Paper  doi  abstract   bibtex   

@inproceedings{10.1145/3491102.3501911,
author = {Kim, Raphael and Linehan, Conor and Pschetz, Larissa},
title = {Navigating Imaginaries of DNA-Based Digital Data Storage},
year = {2022},
isbn = {9781450391573},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3491102.3501911},
doi = {10.1145/3491102.3501911},
abstract = {DNA-based digital data storage technology is hailed as a potential solution for the issues around exponential global data production. However, while the technology continues to strive towards its full commercialization, there is a lack of discourse on how it could be applied to facilitate interactions that are meaningful, ethical, and socially sustainable. As an approach to address this gap, we hosted a series of online workshops, soliciting 15 participants to engage in grounded speculations on plausible futures of DNA data storage. Themes drawn from the resulting imaginaries and discussions were situated within a selection of existing HCI literature, to generate an initial set of design opportunities and challenges for DNA data storage. Early analysis suggests that the system could be designed to 1) facilitate meaningful interactions that are intangible and molecular, and 2) foster better human relationship with more-than-human entities. Furthermore, we highlight the imperative for cross-disciplinary collaborations and pedagogy, to ensure fair and high quality access to the technology.},
booktitle = {Proceedings of the 2022 CHI Conference on Human Factors in Computing Systems},
articleno = {616},
numpages = {15},
keywords = {DNA, archives, bio-design, bio-digital, biological-HCI, data, futures},
location = {<conf-loc>, <city>New Orleans</city>, <state>LA</state>, <country>USA</country>, </conf-loc>},
series = {CHI '22}
}

Paper  doi  abstract   bibtex   

@article{Kieswetter2022,
abstract = {Background: Previously, we evaluated the intracellular mycobactericidal activity of the minor groove binder, S-MGB-364 against the clinical Mycobacterium tuberculosis (Mtb) strain HN878 in macrophages. Objectives: To assess the mycobactericidal activity of S-MGB-364 in Mtb-infected mice. Further, we investigated a plausible DNA binding mechanism of action of S-MGB-364. Methods: The anti-TB and host immune effects of intranasal S-MGB-364 or S-MGB-364 encapsulated in non-ionic surfactant vesicles (NIV) were assessed in Mtb-infected mice by cfu enumeration, ELISA, histology, and flow cytometry. DNA binding was examined using native mass spectrometry and UV-vis thermal melt determination. S-MGB interference with DNA-centric biological events was assessed using a representative panel of Mtb and human topoisomerase I, and gyrase assays. Results: S-MGB-364 bound strongly to DNA as a dimer, significantly increasing the stability of the DNA:S-MGB complex compared with DNA alone. Moreover, S-MGB-364 inhibited the relaxation of Mtb topoisomerase I but not the human form. In macrophages, S-MGB-364 or S-MGB-364-NIV did not cause DNA damage as shown by the low $\gamma$-H2AX expression. Importantly, in the lungs, the intranasal administration of S-MGB-364 or S-MGB-364-NIV formulation in Mtb-infected mice was non-toxic and resulted in a 1 log cfu reduction in mycobacter-ial burden, reduced the expression of proinflammatory cytokines/chemokines, altered immune cell recruitment, and importantly reduced recruitment of neutrophils. Conclusions: Together, these data provide proof of concept for S-MGBs as novel anti-TB therapeutics in vivo.},
author = {Kieswetter, Nathan S and Ozturk, Mumin and Hlaka, Lerato and Chia, Julius Ebua and Nichol, Ryan J O and Cross, Jasmine M and McGee, Leah M C and Tyson-Hirst, Izaak and Beveridge, Rebecca and Brombacher, Frank and Carter, Katharine C and Suckling, Colin J and Scott, Fraser J and Guler, Reto},
doi = {10.1093/JAC/DKAC001},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Kieswetter et al. - 2022 - Intranasally administered S-MGB-364 displays antitubercular activity and modulates the host immune response t.pdf:pdf},
issn = {0305-7453},
journal = {Journal of Antimicrobial Chemotherapy},
keywords = {OA,antitubercular agents,chemical surfactants,chemokines,cytokine,dimers,dna,dna topoisomerases,enzyme-linked immunosorbent assay,flow cytometry,fund{\_}ack,histology,immune response,infections,intranasal administration,lung,macrophages,mass spectrometry,mice,mycobacterium tuberculosis,neutrophils,noninvasive ventilation,original,pharmacokinetics,proof of concept studies,pulmonary surfactants,tuberculosis,type i,vaccine information sheets,vesicle},
mendeley-tags = {OA,fund{\_}ack,original},
month = {jan},
number = {4},
pages = {1061--1071},
pmid = {35084027},
publisher = {Oxford University Press (OUP)},
title = {{Intranasally administered S-MGB-364 displays antitubercular activity and modulates the host immune response to \textit{Mycobacterium tuberculosis} infection}},
url = {https://academic.oup.com/jac/advance-article/doi/10.1093/jac/dkac001/6515318},
volume = {77},
year = {2022}
}

Paper  doi  abstract   bibtex   

@article{weedon_compositional_2017,
	title = {Compositional {Stability} of the {Bacterial} {Community} in a {Climate}-{Sensitive} {Sub}-{Arctic} {Peatland}},
	volume = {8},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.00317/full},
	doi = {10.3389/fmicb.2017.00317},
	abstract = {{\textless}p{\textgreater}The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100\% increases) in a sub-arctic {\textless}italic{\textgreater}Sphagnum{\textless}/italic{\textgreater} peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15\% of variance explained) \> temporal variation (7–11\%) \> climate treatment (4–9\%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-03-27},
	journal = {Frontiers in Microbiology},
	author = {Weedon, James T. and Kowalchuk, George A. and Aerts, Rien and Freriks, Stef and Röling, Wilfred F. M. and van Bodegom, Peter M.},
	month = mar,
	year = {2017},
	note = {Publisher: Frontiers},
	keywords = {\#nosource, 16S, Bacteria, Carbon, Climate Change, DNA, Nitrogen, Peatlands, RNA, Seasonality},
	pages = {00317},
}

@article{Keane2016,
	title = {Long-lived excited-state dynamics of i-{Motif} structures probed by time-resolved infrared spectroscopy},
	volume = {17},
	issn = {14397641},
	doi = {10.1002/cphc.201501183},
	abstract = {© 2016 WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim.UV-generated excited states of cytosine (C) nucleobases are precursors to mutagenic photoproduct formation. The i-motif formed from C-rich sequences is known to exhibit high yields of long-lived excited states following UV absorption. Here the excited states of several i-motif structures have been characterized following 267 nm laser excitation using time-resolved infrared spectroscopy (TRIR). All structures possess a long-lived excited state of ∼300 ps and notably in some cases decays greater than 1 ns are observed. These unusually long-lived lifetimes are attributed to the interdigitated DNA structure which prevents direct base stacking overlap.},
	number = {9},
	journal = {ChemPhysChem},
	author = {Keane, Páraic M. and Baptista, Frederico R. and Gurung, Sarah P. and Devereux, Stephen J. and Sazanovich, Igor V. and Towrie, Michael and Brazier, John A. and Cardin, Christine J. and Kelly, John M. and Quinn, Susan J.},
	year = {2016},
	pmid = {26879336},
	note = {tex.ids= keaneLongLivedExcitedStateDynamics2016},
	keywords = {DNA, cytosine, excited states, i-motifs, time-resolved infrared spectroscopy},
	pages = {1281--1287},
}

@article{pascual_bloodstream_2016,
	title = {Bloodstream infections caused by {Escherichia} coli producing {AmpC} β-lactamases: epidemiology and clinical features},
	volume = {35},
	issn = {1435-4373},
	shorttitle = {Bloodstream infections caused by {Escherichia} coli producing {AmpC} β-lactamases},
	doi = {10.1007/s10096-016-2752-3},
	abstract = {The aim of the study was to investigate the epidemiology and clinical features of bloodstream infections due to Escherichia coli producing AmpC β-lactamases (AmpC-Ec-BSI). In a multi-centre case-control study, all third-generation-cephalosporin-resistant Escherichia coli BSI (3GC-Ec-BSI) isolates were analysed. Acquired bla AmpC (bla ac-AmpC) detection was done by polymerase chain reaction (PCR) and sequencing. Chromosomal bla AmpC (bla c-AmpC) expression was quantified by real-time PCR. Cases were patients with AmpC-Ec-BSI. Controls were patients with cephalosporin-susceptible E. coli BSI, matched 1:1 by sex and age. Demographics, comorbidities, intrinsic and extrinsic risk factors for antimicrobial resistance, clinical presentation and outcomes were investigated. Among 841 E. coli BSI, 17 were caused by AmpC-Ec (2 \%). Eleven isolates (58.8 \%) had bla ac-AmpC and six were bla c-AmpC overproducers. The mean age of cases was 66.2 years and 71 \% were men. Cases were more frequently healthcare-related (82 vs. 52 \% controls, p {\textless} 0.05) and presented more intrinsic and extrinsic risk factors. At least one risk factor was present in 94.1 \% of cases vs. 41.7 \% of controls (p = 0.002). Severity and length of stay (LOS) were higher among cases (mean Pitt Score 2.6 vs. 0.38 in controls, p = 0.03; LOS 17.5 days vs. 6 in controls, p = 0.02). Inappropriate empirical therapy (IET) was administered to 70.6 \% of cases and 23.5 \% of controls (p {\textless} 0.003). No differences were found in terms of cure rate at the 14th day and mortality. Bloodstream infections due to AmpC-Ec (mostly plasmid-mediated) are infrequent in our area. AmpC-Ec-BSI affects mainly patients with intrinsic risk factors and those with previous antibiotic exposure. A high proportion received IET.},
	language = {eng},
	number = {12},
	journal = {European Journal of Clinical Microbiology \& Infectious Diseases: Official Publication of the European Society of Clinical Microbiology},
	author = {Pascual, V. and Alonso, N. and Simó, M. and Ortiz, G. and Garcia, M. C. and Xercavins, M. and Rivera, A. and Morera, M. A. and Miró, E. and Espejo, E. and Navarro, F. and Gurguí, M. and Pérez, J. and Rodríguez-Carballeira, M. and Garau, J. and Calbo, E.},
	year = {2016},
	pmid = {27549108},
	keywords = {Adult, Age Distribution, Aged, Aged, 80 and over, Anti-Bacterial Agents, Bacteremia, Bacterial Proteins, Case-Control Studies, DNA, Bacterial, Escherichia coli, Escherichia coli Infections, Female, Humans, Length of Stay, Male, Middle Aged, Polymerase Chain Reaction, Risk Factors, Sequence Analysis, DNA, Severity of Illness Index, Treatment Outcome, beta-Lactamases},
	pages = {1997--2003},
}

@article{greco_scr7_2016,
	title = {{SCR7} is neither a selective nor a potent inhibitor of human {DNA} ligase {IV}},
	volume = {43},
	issn = {1568-7856},
	doi = {10.1016/j.dnarep.2016.04.004},
	abstract = {DNA ligases are attractive therapeutics because of their involvement in completing the repair of almost all types of DNA damage. A series of DNA ligase inhibitors with differing selectivity for the three human DNA ligases were identified using a structure-based approach with one of these inhibitors being used to inhibit abnormal DNA ligase IIIα-dependent repair of DNA double-strand breaks (DSB)s in breast cancer, neuroblastoma and leukemia cell lines. Raghavan and colleagues reported the characterization of a derivative of one of the previously identified DNA ligase inhibitors, which they called SCR7 (designated SCR7-R in our experiments using SCR7). SCR7 appeared to show increased selectivity for DNA ligase IV, inhibit the repair of DSBs by the DNA ligase IV-dependent non-homologous end-joining (NHEJ) pathway, reduce tumor growth, and increase the efficacy of DSB-inducing therapeutic modalities in mouse xenografts. In attempting to synthesize SCR7, we encountered problems with the synthesis procedures and discovered discrepancies in its reported structure. We determined the structure of a sample of SCR7 and a related compound, SCR7-G, that is the major product generated by the published synthesis procedure for SCR7. We also found that SCR7-G has the same structure as the compound (SCR7-X) available from a commercial vendor (XcessBio). The various SCR7 preparations had similar activity in DNA ligation assay assays, exhibiting greater activity against DNA ligases I and III than DNA ligase IV. Furthermore, SCR7-R failed to inhibit DNA ligase IV-dependent V(D)J recombination in a cell-based assay. Based on our results, we conclude that SCR7 and the SCR7 derivatives are neither selective nor potent inhibitors of DNA ligase IV.},
	language = {eng},
	journal = {DNA repair},
	author = {Greco, George E. and Matsumoto, Yoshihiro and Brooks, Rhys C. and Lu, Zhengfei and Lieber, Michael R. and Tomkinson, Alan E.},
	year = {2016},
	pmid = {27235626},
	pmcid = {PMC5042453},
	keywords = {Animals, Antineoplastic Agents, Cell Line, Tumor, Cell Survival, DNA, DNA Breaks, Double-Stranded, DNA End-Joining Repair, DNA Ligase ATP, DNA double strand break repair, DNA ligase inhibitors, Enzyme Inhibitors, Epithelial Cells, Escherichia coli, Gene Expression, Human DNA ligases, Humans, Leukocytes, Mice, Neurons, Non-homologous end-joining, Pyrimidines, Recombinant Proteins, Schiff Bases, Substrate Specificity, Tumor Burden, V(D)J Recombination, Xenograft Model Antitumor Assays},
	pages = {18--23},
}

@article{afiahayati_metavelvet-sl:_2015,
	title = {{MetaVelvet}-{SL}: an extension of the {Velvet} assembler to a de novo metagenomic assembler utilizing supervised learning},
	volume = {22},
	issn = {1756-1663},
	shorttitle = {{MetaVelvet}-{SL}},
	doi = {10.1093/dnares/dsu041},
	abstract = {The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program (assembler) is not capable of resolving metagenome sequences, so assemblers designed specifically for metagenomics have been developed. MetaVelvet is an extension of the single-genome assembler Velvet. It has been proved to generate assemblies with higher N50 scores and higher quality than single-genome assemblers such as Velvet and SOAPdenovo when applied to metagenomic sequence reads and is frequently used in this research community. One important open problem for MetaVelvet is its low accuracy and sensitivity in detecting chimeric nodes in the assembly (de Bruijn) graph, which prevents the generation of longer contigs and scaffolds. We have tackled this problem of classifying chimeric nodes using supervised machine learning to significantly improve the performance of MetaVelvet and developed a new tool, called MetaVelvet-SL. A Support Vector Machine is used for learning the classification model based on 94 features extracted from candidate nodes. In extensive experiments, MetaVelvet-SL outperformed the original MetaVelvet and other state-of-the-art metagenomic assemblers, IDBA-UD, Ray Meta and Omega, to reconstruct accurate longer assemblies with higher N50 scores for both simulated data sets and real data sets of human gut microbial sequences.},
	language = {eng},
	number = {1},
	journal = {DNA research: an international journal for rapid publication of reports on genes and genomes},
	author = {Afiahayati, null and Sato, Kengo and Sakakibara, Yasubumi},
	month = feb,
	year = {2015},
	pmid = {25431440},
	pmcid = {PMC4379979},
	keywords = {Genome, Humans, Metagenome, Metagenomic, Sequence Analysis, DNA, Software, Support Vector Machine, de novo assembler, microbial community, short read, supervised learning},
	pages = {69--77}
}

Paper  doi  abstract   bibtex   

@article{RN16,
   author = {Acinas, S. G. and Ferrera, I. and Sarmento, H. and Diez-Vives, C. and Forn, I. and Ruiz-Gonzalez, C. and Cornejo-Castillo, F. M. and Salazar, G. and Gasol, J. M.},
   title = {Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations},
   journal = {Environ Microbiol},
   volume = {17},
   number = {10},
   pages = {3557-69},
   note = {Acinas, Silvia G
Ferrera, Isabel
Sarmento, Hugo
Diez-Vives, Cristina
Forn, Irene
Ruiz-Gonzalez, Clara
Cornejo-Castillo, Francisco M
Salazar, Guillem
Gasol, Josep M
eng
Comparative Study
Research Support, Non-U.S. Gov't
Validation Study
England
Environ Microbiol. 2015 Oct;17(10):3557-69. doi: 10.1111/1462-2920.12517. Epub 2014 Jul 7.},
   abstract = {Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequences from the Rhodobacteraceae and Alteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory (NW Mediterranean). We also compared the CARD-FISH data with the Bacteroidetes 16S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319a targeted some unspecific sequences and both probes displayed different abundances of specific Bacteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions (Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine Bacteroidetes, notably large differences between summer and winter that is overlooked by CF319a. We propose CF968 as an alternative to CF319a for targeting the whole Bacteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine Bacteroidetes.},
   keywords = {Alteromonadaceae/genetics
Bacteroidetes/*classification/genetics
DNA Probes/*genetics
DNA, Bacterial/*genetics
In Situ Hybridization, Fluorescence/*methods
Mediterranean Sea
RNA, Ribosomal, 16S/genetics
Rhodobacteraceae/genetics
Seasons
Seawater/microbiology
Sequence Analysis, DNA},
   ISSN = {1462-2920 (Electronic)
1462-2912 (Linking)},
   DOI = {10.1111/1462-2920.12517},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24890225},
   year = {2015},
   type = {Journal Article}
}

Paper  doi  abstract   bibtex   

@article{ranade_fungal_2015,
	title = {Fungal {Infection} {Increases} the {Rate} of {Somatic} {Mutation} in {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {106},
	issn = {1465-7333 (Electronic) 0022-1503 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25890976},
	doi = {10.1093/jhered/esv017},
	abstract = {Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {J Hered},
	author = {Ranade, S. S. and Ganea, L. S. and Razzak, A. M. and Garcia Gil, M. R.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/04/22},
	keywords = {*Mutation Rate, Basidiomycota/*pathogenicity, DNA, Plant/genetics, Genetic Markers, Genetics, Population, Genome, Plant, Genomic Instability, Genotype, Host-Pathogen Interactions/*genetics, Microsatellite Repeats, Mutation, Pinus sylvestris/*genetics/microbiology, Plant Diseases/genetics/*microbiology, Scots pine, Sequence Analysis, DNA, Somatic mutation., Sweden, abiotic stress, microsatellite, simple sequence repeats},
	pages = {386--94},
}

@article{ kidd_influenza_2014,
  title = {Influenza viruses: update on epidemiology, clinical features, treatment and vaccination},
  volume = {20},
  issn = {1531-6971},
  shorttitle = {Influenza viruses},
  doi = {10.1097/MCP.0000000000000049},
  abstract = {PURPOSE OF REVIEW: In the last decade, sporadic and lethal human disease caused by zoonotic avian influenza viruses, and the seasonal activity of human H1N1 2009 pandemic type have driven intense epidemiological and laboratory studies into the virus life cycle. This article highlights major developments from mid-2012 to early 2014.
RECENT FINDINGS: Advances in molecular techniques and efficient rollout of diagnostic tests have enabled the rapid identification of clinical cases and detailed genetic sequencing of viral genomes. Studies have contributed widely to the understanding of how and when influenza viruses circulate, what determines their innate pathogenicity in particular hosts and whether host cofactors influence disease severity. Other imperatives include investigations into how influenza can be better prevented by vaccination, or treated with antiviral drugs.
SUMMARY: Avian influenza viruses present a continuous threat to human populations. There is a need for sustained surveillance and downstream research to evaluate the potential for future pandemics.},
  language = {eng},
  number = {3},
  journal = {Current Opinion in Pulmonary Medicine},
  author = {Kidd, Mike},
  month = {May},
  year = {2014},
  pmid = {24637227},
  keywords = {Animals, Antiviral Agents, DNA, Viral, Drug Resistance, Viral, Female, Humans, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H5N1 Subtype, Influenza A Virus, H7N9 Subtype, Influenza A virus, Influenza in Birds, Influenza, Human, Male, Pandemics, Poultry, Seasons, Sentinel Surveillance, Sequence Analysis, DNA, Viral Vaccines, Zanamivir},
  pages = {242--246}
}

Paper  abstract   bibtex   

@electronic{citeulike:13075038,
    abstract = {List of indexed keywords within the transdisciplinary set of domains which relate to the Integrated Natural Resources Modelling and Management ({INRMM}). In particular, the list of keywords maps the semantic tags in the {INRMM} Meta-information Database ({INRMM}-{MiD}). [\n] The {INRMM}-{MiD} records providing this list are accessible by the special tag: inrmm-list-of-tags ( {http://mfkp.org/INRMM}/tag/inrmm-list-of-tags ).},
    author = {{M.R.I.}},
    citeulike-article-id = {13075038},
    citeulike-linkout-0 = {http://mfkp.org/INRMM/tag/inrmm-list-of-tags},
    citeulike-linkout-1 = {http://www.citeulike.org/group/15400/tag/inrmm-list-of-tags},
    keywords = {database, dataset, dating, dddas, de-facto-standard, dead-wood, debris, debris-floods, debris-flows, deciduous, deciduous-forest, decision-making, decision-making-procedure, decision-support-system, decline, decline-effect, decline-symptomology, deep-reproducible-research, deep-uncertainty, definition, deforestation, degenerated-soil, deglaciation, degradation, degradation-velocity, dehesas, delonix-regia, democracy, dendrochronology, dendroctonus, dendroctonus-frontalis, dendroctonus-micans, dendroctonus-ponderosae, dendroctonus-pseudotsugae, dendroecology, dendrology, denmark, density-related-behaviour, deposition, derived-data, desalinisation, description, desertification, deserts, design-diversity, devil-in-details, diabetes, diabetes-mellitus, diagram-data, diameter-differentiation, dictionary, die-off, dieback, diesel, differentiation, digital-preservation, digital-society, dimensional-analysis, dimensionality-reduction, dimensionless, dioryctria-splendidella, diospyros-kaki, diospyros-spp, diospyros-virginiana, diplodia-pinea, diprion-pini, dipteryx-panamensis, direct-reciprocity, disaster-recovery, disaster-response, disasters, discharge, disciplinary-barrier, disconcerting-learning, discount-rate, disease, diseases, disjunction, dispersal, dispersal-limitation, dispersal-models, dissent, distance-analysis, distance-correlation, distilled-gin, distribution, distribution-limit, disturbance-ecology, disturbance-interactions, disturbances, diversity, django, dna, dna-fingerprinting, dobrogea, dodonaea-viscosa, dormancy, dormouse, inrmm-list-of-tags},
    month = feb,
    posted-at = {2014-02-28 14:09:03},
    priority = {2},
    title = {List of keywords of the {INRMM} meta-information database - part 10},
    url = {http://mfkp.org/INRMM/tag/inrmm-list-of-tags},
    year = {2014}
}

@article{adamsPhylogenyJuniperusUsing2013a,
  title = {Phylogeny of {{Juniperus}} Using {{nrDNA}} and Four {{cpDNA}} Regions},
  author = {Adams, R. P. and Schwarzbach, A. E.},
  year = {2013},
  volume = {95},
  pages = {179--187},
  abstract = {The Phylogeny of Juniperusis presented based on nrDNA (ITS), petN-psbM, trnS-trnG, trnD-trnT, trnL-trnF sequencing (4411 bp) utilizing all currently recognized species. The major clades of the phylogenetic tree were congruent with the previouslypublished phylogenetic tree of Mao et al. (2010) that had a subset of taxa of the current study. The lone species with serrate leaves in the eastern hemisphere, J. phoenicea, was found to be in a clade quite separated from the serrate junipers of North America. Juniperus phoeniceais referred to as 'pseudoserrate' to distinguish it from the semi-arid, serrate leaf junipers of the western hemisphere. Section Sabinais the most derived group and has radiated into niches in both the eastern and western hemispheres with approx. 60 species.},
  journal = {Phytologia},
  keywords = {*imported-from-citeulike-INRMM,~INRMM-MiD:c-13699749,forest-resources,juniperus-spp,phylogenetics,taxonomy},
  lccn = {INRMM-MiD:c-13699749},
  number = {2}
}

@article{tan_identification_2013,
	title = {Identification of a new cyclovirus in cerebrospinal fluid of patients with acute  central nervous system infections.},
	volume = {4},
	issn = {2150-7511},
	doi = {10.1128/mBio.00231-13},
	abstract = {Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4\% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58\%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.},
	language = {eng},
	number = {3},
	journal = {mBio},
	author = {Tan, Le Van and van Doorn, H. Rogier and Nghia, Ho Dang Trung and Chau, Tran Thi Hong and Tu, Le Thi Phuong and de Vries, Michel and Canuti, Marta and Deijs, Martin and Jebbink, Maarten F. and Baker, Stephen and Bryant, Juliet E. and Tham, Nguyen Thi and BKrong, Nguyen Thi Thuy Chinh and Boni, Maciej F. and Loi, Tran Quoc and Phuong, Le Thi and Verhoeven, Joost T. P. and Crusat, Martin and Jeeninga, Rienk E. and Schultsz, Constance and Chau, Nguyen Van Vinh and Hien, Tran Tinh and van der Hoek, Lia and Farrar, Jeremy and de Jong, Menno D.},
	month = jun,
	year = {2013},
	pmid = {23781068},
	pmcid = {PMC3684831},
	keywords = {Adolescent, Adult, Aged, Animals, Central Nervous System Infections/epidemiology/*virology, Child, Child, Preschool, Circoviridae Infections/epidemiology/*virology, Circoviridae/*classification/genetics/*isolation \& purification, Cluster Analysis, DNA, Viral/chemistry/genetics, Female, Genome, Viral, Humans, Infant, Male, Middle Aged, Molecular Sequence Data, Phylogeny, Prevalence, Prospective Studies, Sequence Analysis, DNA, Vietnam, Young Adult},
	pages = {e00231--00213},
}

Paper  doi  abstract   bibtex   

@article{Biffi2013,
	title = {Quantitative visualization of {DNA} {G}-quadruplex structures in human cells.},
	volume = {5},
	issn = {1755-4349},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3622242&tool=pmcentrez&rendertype=abstract},
	doi = {10.1038/nchem.1548},
	abstract = {Four-stranded G-quadruplex nucleic acid structures are of great interest as their high thermodynamic stability under near-physiological conditions suggests that they could form in cells. Here we report the generation and application of an engineered, structure-specific antibody employed to quantitatively visualize DNA G-quadruplex structures in human cells. We show explicitly that G-quadruplex formation in DNA is modulated during cell-cycle progression and that endogenous G-quadruplex DNA structures can be stabilized by a small-molecule ligand. Together these findings provide substantive evidence for the formation of G-quadruplex structures in the genome of mammalian cells and corroborate the application of stabilizing ligands in a cellular context to target G-quadruplexes and intervene with their function.},
	number = {3},
	journal = {Nature chemistry},
	author = {Biffi, Giulia and Tannahill, David and McCafferty, John and Balasubramanian, Shankar},
	month = mar,
	year = {2013},
	pmid = {23422559},
	keywords = {\#nosource, Animals, Bone Neoplasms, Bone Neoplasms: genetics, Cell Cycle, Cell Line, DNA, DNA: chemistry, Enzyme-Linked Immunosorbent Assay, G-Quadruplexes, Humans, Male, Osteosarcoma, Osteosarcoma: genetics, Salmon, Spermatozoa, Spermatozoa: chemistry, Thermodynamics, Tumor},
	pages = {182--6},
}

@article{Matsumoto2013,
	title = {A peptide nucleic acid ( {PNA} ) heteroduplex probe containing an inosine –},
	doi = {10.1002/chem.201204183},
	journal = {Chemistry - A European Journal},
	author = {Matsumoto, Katsuhiko and Nakata, Eiji and Tamura, Tomoki and Saito, Isao},
	year = {2013},
	keywords = {\#nosource, dna},
}

Paper  doi  bibtex   

@article{gomez-pinto_carbohydrate-dna_2013,
	title = {Carbohydrate-dna interactions at g-quadruplexes: {Folding} and stability changes by attaching sugars at the 5′-{End}},
	issn = {09476539},
	url = {http://doi.wiley.com/10.1002/chem.201203902},
	doi = {10.1002/chem.201203902},
	journal = {Chemistry - A European Journal},
	author = {Gómez-Pinto, Irene and Vengut-Climent, Empar and Lucas, Ricardo and Aviñó, Anna and Eritja, Ramón and González, Carlos and Morales, Juan Carlos},
	month = jan,
	year = {2013},
	keywords = {\#nosource, carbohydrates, contacts, dna, g-quadruplexes, hydrogen bonds, molecular interactions, stacking, that at-, we have also shown},
	pages = {n/a--n/a},
}

Paper  doi  abstract   bibtex   

@article{Fujimoto2013,
	title = {Thermodynamics-hydration relationships within loops that affect {G}-quadruplexes under molecular crowding conditions.},
	volume = {117},
	issn = {1520-5207},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/23153339},
	doi = {10.1021/jp308402v},
	abstract = {We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.},
	number = {4},
	journal = {The journal of physical chemistry. B},
	author = {Fujimoto, Takeshi and Nakano, Shu-ichi and Sugimoto, Naoki and Miyoshi, Daisuke},
	month = jan,
	year = {2013},
	pmid = {23153339},
	keywords = {\#nosource, DNA, DNA: chemistry, G-Quadruplexes, Models, Molecular, Sodium, Sodium: chemistry, Thermodynamics, Water, Water: chemistry},
	pages = {963--72},
}

Paper  doi  abstract   bibtex   

@article{Tarsounas2013,
	title = {Genomes and {G}-quadruplexes: {For} better or for worse},
	volume = {425},
	issn = {00222836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24076189 http://linkinghub.elsevier.com/retrieve/pii/S0022283613006104 http://dx.doi.org/10.1016/j.jmb.2013.09.026},
	doi = {10.1016/j.jmb.2013.09.026},
	abstract = {Genomic integrity is crucial for correct chromosome segregation and physiological rates of cell proliferation. Mutations, deletions and translocations, hallmarks of human tumors, drive the aberrant proliferation and metastatic behavior of cancer cells. These chromosomal rearrangements often occur at genomic sites susceptible to breakage during DNA replication, including regions with G-quadruplex (G4)-forming potential. G4s are stable secondary structures that guanine-rich single-stranded DNA can readily adopt in vitro. However, their formation in eukaryotic cells has remained elusive and thus a subject of debate ever since they were first described. Recent work has more convincingly implicated G4s in a variety of biological processes including telomere maintenance, gene expression, epigenetic regulation and DNA replication. However, the downside of employing thermodynamically very stable alternative DNA structures as regulatory entities lies in their potential to also interfere with normal DNA metabolic processes, such as transcription and replication, which require readability of each base to faithfully transmit genetic information. Indeed, it has become clear that G4 structures can pose prominent barriers to replication fork progression and that they are also intrinsically recombinogenic. Here, we discuss mechanisms that cells evolved to counteract these detrimental effects, thereby ensuring the faithful inheritance of G4-containing genomes.},
	number = {23},
	journal = {Journal of Molecular Biology},
	author = {Tarsounas, Madalena and Tijsterman, Marcel},
	month = sep,
	year = {2013},
	pmid = {24076189},
	note = {tex.ids= tarsounasGenomesGQuadruplexesBetter2013, tarsounasGenomesGQuadruplexesBetter2013a
ISBN: 00222836
publisher: Elsevier B.V.},
	keywords = {DNA, DNA Replication, DNA replication, DNA-Directed DNA Polymerase, DNA: chemistry, DNA: metabolism, Eukaryota, Eukaryota: genetics, Eukaryota: physiology, G-Quadruplexes, G-quadruplex, Genetic, Genomic Instability, Transcription, genomic instability},
	pages = {4782--9},
}

Website  abstract   bibtex   

@article{
 title = {Molecular recognition between DNA and a copper-based anticancer complex.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Antineoplastic Agents,Antineoplastic Agents: chemistry,Antineoplastic Agents: pharmacology,Copper,Copper: chemistry,DNA,DNA: chemistry,DNA: drug effects,Ligands,Molecular Dynamics Simulation,Organometallic Compounds,Organometallic Compounds: chemistry,Organometallic Compounds: pharmacology,Structure-Activity Relationship},
 pages = {15539-46},
 volume = {14},
 websites = {http://pubs.rsc.org/en/content/articlehtml/2012/cp/c2cp42185b},
 month = {11},
 publisher = {The Royal Society of Chemistry},
 day = {28},
 id = {71db2563-a07f-3450-9e24-c4f3c79f9787},
 created = {2013-04-01T20:34:59.000Z},
 accessed = {2013-04-01},
 file_attached = {false},
 profile_id = {f6dc1d9a-3905-3337-924c-214414352692},
 last_modified = {2015-08-21T05:42:19.000Z},
 read = {false},
 starred = {true},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Galindo-Murillo2012},
 language = {en},
 folder_ids = {49690701,49946861},
 abstract = {The aim of this work is to describe the specific recognition site between DNA and an anticancer copper complex by means of computational methods. Molecular dynamics were used to find the preferred site of binding between selected DNA chains and [Cu(2,2'-bipyridine)(acetylacetonate)(H(2)O)](+) (Cas). Full DFT optimizations of selected geometries extracted from simulations, followed by a topological analysis of electron density allowed us to define the specific interactions inside the recognition site. Cas links deoxyribose-phosphate by a coordination bond between metal and the phosphate group. There are several C-H···π, O···π(C) and O···π(N) interactions between the sugar group and the aromatic ligand of Cas. The results indicate that the adduct Cas-deoxyribose-phosphate may be an initial step toward the hydrolysis of DNA chains. Overall, this study provides insights into the initial step of the action mechanism of copper complexes as apoptosis-inducing agents and provides guidelines for the design of this kind of drugs.},
 bibtype = {article},
 author = {Galindo-Murillo, R. and Ruiz-Azuara, L. and Moreno-Esparza, R. and Cortés-Guzmán, F.},
 journal = {Physical chemistry chemical physics : PCCP},
 number = {44}
}

Paper  doi  abstract   bibtex   

@article{Anand2012,
	title = {Overcoming natural replication barriers: differential helicase requirements.},
	volume = {40},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3273818&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkr836},
	abstract = {DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. Srs2 helicase activity is required for hairpin unwinding and fork progression. Also, the PCNA binding domain of Srs2 is required for its in vivo role of replication through hairpins. In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric protein barrier. Interestingly, replication through a protein barrier but not a DNA structure barrier was modulated by nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through protein-mediated stall sites. Our analyses reveal fundamental differences in the replication of DNA structural versus protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures.},
	number = {3},
	journal = {Nucleic acids research},
	author = {Anand, Ranjith P and Shah, Kartik a and Niu, Hengyao and Sung, Patrick and Mirkin, Sergei M and Freudenreich, Catherine H},
	month = mar,
	year = {2012},
	pmid = {21984413},
	keywords = {\#nosource, Chromosome Breakage, DNA, DNA Helicases, DNA Helicases: metabolism, DNA Helicases: physiology, DNA Replication, DNA-Binding Proteins, DNA-Binding Proteins: metabolism, DNA: chemistry, G-Quadruplexes, Nucleic Acid, Nucleic Acid Conformation, Proliferating Cell Nuclear Antigen, Proliferating Cell Nuclear Antigen: metabolism, RecQ Helicases, RecQ Helicases: physiology, Repetitive Sequences, Saccharomyces cerevisiae Proteins, Saccharomyces cerevisiae Proteins: metabolism, Saccharomyces cerevisiae Proteins: physiology, Telomere, Telomere: metabolism},
	pages = {1091--105},
}

Paper  doi  abstract   bibtex   

@article{perez_frontiers_2012,
	title = {Frontiers in molecular dynamics simulations of {DNA}.},
	volume = {45},
	issn = {1520-4898},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21830782},
	doi = {10.1021/ar2001217},
	abstract = {It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global thermodynamic and kinetic picture of the binding landscape of DNA will become available in a few years. MD will become a crucial tool in areas such as biomolecular engineering and synthetic biology. MD has also been shown to be an excellent source of parameters for mesoscopic models of DNA flexibility. Such models can be refined through atomistic MD simulations on small duplexes and then applied to the study of entire chromosomes. Recent evidence suggests that MD-derived elastic models can successfully predict the position of regulatory regions in DNA and can help advance our understanding of nucleosome positioning and chromatin plasticity. If these results are confirmed, MD simulations can become the ultimate tool to decipher a physical code that can contribute to gene regulation. We are entering the golden age of MD simulations of DNA. Undoubtedly, the expectations are high, but the challenges are also enormous. These include the need for more accurate potential energy functionals and for longer and more complex simulations in more realistic systems. The joint research effort of several groups will be crucial for adapting the technique to the requirements of the coming decade.},
	number = {2},
	journal = {Accounts of chemical research},
	author = {Pérez, Alberto and Luque, F Javier and Orozco, Modesto},
	month = feb,
	year = {2012},
	pmid = {21830782},
	keywords = {\#nosource, DNA, DNA: chemistry, DNA: metabolism, Models, Molecular, Molecular Dynamics Simulation, Nucleic Acid Conformation, Protein Conformation, Proteins, Proteins: chemistry, Proteins: metabolism, Thermodynamics, X-Ray Diffraction},
	pages = {196--205},
}

@article{
 title = {Metagenomes of the Picoalga Bathycoccus from the Chile coastal upwelling},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Chile,Chlorophyta,Chlorophyta: genetics,DNA,Metagenomics,Metagenomics: methods,Molecular Sequence Data,Oceans and Seas,RCC,SBR_Phyto_DIPO,Sequence Analysis},
 pages = {e39648},
 volume = {7},
 websites = {http://dx.plos.org/10.1371/journal.pone.0039648,http://figshare.com/articles/Metagenomes_of_the_Picoalga_Bathycoccus_from_the_Chile_Coastal_Upwelling/123702},
 month = {1},
 publisher = {Public Library of Science},
 editors = {[object Object]},
 id = {628d98fc-f70b-33e2-9b78-33543927cc62},
 created = {2015-11-02T11:41:37.000Z},
 accessed = {2014-11-27},
 file_attached = {false},
 profile_id = {9e8929f8-811d-3561-b42b-6003aef71c7c},
 group_id = {98cf6291-ef58-3f8a-a4b6-c8754044662f},
 last_modified = {2015-11-02T11:41:37.000Z},
 tags = {2012,microb3,sbr_phyto_dipo},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 abstract = {Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome.},
 bibtype = {article},
 author = {Vaulot, Daniel and Lepère, Cécile and Toulza, Eve and de la Iglesia, Rodrigo and Poulain, Julie and Gaboyer, Frédéric and Moreau, Hervé and Vandepoele, Klaas and Ulloa, Osvaldo and Gavory, Frederick and Piganeau, Gwenael},
 journal = {PLoS ONE},
 number = {6}
}

Paper  doi  abstract   bibtex   

@article{Kim2012,
	title = {A pyrene-imidazolium derivative that selectively recognizes {G}-quadruplex {DNA}.},
	volume = {33},
	issn = {1878-5905},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22196901},
	doi = {10.1016/j.biomaterials.2011.11.073},
	abstract = {G-quadruplexes, formed of four stranded guanine bases stabilized by monovalent cations, serve important role in cancer cell growth and control gene expression in telomere. Since there are various types of quadruplex structures, rapid and simple screening methods with high selectivity, sensitivity and nontoxicity are required for understanding about the biological roles of quadruplex DNA as well as in designing therapeutics. Herein, we report a pyrene-imidazolium derivative, JY-1, which can with high selectivity recognize G-quadruplex using fluorescence and NMR spectroscopy. This is the first example based on the imidazolium derivative, which can detect the G-quadruplex directly to utilize the excimer/monomer emission change in pyrene fluorophore. The selectivity of strong binding to a specific sequence can allow for quadruplex sensing and the detection method presented here is very simple, using fluorescence and NMR study. Also, the groove binding characteristic of JY-1 to the G-quadruplex has a relatively low nonspecific toxicity and the structure-specific differences in fluorescent character between DNA duplex and G-quadruplex may offer more discovery and application in biological study.},
	number = {7},
	journal = {Biomaterials},
	author = {Kim, Ha Na and Lee, Eun-Hae and Xu, Zhaochao and Kim, Hee-Eun and Lee, Hee-Seung and Lee, Joon-Hwa and Yoon, Juyoung},
	month = mar,
	year = {2012},
	pmid = {22196901},
	note = {Publisher: Elsevier Ltd},
	keywords = {\#nosource, Circular Dichroism, DNA, DNA: chemistry, Fluorescence, Fluorescence: methods, Fluorescent Dyes, Fluorescent Dyes: chemistry, G-Quadruplexes, Imidazoles, Imidazoles: chemistry, Magnetic Resonance Spectroscopy, Magnetic Resonance Spectroscopy: methods, Models, Molecular, Molecular Structure, Nucleic Acid Conformation, Pyrenes, Pyrenes: chemistry, Spectrometry},
	pages = {2282--8},
}

Paper  doi  abstract   bibtex   

@article{ruiz-castelar_combination_2012,
	title = {Combination of chromatographic and chemometric methods to study the interactions between {DNA} strands.},
	volume = {722},
	issn = {1873-4324},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22444532},
	doi = {10.1016/j.aca.2012.02.005},
	abstract = {This work describes the combination of size-exclusion chromatography and chemometric resolution methods to study the formation of complex DNA structures from individual strands. This combined procedure has been applied to two different experimental data. Firstly, the formation of an intermolecular Watson-Crick duplex structure formed by the individual unstructured strands. Secondly, the competition between the intermolecular Watson-Crick duplex and intramolecular quadruplex structures formed by two sequences found in the hTERT gene has been studied. The analysis of the recorded chromatograms at just one single wavelength may not always be enough to confirm the existence of a higher order structure. In these cases, recording the entire spectrum at each point of the chromatogram and applying appropriate chemometric resolution methods has shown to be a useful tool to resolve and quantify the contribution of all DNA structures to the analytical signal. In this work, the Multivariate Curve Resolution based on Alternating Least Squares (MCR-ALS) has been used to analyze the three-way data sets acquired along chromatographic runs.},
	journal = {Analytica chimica acta},
	author = {Ruiz-Castelar, Sara and Checa, Antonio and Gargallo, Raimundo and Jaumot, Joaquim},
	month = may,
	year = {2012},
	pmid = {22444532},
	note = {Publisher: Elsevier B.V.},
	keywords = {\#nosource, Chromatography, Circular Dichroism, DNA, DNA: chemistry, DNA: metabolism, G-Quadruplexes, Gel, Humans, Least-Squares Analysis, Nucleic Acid Conformation, Telomerase, Telomerase: chemistry, Telomerase: metabolism},
	pages = {34--42},
}

Paper  doi  abstract   bibtex   

@article{vorlickova_8-oxoguanine_2012,
	title = {8-oxoguanine in a quadruplex of the human telomere {DNA} sequence.},
	volume = {279},
	issn = {1742-4658},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22008383},
	doi = {10.1111/j.1742-4658.2011.08396.x},
	abstract = {8-Oxoguanine is a ubiquitous oxidative base lesion. We report here on the effect of this lesion on the structure and stability of quadruplexes formed by the human telomeric DNA sequence 5'-dG(3)(TTAG(3))(3) in NaCl and KCl. CD, PAGE and absorption-based thermodynamic stability data showed that replacement of any of the tetrad-forming guanines by 8-oxoguanine did not hinder the formation of monomolecular, antiparallel quadruplexes in NaCl. The modified quadruplexes were, however, destabilized in both salts, the extent of this depending on the position of the lesion. These results and the results of previous studies on guanine-to-adenine exchanges and guanine abasic lesions in the same quadruplex show a noticeable trend: it is not the type of the lesion but the position of the modification that determines the effect on the conformation and stability of the quadruplex. The type of lesion only governs the extent of changes, such as of destabilization. Most sensitive sites were found in the middle tetrad of the three-tetrad quadruplex, and the smallest alterations were observed if guanines of the terminal tetrad with the diagonal TTA loop were substituted, although even these substitutions brought about unfavorable enthalpic changes. Interestingly, the majority of these base-modified quadruplexes did not adopt the rearranged folding induced in the unmodified dG(3)(TTAG(3))(3) by potassium ions, an observation that could imply biological relevance of the results.},
	number = {1},
	journal = {The FEBS journal},
	author = {Vorlícková, Michaela and Tomasko, Martin and Sagi, Andras J and Bednarova, Klara and Sagi, Janos},
	month = jan,
	year = {2012},
	pmid = {22008383},
	keywords = {\#nosource, Biomolecular, Circular Dichroism, DNA, DNA: chemistry, DNA: genetics, Guanine, Guanine: analogs \& derivatives, Guanine: chemistry, Humans, Models, Molecular, Nuclear Magnetic Resonance, Nucleic Acid Conformation, Potassium, Potassium: chemistry, Telomere, Telomere: chemistry, Thermodynamics},
	pages = {29--39},
}

@article{galvao_synteny-based_2012,
	title = {Synteny-based mapping-by-sequencing enabled by targeted enrichment},
	volume = {71},
	issn = {1365-313X},
	doi = {10/gkgdms},
	abstract = {Mapping-by-sequencing, as implemented in SHOREmap ('SHOREmapping'), is greatly accelerating the identification of causal mutations. The original SHOREmap approach based on resequencing of bulked segregants required a highly accurate and complete reference sequence. However, current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed using a reduced number of markers, and how the associated decrease in the number of markers can be compensated for by enrichment of marker sequences. As proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, whose genome has several large-scale rearrangements relative to A. thaliana. Our approach provides an alternative method for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals.},
	language = {eng},
	number = {3},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Galvão, Vinicius C. and Nordström, Karl J. V. and Lanz, Christa and Sulz, Patric and Mathieu, Johannes and Posé, David and Schmid, Markus and Weigel, Detlef and Schneeberger, Korbinian},
	month = aug,
	year = {2012},
	pmid = {22409706},
	keywords = {Arabidopsis, Arabidopsis Proteins, Brassica rapa, Chromosome Mapping, DNA Mutational Analysis, DNA, Plant, Flowers, Gene Frequency, Gene Library, Genetic Linkage, Genome, Plant, High-Throughput Nucleotide Sequencing, MADS Domain Proteins, Mutation, Sequence Analysis, DNA, Synteny, Transcriptome},
	pages = {517--526},
}

Paper  doi  abstract   bibtex   

@article{Kuzuya2011,
	title = {Nanomechanical {DNA} origami 'single-molecule beacons' directly imaged by atomic force microscopy.},
	volume = {2},
	issn = {2041-1723},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3265375&tool=pmcentrez&rendertype=abstract},
	doi = {10.1038/ncomms1452},
	abstract = {DNA origami involves the folding of long single-stranded DNA into designed structures with the aid of short staple strands; such structures may enable the development of useful nanomechanical DNA devices. Here we develop versatile sensing systems for a variety of chemical and biological targets at molecular resolution. We have designed functional nanomechanical DNA origami devices that can be used as 'single-molecule beacons', and function as pinching devices. Using 'DNA origami pliers' and 'DNA origami forceps', which consist of two levers  170 nm long connected at a fulcrum, various single-molecule inorganic and organic targets ranging from metal ions to proteins can be visually detected using atomic force microscopy by a shape transition of the origami devices. Any detection mechanism suitable for the target of interest, pinching, zipping or unzipping, can be chosen and used orthogonally with differently shaped origami devices in the same mixture using a single platform.},
	journal = {Nature communications},
	author = {Kuzuya, Akinori and Sakai, Yusuke and Yamazaki, Takahiro and Xu, Yan and Komiyama, Makoto},
	month = jan,
	year = {2011},
	pmid = {21863016},
	note = {Publisher: Nature Publishing Group},
	keywords = {\#nosource, Atomic Force, Atomic Force: methods, Base Sequence, DNA, DNA: chemistry, Microscopy, Molecular Sequence Data, Nanotechnology, Nanotechnology: methods, Nucleic Acid Conformation, Proteins, Proteins: chemistry, Single-Stranded, Single-Stranded: chemistry},
	pages = {449},
}

@article{ gkikopoulos_swi/snf_2011,
  title = {The {SWI}/{SNF} complex acts to constrain distribution of the centromeric histone variant {Cse}4},
  volume = {30},
  issn = {1460-2075},
  doi = {10.1038/emboj.2011.112},
  abstract = {In order to gain insight into the function of the Saccharomyces cerevisiae SWI/SNF complex, we have identified DNA sequences to which it is bound genomewide. One surprising observation is that the complex is enriched at the centromeres of each chromosome. Deletion of the gene encoding the Snf2 subunit of the complex was found to cause partial redistribution of the centromeric histone variant Cse4 to sites on chromosome arms. Cultures of snf2Δ yeast were found to progress through mitosis slowly. This was dependent on the mitotic checkpoint protein Mad2. In the absence of Mad2, defects in chromosome segregation were observed. In the absence of Snf2, chromatin organisation at centromeres is less distinct. In particular, hypersensitive sites flanking the Cse4 containing nucleosomes are less pronounced. Furthermore, SWI/SNF complex was found to be especially effective in the dissociation of Cse4 containing chromatin in vitro. This suggests a role for Snf2 in the maintenance of point centromeres involving the removal of Cse4 from ectopic sites.},
  language = {eng},
  number = {10},
  journal = {The EMBO journal},
  author = {Gkikopoulos, Triantaffyllos and Singh, Vijender and Tsui, Kyle and Awad, Salma and Renshaw, Matthew J. and Scholfield, Pieta and Barton, Geoffrey J. and Nislow, Corey and Tanaka, Tomoyuki U. and Owen-Hughes, Tom},
  month = {May},
  year = {2011},
  pmid = {21505420},
  pmcid = {PMC3098484},
  keywords = {Adenosine Triphosphatases, Binding Sites, Centromere, Chromatin Assembly and Disassembly, Chromosomal Proteins, Non-Histone, Chromosome Segregation, DAG, DNA, Fungal, DNA-Binding Proteins, Gene Deletion, Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors},
  pages = {1919--1927}
}

Paper  doi  abstract   bibtex   

@article{Chiou2011,
	title = {Monitoring triplex {DNA} formation with fluorescence resonance energy transfer between a fluorophore-labeled probe and intercalating dyes.},
	volume = {416},
	issn = {1096-0309},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21609711},
	doi = {10.1016/j.ab.2011.05.002},
	abstract = {Triplex-forming oligonucleotides (TFOs) are sequence-dependent DNA binders that may be useful for DNA targeting and detection. A sensitive and convenient method to monitor triplex formation by a TFO and its target DNA duplex is required for the application of TFO probes. Here we describe a novel design by which triplex formation can be monitored homogeneously without prelabeling the target duplex. The design uses a TFO probe tagged with a fluorophore that undergoes fluorescence resonance energy transfer with fluorescent dyes that intercalate into the target duplex. Through color compensation analysis, the specific emission of the TFO probe reveals the status of the triple helices. We used this method to show that triple helix formation with TFOs is magnesium dependent. We also demonstrated that the TFO probe can be used for detection of sequence variation in melting analysis and for DNA quantitation in real-time polymerase chain reaction.},
	number = {1},
	journal = {Analytical biochemistry},
	author = {Chiou, Chiuan-Chian and Chen, Shiau-Wen and Luo, Ji-Dung and Chien, Yu-Tzu},
	month = sep,
	year = {2011},
	pmid = {21609711},
	note = {Publisher: Elsevier Inc.},
	keywords = {\#nosource, DNA, DNA: analysis, DNA: chemistry, DNA: genetics, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, Fluorescent Dyes: analysis, Fluorescent Dyes: chemical synthesis, Fluorescent Dyes: chemistry, Intercalating Agents, Intercalating Agents: chemistry, Nucleic Acid Denaturation, Oligonucleotides, Oligonucleotides: analysis, Oligonucleotides: chemical synthesis, Oligonucleotides: chemistry, Plasmids, Plasmids: genetics, Reverse Transcriptase Polymerase Chain Reaction, Temperature},
	pages = {1--7},
}

Paper  doi  abstract   bibtex   

@article{Moriyama2011,
	title = {{DNA} assembly and re-assembly activated by cationic comb-type copolymer},
	volume = {32},
	issn = {01429612},
	url = {http://dx.doi.org/10.1016/j.biomaterials.2010.11.064 http://www.ncbi.nlm.nih.gov/pubmed/21186054 http://www.sciencedirect.com/science/article/B6TWB-51ST6V0-4/2/93fada36d0fba3cbb3bb39227dba8ee0},
	doi = {10.1016/j.biomaterials.2010.11.064},
	abstract = {Guanine-rich oligonucleotides, such as TG4T and TG5T, assemble into a tetramolecular quadruplexes with layers of G-quartets stabilized by coordination to monovalent cations. Association rates of the quadruplexes are extremely slow, likely owing to electrostatic repulsion among the four strands. We have shown that comb-type copolymers with a polycation backbone and abundant hydrophilic graft chains form water-soluble polyelectrolyte complexes with DNA and promote DNA hybridization. Here, we report the effect of cationic comb-type copolymers on the kinetics of tetramolecular quadruplex formation. The copolymer significantly increased the association rate of tetramolecular quadruplexes without altering kinetic effects of metal cations in quadruplex formation. Dissociation rates of the quadruplexes were also accelerated by the copolymer suggesting that the copolymer has chaperone-like activity that reduces the energy barriers associated with dissociation and re-assembly of base pairs. This hypothesis was further supported by the observation that the copolymer activated the strand exchange reaction between the quadruplex and a constituting single-stranded. © 2010 Elsevier Ltd.},
	number = {9},
	journal = {Biomaterials},
	author = {Moriyama, Rui and Shimada, Naohiko and Kano, Arihiro and Maruyama, Atsushi},
	month = mar,
	year = {2011},
	pmid = {21186054},
	note = {tex.ids= moriyamaDNAAssemblyReassembly2011, moriyamaDNAAssemblyReassembly2011a
ISBN: 1878-5905 (Electronic)0̊142-9612 (Linking)
publisher: Elsevier Ltd},
	keywords = {Cationic comb-type copolymer, Cationic comb-type copolymer G-quadruplex Interpol, Cations, DNA, DNA: chemistry, DNA: metabolism, Dextrans, Dextrans: chemistry, Fluorescence, G-Quadruplexes, G-quadruplex, Interpolyelectrolyte complex, Kinetics, Nucleic Acid Denaturation, Nucleic Acid Denaturation: drug effects, Polylysine, Polylysine: pharmacology, Polymers, Polymers: pharmacology, Spectrometry, Strand exchange reaction, Temperature},
	pages = {2351--2358},
}

Paper  doi  abstract   bibtex   

@article{Sun2010,
	title = {Stable anticancer gold({III})-porphyrin complexes: effects of porphyrin structure.},
	volume = {16},
	issn = {1521-3765},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20162647},
	doi = {10.1002/chem.200902741},
	abstract = {In the design of physiologically stable anticancer gold(III) complexes, we have employed strongly chelating porphyrinato ligands to stabilize a gold(III) ion [Chem. Commun. 2003, 1718; Coord. Chem. Rev. 2009, 253, 1682]. In this work, a family of gold(III) tetraarylporphyrins with porphyrinato ligands containing different peripheral substituents on the meso-aryl rings were prepared, and these complexes were used to study the structure-bioactivity relationship. The cytotoxic IC(50) values of [Au(Por)](+) (Por=porphyrinato ligand), which range from 0.033 to ¿100 microM, correlate with their lipophilicity and cellular uptake. Some of them induce apoptosis and display preferential cytotoxicity toward cancer cells than to normal noncancerous cells. A new gold(III)-porphyrin with saccharide conjugation [Au(4-glucosyl-TPP)]Cl (2a; H(2)(4-glucosyl-TPP)=meso-tetrakis(4-beta-D-glucosylphenyl)porphyrin) exhibits significant cytostatic activity to cancer cells (IC(50)=1.2-9.0 microM) without causing cell death and is much less toxic to lung fibroblast cells (IC(50)¿100 microM). The gold(III)-porphyrin complexes induce S-phase cell-cycle arrest of cancer cells as indicated by flow cytometric analysis, suggesting that the anticancer activity may be, in part, due to termination of DNA replication. The gold(III)-porphyrin complexes can bind to DNA in vitro with binding constants in the range of 4.9 x 10(5) to 4.1 x 10(6) dm(3) mol(-1) as determined by absorption titration. Complexes 2a and [Au(TMPyP)]Cl(5) (4a; [H(2)TMPyP](4+)=meso-tetrakis(N-methylpyridinium-4-yl)porphyrin) interact with DNA in a manner similar to the DNA intercalator ethidium bromide as revealed by gel mobility shift assays and viscosity measurements. Both of them also inhibited the topoisomerase I induced relaxation of supercoiled DNA. Complex 4a, a gold(III) derivative of the known G-quadruplex-interactive porphyrin [H(2)TMPyP](4+), can similarly inhibit the amplification of a DNA substrate containing G-quadruplex structures in a polymerase chain reaction stop assay. In contrast to these reported complexes, complex 2a and the parental gold(III)-porphyrin 1a do not display a significant inhibitory effect (¡10\%) on telomerase. Based on the results of protein expression analysis and computational docking experiments, the anti-apoptotic bcl-2 protein is a potential target for those gold(III)-porphyrin complexes with apoptosis-inducing properties. Complex 2a also displays prominent anti-angiogenic properties in vitro. Taken together, the enhanced stabilization of the gold(III) ion and the ease of structural modification render porphyrins an attractive ligand system in the development of physiologically stable gold(III) complexes with anticancer and anti-angiogenic activities.},
	number = {10},
	journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
	author = {Sun, Raymond Wai-Yin and Li, Carrie Ka-Lei and Ma, Dik-Lung and Yan, Jessie Jing and Lok, Chun-Nam and Leung, Chung-Hang and Zhu, Nianyong and Che, Chi-Ming},
	month = mar,
	year = {2010},
	pmid = {20162647},
	keywords = {\#nosource, Animals, Antineoplastic Agents, Antineoplastic Agents: chemistry, Antineoplastic Agents: pharmacology, Binding Sites, Cell Cycle, Cell Cycle: drug effects, Cell Line, Crystallography, DNA, DNA: chemistry, DNA: metabolism, G-Quadruplexes, G-Quadruplexes: drug effects, Gold, Gold: chemistry, Gold: pharmacology, Humans, Ligands, Mice, Organogold Compounds, Organogold Compounds: chemistry, Organogold Compounds: pharmacology, Porphyrins, Porphyrins: chemistry, Porphyrins: metabolism, Porphyrins: pharmacology, Tumor, X-Ray},
	pages = {3097--113},
}

Paper  doi  abstract   bibtex   

@article{Hudson2009,
	title = {Interactions of actinomycin {D} with human telomeric {G}-quadruplex {DNA}.},
	volume = {48},
	issn = {1520-4995},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3021945&tool=pmcentrez&rendertype=abstract},
	doi = {10.1021/bi900203z},
	abstract = {The G-quadruplex structural motif of DNA has emerged as a novel and exciting target for anticancer drug discovery. The human telomeric G-quadruplex consists of a single strand repeat of d[AGGG(TTAGGG)(3)] that can fold into higher-order DNA structures. Small molecules that selectively target and stabilize the G-quadruplex structure(s) may serve as potential therapeutic agents and have garnered significant interest in recent years. In the work presented here, the anticancer agent, actinomycin D, is demonstrated to bind to and induce changes in both structure and stability in both the Na(+) and K(+) forms of the G-quadruplex DNA. The binding of actinomycin D to the G-quadruplex DNAs is characterized by intrinsic association constants of approximately 2 x 10(5) M(-1) (strand) and 2:1 molecularity, and are shown to be enthalpically driven with binding enthalpies of approximately -7 kcal/mol. The free Na(+) or K(+) forms of the quadruplex structures differ in melting temperatures by approximately 8 degrees C (60 and 68 degrees C, respectively), whereas both forms, when complexed with actinomycin D are stabilized with melting temperatures of approximately 79 degrees C. The induced CD signals observed for the actinomycin D-G-quadruplex complexes may indicate that the phenoxazone ring of actinomycin D is stacked on the G-tetrad rather than intercalated between adjacent G-tetrads. Complex formation with actinomycin D results in changes to both the Na(+) or K(+) structural isoforms to ligand-bound complexes having similar structural properties and stabilities.},
	number = {21},
	journal = {Biochemistry},
	author = {Hudson, Jason S and Brooks, Sonja C and Graves, David E},
	month = jul,
	year = {2009},
	pmid = {19348506},
	keywords = {\#nosource, Base Sequence, Calorimetry, Circular Dichroism, DNA, DNA: chemistry, DNA: genetics, DNA: metabolism, Dactinomycin, Dactinomycin: metabolism, Differential Scanning, G-Quadruplexes, Humans, Ligands, Oligodeoxyribonucleotides, Oligodeoxyribonucleotides: chemistry, Oligodeoxyribonucleotides: genetics, Oligodeoxyribonucleotides: metabolism, Telomere, Telomere: metabolism, Thermodynamics},
	pages = {4440--7},
}

Paper  doi  abstract   bibtex   

@article{Zhang2009,
	title = {Conformational conversion of {DNA} {G}-quadruplex induced by a cationic porphyrin.},
	volume = {74},
	issn = {1873-3557},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19577954 http://www.sciencedirect.com/science/article/B6VNG-4WJ3F0B-9/2/94613944cc41c548a9d1baae6e32aa56},
	doi = {10.1016/j.saa.2009.06.018},
	abstract = {The interactions between cationic meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the G-quadruplex (G4) of human telomeric single-strand oligonucleotide d(TTAGGG)(2) (S12) have been investigated by means of circular dichroism (CD), UV-visible absorption and fluorescence spectroscopies. It is found that TMPyP4 can preferentially induce the conformational conversion of the G4 structure from the parallel type to the parallel/antiparallel mixture in the presence of K(+), and that it can directly induce the formation of antiparallel G4 structure from the single-strand oligonucleotide S12 in the absence of K(+). Furthermore, the comparable experiments of TMPyP4 with two single-strand oligonucleotides S6 d(TTAGGG) and S24 d(TAGGG(TTAGGG)(3)T) in the absence of K(+) show that TMPyP4 can also induce the formation of antiparallel G4 from S24 but not from S6, indicating that the end-loops of the G4 structure are the key factors for the formation of G4 induced by TMPyP4.},
	number = {1},
	journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
	author = {Zhang, Huijuan and Xiao, Xiao and Wang, Peng and Pang, Siping and Qu, Feng and Ai, Xicheng and Zhang, Jianping},
	month = sep,
	year = {2009},
	pmid = {19577954},
	note = {tex.ids= zhangConformationalConversionDNA2009
publisher: Elsevier B.V.},
	keywords = {Biological, Circular Dichroism, DNA, G-Quadruplexes, G-quadruplex (G4) TMPyP4 Conformational conversion, Humans, Models, Molecular Structure, Nucleic Acid Conformation, Nucleic Acid Conformation: drug effects, Porphyrins, Porphyrins: chemistry, Porphyrins: metabolism, Porphyrins: pharmacology, Potassium, Potassium: chemistry, Potassium: pharmacology, Single-Stranded, Single-Stranded: chemistry, Single-Stranded: drug effects, Single-Stranded: metabolism},
	pages = {243--7},
}

Paper  doi  abstract   bibtex   

@article{Bomble2008,
	title = {Multiscale modeling of nucleic acids: insights into {DNA} flexibility.},
	volume = {89},
	issn = {0006-3525},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2561918&tool=pmcentrez&rendertype=abstract},
	doi = {10.1002/bip.21000},
	abstract = {The elastic rod theory is used together with all-atom normal mode analysis in implicit solvent to characterize the mechanical flexibility of duplex DNA. The bending, twisting, stretching rigidities extracted from all-atom simulations (on linear duplexes from 60 to 150 base pairs in length and from 94-bp minicircles) are in reasonable agreement with experimental results. We focus on salt concentration and sequence effects on the overall flexibility. Bending persistence lengths are about 20\% higher than most experimental estimates, but the transition from low-salt to high-salt behavior is reproduced well, as is the dependence of the stretching modulus on salt (which is opposite to that of bending). CTG and CGG trinucleotide repeats, responsible for several degenerative disorders, are found to be more flexible than random DNA, in agreement with several recent studies, whereas poly(dA).poly(dT) is the stiffest sequence we have encountered. The results suggest that current all-atom potentials, which were parameterized on small molecules and short oligonucleotides, also provide a useful description of duplex DNA at much longer length scales.},
	number = {9},
	journal = {Biopolymers},
	author = {Bomble, Yannick J and Case, David a},
	month = sep,
	year = {2008},
	pmid = {18412139},
	keywords = {\#nosource, Circular, Circular: chemistry, Computer Simulation, DNA, Models, Molecular, Nucleic Acid Conformation, Trinucleotide Repeats},
	pages = {722--31},
}

@article{dong_exploring_2008,
	title = {Exploring marine bacterial diversity in coastal {Georgia} salt marshes using {DNA} technology},
	volume = {70},
	abstract = {An important aspect of teaching biology is to expose students to the concept of biodiversity. For this purpose, bacteria are excellent examples. Prokaryotes were the first inhabitants on Earth, surviving and even thriving under very harsh conditions as new species continuously evolved. In fact, it is believed that there are more than 5 x 10{\textasciicircum}30 prokaryotes living on Earth today (Whitman et al., 1998). Our current knowledge of these tiny organisms is very limited, and less than 1\% of all bacterial species have been described (Horner-Devine et al., 2004). However, the prominent roles bacteria play in nature are not easy to overlook: Their functions range from providing essential nutrients to plants through nitrogen-fixation (such as for Rhizobium leguminosarum) to enhancement of nutrient absorption in animal intestines (such as for Escherichia coli). As a result, identifying unknown species of bacteria and extending our understanding of known ones are important tasks for 21st Century scientists.},
	journal = {The American Biology Teacher},
	author = {Dong, Yihe. and Guerrero, Stella. and Moran, Mary Ann.},
	year = {2008},
	keywords = {GCE, microbial ecology, salt marshes, diversity, bacteria, dna, education, molecular biology}
}

Paper  doi  abstract   bibtex   

@article{Yu2008,
	title = {Chiral metallo-supramolecular complexes selectively recognize human telomeric {G}-quadruplex {DNA}.},
	volume = {36},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2553577&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkn569},
	abstract = {Here, we report the first example that one enantiomer of a supramolecular cylinder can selectively stabilize human telomeric G-quadruplex DNA. The P-enantiomer of this cylinder has a strong preference for G-quadruplex over duplex DNA and, in the presence of sodium, can convert G-quadruplexes from an antiparallel to a hybrid structure. The compound's chiral selectivity and its ability to discriminate quadruplex DNA have been studied by DNA melting, circular dichroism, gel electrophoresis, fluorescence spectroscopy and S1 nuclease cleavage. The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif. The complex is also convenient to synthesize and separate enantiomers. These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.},
	number = {17},
	journal = {Nucleic acids research},
	author = {Yu, Haijia and Wang, Xiaohui and Fu, Manliang and Ren, Jinsong and Qu, Xiaogang},
	month = oct,
	year = {2008},
	pmid = {18776218},
	keywords = {\#nosource, Antineoplastic Agents, Antineoplastic Agents: chemistry, DNA, DNA: chemistry, Ferrous Compounds, Ferrous Compounds: chemistry, G-Quadruplexes, Humans, Stereoisomerism, Telomere, Telomere: chemistry},
	pages = {5695--703},
}

Paper  doi  abstract   bibtex   

@article{Cheng2008,
	title = {Antitumor polycyclic acridines. 20. {Search} for {DNA} quadruplex binding selectivity in a series of 8,13-dimethylquino[4,3,2-kl]acridinium salts: telomere-targeted agents.},
	volume = {51},
	issn = {0022-2623},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18247546},
	doi = {10.1021/jm070587t},
	abstract = {The growth-inhibitory activities of an extensive series of quaternized quino[4,3,2- kl]acridinium salts against tumor cell lines in vitro have been measured and their biological properties interpreted in the light of differential binding to different DNA isoforms. Selectivity for quadruplex DNA binding and stabilization by compounds were explored through an array of methods: UV absorption and fluorescence emission spectroscopy, surface plasmon resonance, and competition dialysis. Quadruplex DNA interaction was further characterized through FRET and DNA polymerase arrest assays. Telomerase inhibition, inferred from the TRAP assay, is attributed to quadruplex stabilization, supported by the strong correlation (R(2) = 0.81) across the series between quadruplex DNA binding affinity and TRAP inhibition potency. Growth inhibition potency in the NCI60 human tumor cell line panel is more marked in compounds with greater DNA duplex binding affinity (R(2) = 0.82). Quantification of relative quadruplex and duplex binding affinity constants puts some of these ligands among the most selective quadruplex DNA interactive agents reported to date.},
	number = {4},
	journal = {Journal of medicinal chemistry},
	author = {Cheng, Mai-Kim and Modi, Chetna and Cookson, Jennifer C and Hutchinson, Ian and Heald, Robert a and McCarroll, Andrew J and Missailidis, Sotiris and Tanious, Farial and Wilson, W David and Mergny, Jean-Louis and Laughton, Charles a and Stevens, Malcolm F G},
	month = feb,
	year = {2008},
	pmid = {18247546},
	keywords = {\#nosource, Acridines, Acridines: chemical synthesis, Acridines: chemistry, Acridines: pharmacology, Antineoplastic Agents, Antineoplastic Agents: chemical synthesis, Antineoplastic Agents: chemistry, Antineoplastic Agents: pharmacology, Antitumor, Cell Line, Cell Proliferation, Cell Proliferation: drug effects, DNA, DNA: chemistry, Drug Screening Assays, Fluorescence Resonance Energy Transfer, G-Quadruplexes, Heterocyclic Compounds with 4 or More Rings, Heterocyclic Compounds with 4 or More Rings: chemi, Heterocyclic Compounds with 4 or More Rings: pharm, Humans, Quaternary Ammonium Compounds, Quaternary Ammonium Compounds: chemical synthesis, Quaternary Ammonium Compounds: chemistry, Quaternary Ammonium Compounds: pharmacology, Structure-Activity Relationship, Surface Plasmon Resonance, Telomerase, Telomerase: antagonists \& inhibitors, Telomere, Telomere: metabolism, Tumor},
	pages = {963--75},
}

Paper  doi  abstract   bibtex   

@article{Gray2008,
	title = {Kinetics and mechanism of {K}+- and {Na}+-induced folding of models of human telomeric {DNA} into {G}-quadruplex structures.},
	volume = {36},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2475619&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkn379},
	abstract = {Cation-induced folding into quadruplex structures for three model human telomeric oligonucleotides, d[AGGG(TTAGGG)(3)], d[TTGGG(TTAGGG)(3)A] and d[TTGGG(TTAGGG)(3)], was characterized by equilibrium titrations with KCl and NaCl and by multiwavelength stopped flow kinetics. Cation binding was cooperative with Hill coefficients of 1.5-2.2 in K(+) and 2.4-2.9 in Na(+) with half-saturation concentrations of 0.5-1 mM for K(+) and 4-13 mM for Na(+) depending on the oligonucleotide sequence. Oligonucleotide folding in 50 mM KCl at 25 degrees C consisted of single exponential processes with relaxation times tau of 20-60 ms depending on the sequence. In contrast, folding in100 mM NaCl consisted of three exponentials with tau-values of 40-85 ms, 250-950 ms and 1.5-10.5 s. The folding rate constants approached limiting values with increasing cation concentration; in addition, the rates of folding decreased with increasing temperature over the range 15-45 degrees C. Taken together, these results suggest that folding of G-rich oligonucleotides into quadruplex structures proceeds via kinetically significant intermediates. These intermediates may consist of antiparallel hairpins in rapid equilibrium with less ordered structures. The hairpins may subsequently form nascent G-quartets stabilized by H-bonding and cation binding followed by relatively slow strand rearrangements to form the final completely folded topologies. Fewer kinetic intermediates were evident with K(+) than Na(+), suggesting a simpler folding pathway in K(+) solutions.},
	number = {12},
	journal = {Nucleic acids research},
	author = {Gray, Robert D and Chaires, Jonathan B},
	month = jul,
	year = {2008},
	pmid = {18567908},
	keywords = {\#nosource, Cations, Cations: chemistry, DNA, DNA: chemistry, G-Quadruplexes, Humans, Kinetics, Models, Molecular, Oligodeoxyribonucleotides, Oligodeoxyribonucleotides: chemistry, Potassium, Potassium Chloride, Potassium Chloride: pharmacology, Potassium: chemistry, Sodium, Sodium Chloride, Sodium Chloride: pharmacology, Sodium: chemistry, Telomere, Telomere: chemistry, Temperature},
	pages = {4191--203},
}

Paper  doi  abstract   bibtex   

@article{lesch_molecular_2008,
	title = {Molecular genetics of adult {ADHD}: converging evidence from genome-wide association and extended pedigree linkage studies.},
	volume = {115},
	issn = {0300-9564},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18839057},
	doi = {10.1007/s00702-008-0119-3},
	abstract = {A genome-wide association (GWA) study with pooled DNA in adult attention-deficit/hyperactivity disorder (ADHD) employing approximately 500K SNP markers identifies novel risk genes and reveals remarkable overlap with findings from recent GWA scans in substance use disorders. Comparison with results from our previously reported high-resolution linkage scan in extended pedigrees confirms several chromosomal loci, including 16q23.1-24.3 which also reached genome-wide significance in a recent meta-analysis of seven linkage studies (Zhou et al. in Am J Med Genet Part B, 2008). The findings provide additional support for a common effect of genes coding for cell adhesion molecules (e.g., CDH13, ASTN2) and regulators of synaptic plasticity (e.g., CTNNA2, KALRN) despite the complex multifactorial etiologies of adult ADHD and addiction vulnerability.},
	number = {11},
	urldate = {2015-05-16},
	journal = {Journal of neural transmission (Vienna, Austria : 1996)},
	author = {Lesch, Klaus-Peter and Timmesfeld, Nina and Renner, Tobias J and Halperin, Rebecca and Röser, Christoph and Nguyen, T Trang and Craig, David W and Romanos, Jasmin and Heine, Monika and Meyer, Jobst and Freitag, Christine and Warnke, Andreas and Romanos, Marcel and Schäfer, Helmut and Walitza, Susanne and Reif, Andreas and Stephan, Dietrich A and Jacob, Christian},
	month = nov,
	year = {2008},
	pmid = {18839057},
	keywords = {Adult, Attention Deficit Disorder with Hyperactivity, Attention Deficit Disorder with Hyperactivity: gen, Cell Adhesion Molecules, Chromosomes, Chromosomes: genetics, DNA, DNA: genetics, Female, Genetic Linkage, Genetic Linkage: genetics, Genome, Genome-Wide Association Study, Genotype, Human, Humans, Male, Molecular Biology, Neuronal Plasticity, Neuronal Plasticity: physiology, Polymorphism, Single Nucleotide, Single Nucleotide: genetics},
	pages = {1573--85},
}

Paper  doi  bibtex   

@article{Jayawickramarajah2007,
	title = {Allosteric control of self-assembly: modulating the formation of guanine quadruplexes through orthogonal aromatic interactions.},
	volume = {46},
	issn = {1433-7851},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17823899},
	doi = {10.1002/anie.200701883},
	number = {40},
	journal = {Angewandte Chemie (International ed. in English)},
	author = {Jayawickramarajah, Janarthanan and Tagore, Debarati M and Tsou, Lun K and Hamilton, Andrew D},
	month = jan,
	year = {2007},
	pmid = {17823899},
	keywords = {\#nosource, Allosteric Regulation, Circular Dichroism, DNA, DNA: chemistry, Electrons, G-Quadruplexes, Guanine, Guanine: chemistry, Molecular Structure, Spectrophotometry},
	pages = {7583--6},
}

Paper  doi  abstract   bibtex   

@article{Paramasivan2007,
	title = {Circular dichroism of quadruplex {DNAs}: applications to structure, cation effects and ligand binding.},
	volume = {43},
	issn = {1046-2023},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17967702},
	doi = {10.1016/j.ymeth.2007.02.009},
	abstract = {Circular dichroism, CD, spectra can be used to gain information about quadruplex structures of DNAs as well as the effects of sequence, cations, chemical modification and ligand binding on quadruplex structure. There is not yet a validated approach to calculate a CD spectrum from a quadruplex structure nor is their one to go from a CD spectrum to a structure. However, it is possible to empirically correlate CD spectra features with quadruplex structural type in many cases. In this article four case studies are presented to indicate the strengths and limitations of CD in investigations of the properties of quadruplex structures formed by telomere repeat sequences. The case studies include determination of the quadruplex structural type present as a function of potassium concentration, the effect of sequence on the equilibrium between quadruplex structural types as a function of potassium concentration, the effect of ligand binding on quadruplex structure and the effect of 5' phosphorylation on quadruplex structural type.},
	number = {4},
	journal = {Methods (San Diego, Calif.)},
	author = {Paramasivan, Sattanathan and Rujan, Iulian and Bolton, Philip H},
	month = dec,
	year = {2007},
	pmid = {17967702},
	keywords = {\#nosource, Circular Dichroism, Circular Dichroism: methods, DNA, DNA: chemistry, G-Quadruplexes, Guanine, Guanine: chemistry, Ligands},
	pages = {324--31},
}

Paper  doi  abstract   bibtex   

@article{foissac_astalavista:_2007,
	title = {{ASTALAVISTA}: dynamic and flexible analysis of alternative splicing events in custom gene datasets.},
	volume = {35},
	issn = {1362-4962},
	url = {http://nar.oxfordjournals.org/content/35/suppl_2/W297.abstract},
	doi = {10.1093/nar/gkm311},
	abstract = {In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade. Consequently, the increasing transcript coverage also revealed the real complexity of some variations in the exon-intron structure between transcript variants and the need for computational tools to address 'complex' AS events. ASTALAVISTA (alternative splicing transcriptional landscape visualization tool) employs an intuitive and complete notation system to univocally identify such events. The method extracts AS events dynamically from custom gene annotations, classifies them into groups of common types and visualizes a comprehensive picture of the resulting AS landscape. Thus, ASTALAVISTA can characterize AS for whole transcriptome data from reference annotations (GENCODE, REFSEQ, ENSEMBL) as well as for genes selected by the user according to common functional/structural attributes of interest: http://genome.imim.es/astalavista.},
	number = {Web Server issue},
	journal = {Nucleic acids research},
	author = {Foissac, Sylvain and Sammeth, Michael},
	month = jul,
	year = {2007},
	pmid = {17485470},
	keywords = {Alternative Splicing, Alternative Splicing: genetics, Chromosome Mapping, Chromosome Mapping: methods, Computational Biology, Computational Biology: methods, DNA, DNA Probes, DNA Probes: genetics, DNA: methods, Databases, Genetic, Genome, Humans, Internet, Messenger, Messenger: metabolism, Oligonucleotide Array Sequence Analysis, Oligonucleotide Array Sequence Analysis: instrumen, Oligonucleotide Array Sequence Analysis: methods, RNA, RNA Splice Sites, RNA Splice Sites: genetics, Sequence Analysis, Software},
	pages = {297}
}

Paper  doi  abstract   bibtex   

@article{Kibbe2007,
	title = {{OligoCalc}: an online oligonucleotide properties calculator.},
	volume = {35},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933198&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkm234},
	abstract = {We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. OligoCalc has a familiar 'calculator' look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900,000 accesses of OligoCalc from nearly 200,000 distinct hosts, excluding search engines. OligoCalc is available at http://basic.northwestern.edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well.},
	number = {Web Server issue},
	journal = {Nucleic acids research},
	author = {Kibbe, Warren a},
	month = jul,
	year = {2007},
	pmid = {17452344},
	keywords = {\#nosource, Algorithms, Animals, Base Composition, Chemical, Computational Biology, Computational Biology: methods, DNA, DNA: chemistry, Humans, Internet, Models, Oligonucleotides, Oligonucleotides: chemistry, Oligonucleotides: genetics, RNA, RNA: chemistry, Software, Temperature, User-Computer Interface},
	pages = {W43--6},
}

Paper  doi  abstract   bibtex   

@article{Wang2007,
	title = {The {POT1}-{TPP1} telomere complex is a telomerase processivity factor.},
	volume = {445},
	issn = {1476-4687},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17237768},
	doi = {10.1038/nature05454},
	abstract = {Telomeres were originally defined as chromosome caps that prevent the natural ends of linear chromosomes from undergoing deleterious degradation and fusion events. POT1 (protection of telomeres) protein binds the single-stranded G-rich DNA overhangs at human chromosome ends and suppresses unwanted DNA repair activities. TPP1 is a previously identified binding partner of POT1 that has been proposed to form part of a six-protein shelterin complex at telomeres. Here, the crystal structure of a domain of human TPP1 reveals an oligonucleotide/oligosaccharide-binding fold that is structurally similar to the beta-subunit of the telomere end-binding protein of a ciliated protozoan, suggesting that TPP1 is the missing beta-subunit of human POT1 protein. Telomeric DNA end-binding proteins have generally been found to inhibit rather than stimulate the action of the chromosome end-replicating enzyme, telomerase. In contrast, we find that TPP1 and POT1 form a complex with telomeric DNA that increases the activity and processivity of the human telomerase core enzyme. We propose that POT1-TPP1 switches from inhibiting telomerase access to the telomere, as a component of shelterin, to serving as a processivity factor for telomerase during telomere extension.},
	number = {7127},
	journal = {Nature},
	author = {Wang, Feng and Podell, Elaine R and Zaug, Arthur J and Yang, Yuting and Baciu, Paul and Cech, Thomas R and Lei, Ming},
	month = mar,
	year = {2007},
	pmid = {17237768},
	keywords = {\#nosource, Crystallography, DNA, Humans, Multiprotein Complexes, Multiprotein Complexes: chemistry, Multiprotein Complexes: metabolism, Nucleic Acid Conformation, Protein, Protein Binding, Protein Structure, Protein Subunits, Protein Subunits: chemistry, Protein Subunits: metabolism, Single-Stranded, Single-Stranded: chemistry, Single-Stranded: genetics, Single-Stranded: metabolism, Structural Homology, Telomerase, Telomerase: antagonists \& inhibitors, Telomerase: chemistry, Telomerase: metabolism, Telomere-Binding Proteins, Telomere-Binding Proteins: chemistry, Telomere-Binding Proteins: metabolism, Tertiary, X-Ray},
	pages = {506--10},
}

@article{Rachwal2007,
  title = {Sequence Effects of Single Base Loops in Intramolecular Quadruplex {{DNA}}.},
  author = {a Rachwal, Phillip and Brown, Tom and Fox, Keith R},
  year = {2007},
  month = may,
  journal = {FEBS letters},
  volume = {581},
  number = {8},
  eprint = {17399710},
  eprinttype = {pubmed},
  pages = {1657--60},
  issn = {0014-5793},
  doi = {10.1016/j.febslet.2007.03.040},
  abstract = {We have examined the properties of intramolecular G-quadruplexes in which the G3 tracts are separated by single base loops. The most stable complex contained 1',2'-dideoxyribose in all three loops, while loops containing T and C were slightly less stable (by about 2 degrees C). Quadruplexes containing loops with single A residues were less stable by 8 degrees C for each T to A substitution. These folded sequences display similar CD spectra, which are consistent with the formation of parallel stranded complexes with double-chain reversal loops. These results demonstrate that loop sequence, and not just length, affects quadruplex stability.},
  pmid = {17399710},
  keywords = {\#nosource,Base Sequence,Deoxyribose,Deoxyribose: analysis,DNA,DNA: chemistry,DNA: genetics,G-Quadruplexes,Nucleic Acid Conformation,Oligonucleotides,Oligonucleotides: chemistry,Oligonucleotides: genetics,Thermodynamics}
}

Paper  Website  abstract   bibtex   

@article{
 title = {High efficiency DNA extraction from bone by total demineralization.},
 type = {article},
 year = {2007},
 identifiers = {[object Object]},
 keywords = {Bone Demineralization Technique,Bone Demineralization Technique: methods,Bone and Bones,Bone and Bones: chemistry,DNA,DNA, Mitochondrial,DNA, Mitochondrial: genetics,DNA, Mitochondrial: isolation & purification,DNA: genetics,DNA: isolation & purification,Forensic Genetics,Forensic Genetics: methods,Humans,Microsatellite Repeats,Tooth,Tooth: chemistry},
 pages = {191-5},
 volume = {1},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/19083754},
 month = {6},
 id = {2aa68071-5255-311a-935f-14249638382d},
 created = {2012-12-06T09:12:59.000Z},
 accessed = {2010-08-18},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Loreille2007a},
 abstract = {In historical cases, missing persons' identification, mass disasters, and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA typing. This is because of the physical and chemical barrier that the protein:mineral matrix of bone poses to environmental deterioration and biological attack. Most bone extraction protocols utilized in the forensic community involve an incubation period of bone powder in extraction buffer for proteinase digestion, followed by the collection of the supernatant, and the disposal of large quantities of undissolved bone powder. Here we present an extremely efficient protocol for recovery of DNA by complete demineralization, resulting in full physical dissolution of the bone sample. This is performed in a manner that retains and concentrates all the reagent volume, for complete DNA recovery. For our study, we selected 14 challenging bone samples. The bones were extracted side-by-side with our new demineralization protocol and the standard extraction protocol in use at AFDIL. A real-time quantification assay based on the amplification of a 143 bp mtDNA fragment showed that this new demineralization protocol significantly enhances the quantity of DNA that can be extracted and amplified from degraded skeletal remains. We have used this technique to successfully recover authentic DNA sequences from extremely challenging samples that failed repeatedly using the standard protocol.},
 bibtype = {article},
 author = {Loreille, Odile M and Diegoli, Toni M and Irwin, Jodi a and Coble, Michael D and Parsons, Thomas J},
 journal = {Forensic science international. Genetics},
 number = {2}
}

@article{RN50,
   author = {Lewis, Z. A. and Shiver, A. L. and Stiffler, N. and Miller, M. R. and Johnson, E. A. and Selker, E. U.},
   title = {High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora},
   journal = {Genetics},
   volume = {177},
   number = {2},
   pages = {1163-71},
   note = {Lewis, Zachary A
Shiver, Anthony L
Stiffler, Nicholas
Miller, Michael R
Johnson, Eric A
Selker, Eric U
GM025690-22/GM/NIGMS NIH HHS/United States
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
United States
2007/07/31
Genetics. 2007 Oct;177(2):1163-71. doi: 10.1534/genetics.107.078147. Epub 2007 Jul 29.},
   abstract = {The wealth of sequence information available for Neurospora crassa and other fungi has greatly facilitated evolutionary and molecular analyses of this group. Although "reverse" genetics, in which genes are first identified by their sequence rather than by their mutant phenotypes, serves as a valuable new approach for elucidating biological processes, classical "forward" genetic analysis is still extremely useful. Unfortunately, mapping mutations and identifying the corresponding genes has typically been slow and laborious. To facilitate forward genetics in Neurospora, we have adapted microarray-based restriction-site-associated DNA (RAD) mapping for use with N. crassa oligonucleotide microarrays. This technique was used to simultaneously detect an unprecedented number of genomewide restriction site polymorphisms from two N. crassa strains: Mauriceville and Oak Ridge. Furthermore, RAD mapping was used to quickly map a previously unknown gene, defective in methylation-7 (dim-7).},
   keywords = {DNA, Fungal/*genetics
Genes, Fungal
Genetic Markers
Genome, Fungal/*genetics
Microarray Analysis
Mutation
Neurospora crassa/*genetics
Polymorphism, Genetic
Restriction Mapping/*methods},
   ISSN = {0016-6731 (Print)
0016-6731},
   DOI = {10.1534/genetics.107.078147},
   year = {2007},
   type = {Journal Article}
}

Paper  doi  abstract   bibtex   

@article{Mergny2006,
	title = {Kinetics of double-chain reversals bridging contiguous quartets in tetramolecular quadruplexes.},
	volume = {34},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1458523&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkl098},
	abstract = {Repetitive 5'GGXGG DNA segments abound in, or near, regulatory regions of the genome and may form unusual structures called G-quadruplexes. Using NMR spectroscopy, we demonstrate that a family of 5'GCGGXGGY sequences adopts a folding topology containing double-chain reversals. The topology is composed of two bistranded quadruplex monomeric units linked by formation of G:C:G:C tetrads. We provide a complete thermodynamic and kinetic analysis of 13 different sequences using absorbance spectroscopy and DSC, and compare their kinetics with a canonical tetrameric parallel-stranded quadruplex formed by TG4T. We demonstrate large differences (up to 10(5)-fold) in the association constants of these quadruplexes depending on primary sequence; the fastest samples exhibiting association rate equal or higher than the canonical TG4T quadruplex. In contrast, all sequences studied here unfold at a lower temperature than this quadruplex. Some sequences have thermodynamic stability comparable to the canonical TG4T tetramolecular quadruplex, but with faster association and dissociation. Sequence effects on the dissociation processes are discussed in light of structural data.},
	number = {8},
	journal = {Nucleic acids research},
	author = {Mergny, Jean-Louis and Cian, Anne De and Amrane, Samir and da Silva, Mateus Webba},
	month = jan,
	year = {2006},
	pmid = {16682446},
	keywords = {\#nosource, Base Sequence, Biomolecular, Calorimetry, DNA, DNA: chemistry, Differential Scanning, G-Quadruplexes, Guanine, Guanine: chemistry, Hydrogen-Ion Concentration, Kinetics, Nuclear Magnetic Resonance, Nucleic Acid Conformation, Osmolar Concentration, Temperature, Thermodynamics},
	pages = {2386--97},
}

Paper  doi  abstract   bibtex   

@article{Moore2006,
	title = {Synthesis of distamycin {A} polyamides targeting {G}-quadruplex {DNA}.},
	volume = {4},
	issn = {1477-0520},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17036143},
	doi = {10.1039/b607707b},
	abstract = {A number of amide-linked oligopyrroles based on distamycin molecules have been synthesized by solid-state methods, and their interactions with a human intramolecular G-quadruplex have been measured by a melting procedure. Several of these molecules show an enhanced ratio of quadruplex vs. duplex DNA binding compared to distamycin itself, including one with a 2,5-disubstituted pyrrole group. Quadruplex affinity increases with the number of pyrrole groups, and it is suggested that this is consistent with a mixed groove/G-quartet stacking binding mode.},
	number = {18},
	journal = {Organic \& biomolecular chemistry},
	author = {Moore, Michael J B and Cuenca, Francisco and Searcey, Mark and Neidle, Stephen},
	month = oct,
	year = {2006},
	pmid = {17036143},
	keywords = {\#nosource, DNA, DNA: chemistry, Dimerization, Distamycins, Distamycins: chemical synthesis, Distamycins: chemistry, Fluorescence Resonance Energy Transfer, G-Quadruplexes, Humans, Models, Molecular, Nylons, Nylons: chemical synthesis, Nylons: chemistry, Thermodynamics},
	pages = {3479--88},
}

Paper  Website  abstract   bibtex   

@article{
 title = {Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus.},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Codon,Consensus Sequence,DNA Primers,DNA Primers: genetics,DNA, Algal,DNA, Algal: genetics,Databases, Nucleic Acid,Expressed Sequence Tags,Genetic Markers,Microsatellite Repeats,Microsatellite Repeats: genetics,Open Reading Frames,Phylogeny,Phytophthora,Phytophthora: genetics,Species Specificity,Transcription, Genetic},
 pages = {245},
 volume = {7},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1594578&tool=pmcentrez&rendertype=abstract},
 month = {1},
 id = {f0612254-194c-38b3-865d-113bae82d407},
 created = {2015-09-09T02:21:59.000Z},
 accessed = {2015-09-09},
 file_attached = {true},
 profile_id = {f95ef69b-8f96-32da-8de9-769c2acf0685},
 last_modified = {2015-09-09T02:22:11.000Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 abstract = {BACKGROUND: Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes.

RESULTS: The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database.

CONCLUSION: In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5%) of primers could be transferred with 90% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.},
 bibtype = {article},
 author = {Garnica, Diana P and Pinzón, Andrés M and Quesada-Ocampo, Lina M and Bernal, Adriana J and Barreto, Emiliano and Grünwald, Niklaus J and Restrepo, Silvia},
 journal = {BMC genomics}
}

Paper  doi  bibtex   

@article{Wieland2006,
	title = {Turning inhibitors into activators: a hammerhead ribozyme controlled by a guanine quadruplex.},
	volume = {45},
	issn = {1433-7851},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16871639},
	doi = {10.1002/anie.200600909},
	number = {35},
	journal = {Angewandte Chemie (International ed. in English)},
	author = {Wieland, Markus and Hartig, Jörg S},
	month = oct,
	year = {2006},
	pmid = {16871639},
	keywords = {\#nosource, Base Sequence, Catalytic, Catalytic: antagonists \& inhibitors, Catalytic: chemistry, DNA, DNA: chemistry, Enzyme Inhibitors, Enzyme Inhibitors: chemistry, Nucleic Acid Conformation, RNA, RNA: chemistry},
	pages = {5875--8},
}

@Article{roch06short,
  author    = {Sebastien Roch},
  title     = {A short proof that phylogenetic tree reconstruction by maximum likelihood is hard.},
  journal   = TCBB,
  year      = {2006},
  volume    = {3},
  number    = {1},
  pages     = {92--94},
  abstract  = {Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel.},
  doi       = {10.1109/TCBB.2006.4},
  keywords  = {Computer Simulation; Genetics, Population; Likelihood Functions; Phylogeny; Recombination; Sequence Analysis, DNA},
  owner     = {Sebastian},
  pmid      = {17048396},
  timestamp = {2006.12.29},
}

Paper  doi  abstract   bibtex   

@article{Ambrus2006,
	title = {Human telomeric sequence forms a hybrid-type intramolecular {G}-quadruplex structure with mixed parallel/antiparallel strands in potassium solution.},
	volume = {34},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1464114&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkl348},
	abstract = {Human telomeric DNA consists of tandem repeats of the sequence d(TTAGGG). The formation and stabilization of DNA G-quadruplexes in the human telomeric sequence have been shown to inhibit the activity of telomerase, thus the telomeric DNA G-quadruplex has been considered as an attractive target for cancer therapeutic intervention. However, knowledge of the intact human telomeric G-quadruplex structure(s) formed under physiological conditions is a prerequisite for structure-based rational drug design. Here we report the folding structure of the human telomeric sequence in K+ solution determined by NMR. Our results demonstrate a novel, unprecedented intramolecular G-quadruplex folding topology with hybrid-type mixed parallel/antiparallel G-strands. This telomeric G-quadruplex structure contains three G-tetrads with mixed G-arrangements, which are connected consecutively with a double-chain-reversal side loop and two lateral loops, each consisting of three nucleotides TTA. This intramolecular hybrid-type telomeric G-quadruplex structure formed in K+ solution is distinct from those reported on the 22 nt Tel22 in Na+ solution and in crystalline state in the presence of K+, and appears to be the predominant conformation for the extended 26 nt telomeric sequence Tel26 in the presence of K+, regardless of the presence or absence of Na+. Furthermore, the addition of K+ readily converts the Na+-form conformation to the K+-form hybrid-type G-quadruplex. Our results explain all the reported experimental data on the human telomeric G-quadruplexes formed in the presence of K+, and provide important insights for understanding the polymorphism and interconversion of various G-quadruplex structures formed within the human telomeric sequence, as well as the effects of sequence and cations. This hybrid-type G-quadruplex topology suggests a straightforward pathway for the secondary structure formation with effective packing within the extended human telomeric DNA. The hybrid-type telomeric G-quadruplex is most likely to be of pharmacological relevance, and the distinct folding topology of this G-quadruplex suggests that it can be specifically targeted by G-quadruplex interactive small molecule drugs.},
	number = {9},
	journal = {Nucleic acids research},
	author = {Ambrus, Attila and Chen, Ding and Dai, Jixun and Bialis, Tiffanie and Jones, Roger a and Yang, Danzhou},
	month = jan,
	year = {2006},
	pmid = {16714449},
	keywords = {Biomolecular, Circular Dichroism, DNA, DNA: chemistry, G-Quadruplexes, Guanine, Guanine: chemistry, Humans, Nuclear Magnetic Resonance, Nucleic Acid, Nucleic Acid Conformation, Potassium, Potassium: chemistry, Protons, Repetitive Sequences, Sodium, Sodium: chemistry, Solutions, Telomere, Telomere: chemistry},
	pages = {2723--35},
}

Paper  doi  abstract   bibtex   

@article{Rawal2006,
	title = {Genome-wide prediction of {G4} {DNA} as regulatory motifs: role in {Escherichia} coli global regulation.},
	volume = {16},
	issn = {1088-9051},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1457047&tool=pmcentrez&rendertype=abstract},
	doi = {10.1101/gr.4508806},
	abstract = {The role of nonlinear DNA in replication, recombination, and transcription has become evident in recent years. Although several studies have predicted and characterized regulatory elements at the sequence level, very few have investigated DNA structure as regulatory motifs. Here, using G-quadruplex or G4 DNA motifs as a model, we have researched the role of DNA structure in transcription on a genome-wide scale. Analyses of ¿61,000 open reading frames (ORFs) across 18 prokaryotes show enrichment of G4 motifs in regulatory regions and indicate its predominance within promoters of genes pertaining to transcription, secondary metabolite biosynthesis, and signal transduction. Based on this, we predict that G4 DNA may present regulatory signals. This is supported by conserved G4 motifs in promoters of orthologous genes across phylogenetically distant organisms. We hypothesized a regulatory role of G4 DNA during supercoiling stress, when duplex destabilization may result in G4 formation. This is in line with our observations from target site analysis for 55 DNA-binding proteins in Escherichia coli, which reveals significant (P¡0.001) association of G4 motifs with target sites of global regulators FIS and Lrp and the sigma factor RpoD (sigma70). These factors together control ¿1000 genes in the early growth phase and are believed to be induced by supercoiled DNA. We also predict G4 motif-induced supercoiling sensitivity for ¿30 operons in E. coli, and our findings implicate G4 DNA in DNA-topology-mediated global gene regulation in E. coli.},
	number = {5},
	journal = {Genome research},
	author = {Rawal, Pooja and Kummarasetti, Veera Bhadra Rao and Ravindran, Jinoy and Kumar, Nirmal and Halder, Kangkan and Sharma, Rakesh and Mukerji, Mitali and Das, Swapan Kumar and Chowdhury, Shantanu},
	month = may,
	year = {2006},
	pmid = {16651665},
	keywords = {\#nosource, Bacterial, Bacterial: chemistry, Chemical, Conserved Sequence, DNA, Escherichia coli, Escherichia coli: genetics, Escherichia coli: metabolism, Gene Expression Regulation, Genes, Genome, Guanine, Guanine: chemistry, Hydrogen Bonding, Models, Nucleic Acid, Nucleic Acid Conformation, Regulator, Regulatory Sequences},
	pages = {644--55},
}

Paper  doi  abstract   bibtex   

@article{Allain2006,
	title = {{FRET} templated by {G}-quadruplex {DNA}: a specific ternary interaction using an original pair of donor/acceptor partners.},
	volume = {128},
	issn = {0002-7863},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16953629},
	doi = {10.1021/ja062193h},
	abstract = {G-quadruplex represents a suitable scaffold for FRET (fluorescence resonance energy transfer) since its two external quartets offer two well-defined binding sites for concomitant trapping of donor/acceptor partners. Combining selective G-quadruplex binders (macrocyclic bis(quinacridine) BOQ(1) or monomeric quinacridine MMQ(1), donor) with a highly fluorescent DNA probe (thiazole orange, acceptor), we designed a structure-specific FRET-system based on an unprecedented noncovalent ternary complex. This system could be potentially usable as a signature for quadruplex-DNA conformation in solution, but also might offer a unique means for observing cation and ligand binding influence on quadruplex topology.},
	number = {36},
	journal = {Journal of the American Chemical Society},
	author = {Allain, Clémence and Monchaud, David and Teulade-Fichou, Marie-Paule},
	month = sep,
	year = {2006},
	pmid = {16953629},
	keywords = {\#nosource, Acridines, Acridines: chemistry, Benzothiazoles, Benzothiazoles: chemistry, Binding Sites, DNA, DNA Probes, DNA Probes: chemistry, DNA: chemistry, Fluorescence, Fluorescence Resonance Energy Transfer, Fluorescence Resonance Energy Transfer: methods, Fluorescent Dyes, Fluorescent Dyes: chemistry, G-Quadruplexes, Nucleic Acid Conformation, Quinolines, Quinolines: chemistry, Spectrometry},
	pages = {11890--3},
}

Paper  doi  abstract   bibtex   

@article{ben-yehuda_defining_2005,
	title = {Defining a centromere-like element in {Bacillus} subtilis by {Identifying} the binding sites for the chromosome-anchoring protein {RacA}},
	volume = {17},
	issn = {1097-2765},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15780934},
	doi = {10.1016/j.molcel.2005.02.023},
	abstract = {Chromosome segregation during sporulation in Bacillus subtilis involves the anchoring of sister chromosomes to opposite ends of the cell. Anchoring is mediated by RacA, which acts as a bridge between a centromere-like element in the vicinity of the origin of replication and the cell pole. To define this element we mapped RacA binding sites by performing chromatin immunoprecipitation in conjunction with gene microarray analysis. RacA preferentially bound to 25 regions spread over 612 kb across the origin portion of the chromosome. Computational and biochemical analysis identified a GC-rich, inverted 14 bp repeat as the recognition sequence. Experiments with single molecules of DNA demonstrated that RacA can condense nonspecific DNA dramatically against appreciable forces to form a highly stable protein-DNA complex. We propose that interactions between DNA bound RacA molecules cause the centromere-like element to fold up into a higher order complex that fastens the chromosome to the cell pole.},
	number = {6},
	urldate = {2009-03-12TZ},
	journal = {Molecular Cell},
	author = {Ben-Yehuda, Sigal and Fujita, Masya and Liu, Xiaole Shirley and Gorbatyuk, Boris and Skoko, Dunja and Yan, Jie and Marko, John F and Liu, Jun S and Eichenberger, Patrick and Rudner, David Z and Losick, Richard},
	month = mar,
	year = {2005},
	pmid = {15780934},
	keywords = {Bacillus subtilis, Bacterial Proteins, Binding Sites, Cell Division, Cell Polarity, Centromere, Chromatin Immunoprecipitation, Chromosomes, Bacterial, DNA, Bacterial, GC Rich Sequence, Gene Expression Regulation, Bacterial, Microarray Analysis, Protein Binding, Replication Origin, Spores, Bacterial},
	pages = {773--82}
}

@article{Phillips2005,
  title = {Water-Soluble Organic Dppz Analogues{\textendash}Tuning {{DNA}} Binding Affinities, Luminescence, and Photo-Redox Properties.},
  author = {Phillips, Tim and Rajput, Chatna and Twyman, Lance and Haq, Ihtshamul and a Thomas, Jim},
  year = {2005},
  month = sep,
  journal = {Chemical communications (Cambridge, England)},
  volume = {44},
  number = {34},
  eprint = {16113737},
  eprinttype = {pubmed},
  pages = {4327--9},
  issn = {1359-7345},
  doi = {10.1039/b506946g},
  abstract = {Three new water-soluble dppz derivatives are reported, one of which binds to DNA with an affinity comparable to any mononuclear metal complex and also displays a high selectivity for GC sites.},
  pmid = {16113737},
  keywords = {\#nosource,DNA,DNA: chemistry,Fast Atom Bombardment,Luminescence,Magnetic Resonance Spectroscopy,Mass,Models,Molecular,Oxidation-Reduction,Phenazines,Phenazines: chemistry,Photochemistry,Solubility,Spectrometry,Spectrophotometry,Ultraviolet,Viscosity}
}

Paper  doi  abstract   bibtex   

@article{Yafe2005,
	title = {Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes.},
	volume = {33},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1133794&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gki606},
	abstract = {Clustered guanine residues in DNA readily generate hairpin or a variety of tetrahelical structures. The myogenic determination protein MyoD was reported to bind to a tetrahelical structure of guanine-rich enhancer sequence of muscle creatine kinase (MCK) more tightly than to its target E-box motif [K. Walsh and A. Gualberto (1992) J. Biol. Chem., 267, 13714-13718], suggesting that tetraplex structures of regulatory sequences of muscle-specific genes could contribute to transcriptional regulation. In the current study we show that promoter or enhancer sequences of various muscle-specific genes display a disproportionately high incidence of guanine clusters. The sequences derived from the guanine-rich promoter or enhancer regions of three muscle-specific genes, human sarcomeric mitochondrial creatine kinase (sMtCK), mouse MCK and alpha7 integrin formed diverse secondary structures. The sMtCK sequence folded into a hairpin structure; the alpha7 integrin oligonucleotide generated a unimolecular tetraplex; and sequences from all three genes associated to generate bimolecular tetraplexes. Furthermore, two neighboring non-contiguous guanine-rich tracts in the alpha7 integrin promoter region also paired to form a tetraplex structure. We also show that homodimeric MyoD bound bimolecular tetraplex structures of muscle-specific regulatory sequences more efficiently than its target E-box motif. These results are consistent with a role of tetrahelical structures of DNA in the regulation of muscle-specific gene expression.},
	number = {9},
	journal = {Nucleic acids research},
	author = {Yafe, Anat and Etzioni, Shulamit and Weisman-Shomer, Pnina and Fry, Michael},
	month = jan,
	year = {2005},
	pmid = {15908587},
	keywords = {\#nosource, Antigens, Base Sequence, CD, CD: genetics, Creatine Kinase, Creatine Kinase: genetics, DNA, DNA: chemistry, E-Box Elements, Enhancer Elements, G-Quadruplexes, Genetic, Guanine, Guanine: analysis, Integrin alpha Chains, Integrin alpha Chains: genetics, Isoenzymes, Isoenzymes: genetics, MM Form, Mitochondrial Form, Molecular Sequence Data, Muscles, Muscles: metabolism, MyoD Protein, MyoD Protein: metabolism, Nucleic Acid Conformation, Porphyrins, Porphyrins: chemistry, Promoter Regions, Temperature},
	pages = {2887--900},
}

Paper  doi  abstract   bibtex   

@article{Ulrich2004,
	title = {{RNA} and {DNA} aptamers in cytomics analysis.},
	volume = {59},
	issn = {1552-4922},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15170601},
	doi = {10.1002/cyto.a.20056},
	abstract = {The systematic evolution of ligands by exponential enrichment (SELEX) technique is a combinatorial library approach in which DNA or RNA molecules (aptamers) are selected by their ability to bind their protein targets with high affinity and specificity, comparable to that of monoclonal antibodies. In contrast to antibodies conventionally selected in animals, aptamers are generated by an in vitro selection process, and can be directed against almost every target, including antigens like toxins or nonimmunogenic targets, against which conventional antibodies cannot be raised.},
	number = {2},
	journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
	author = {Ulrich, Henning and Martins, Antonio Henrique B and Pesquero, João Bosco},
	month = jun,
	year = {2004},
	pmid = {15170601},
	keywords = {\#nosource, Animals, Binding, Combinatorial Chemistry Techniques, Combinatorial Chemistry Techniques: methods, Competitive, DNA, DNA: chemistry, Flow Cytometry, Flow Cytometry: methods, Humans, Ligands, Proteins, Proteins: analysis, Proteins: chemistry, Proteins: physiology, Proteomics, Proteomics: methods, RNA, RNA: chemistry},
	pages = {220--31},
}

Paper  doi  abstract   bibtex   

@article{Phillips2004,
	title = {{DNA} binding of an organic dppz-based intercalator.},
	volume = {43},
	issn = {0006-2960},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15504028},
	doi = {10.1021/bi049146r},
	abstract = {An improved synthesis of a water-soluble derivative of dipyrido[3,2-a:2',3'-c]phenazine (dppz) is reported. The structures of both dppz and the cation ethylene-bipyridyldiylium-phenazine dinitrate [[1][(PF(6))(2)]] have been obtained via X-ray crystallography. Metal complex derivatives of dppz are very well studied. However, using the water soluble [1][(NO(3))(2)], the nature of the interaction of a simple dppz unit with duplex DNA has been investigated for the first time. In both organic solvents and water, 1 displays unstructured luminescence, assigned to an intramolecular charge transfer. The emission is quenched on binding to natural and synthetic duplex DNA, including poly(dA).poly(dT). A variety of techniques reveal that the cation binds to DNA with an affinity comparable to those of many metal dppz complexes, via an intercalative binding mode.},
	number = {43},
	journal = {Biochemistry},
	author = {Phillips, Tim and Haq, Ihtshamul and Meijer, Anthony J H M and Adams, Harry and Soutar, Ian and Swanson, Linda and Sykes, Matthew J and Thomas, Jim a},
	month = nov,
	year = {2004},
	pmid = {15504028},
	keywords = {\#nosource, Binding Sites, Biomolecular, Calorimetry, Crystallography, DNA, DNA: chemistry, Fast Atom Bombardment, Fluorescence, Fluorescence Polarization, Intercalating Agents, Intercalating Agents: chemistry, Luminescent Measurements, Mass, Nuclear Magnetic Resonance, Phenazines, Phenazines: chemistry, Polyribonucleotides, Polyribonucleotides: chemistry, Spectrometry, Structure-Activity Relationship, Thermodynamics, Viscosity, X-Ray},
	pages = {13657--65},
}

Paper  doi  abstract   bibtex   

@article{Jacquemard2004,
	title = {Synthesis of diphenylcarbazoles as cytotoxic {DNA} binding agents.},
	volume = {2},
	issn = {1477-0520},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15136803},
	doi = {10.1039/b401445f},
	abstract = {We report the synthesis of a series of novel diphenylcarbazoles designed to interact with DNA. The compounds bearing two or three dimethylaminoalkyloxy side chains were found to bind much more tightly to DNA, preferentially at AT-rich sites, than the corresponding hydroxy compounds. The DNA binding compounds exhibit potent cytotoxic activity toward P388 leukemia cells. The 3,6-diphenylcarbazole thus represent an interesting scaffold to develop antitumor agents interacting with nucleic acids.},
	number = {10},
	journal = {Organic \& biomolecular chemistry},
	author = {Jacquemard, Ulrich and Routier, Sylvain and Tatibouët, Arnaud and Kluza, Jérôme and Laine, William and Bal, Christine and Bailly, Christian and Mérour, Jean-Yves},
	month = may,
	year = {2004},
	pmid = {15136803},
	keywords = {\#nosource, Alkylation, Animals, Antineoplastic Agents, Antineoplastic Agents: chemical synthesis, Antineoplastic Agents: chemistry, Antineoplastic Agents: pharmacology, Apoptosis, Apoptosis: drug effects, Benzene Derivatives, Benzene Derivatives: chemical synthesis, Benzene Derivatives: chemistry, Benzene Derivatives: pharmacology, Carbazoles, Carbazoles: chemical synthesis, Carbazoles: chemistry, Cell Cycle, Cell Cycle: drug effects, Cell Division, Cell Division: drug effects, Cell Line, DNA, DNA: chemistry, Flow Cytometry, Heterocyclic Compounds with 4 or More Rings, Heterocyclic Compounds with 4 or More Rings: chemi, Heterocyclic Compounds with 4 or More Rings: pharm, Inhibitory Concentration 50, Magnetic Resonance Spectroscopy, Mice, Molecular Structure, Poly dA-dT, Poly dA-dT: chemistry, Structure-Activity Relationship, Transition Temperature, Transition Temperature: drug effects, Tumor},
	pages = {1476--83},
}

Paper  doi  abstract   bibtex   

@article{Carreon2004,
	title = {Thiazole orange-peptide conjugates: sensitivity of {DNA} binding to chemical structure.},
	volume = {6},
	issn = {1523-7060},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/14961612},
	doi = {10.1021/ol0362818},
	abstract = {[structure: see text] Derivatives of the highly fluorescent and DNA-binding dye thiazole orange (TO) are described that feature appended peptides. Functionalization of TO can be achieved at either of the endocyclic nitrogens, and the photophysical properties and DNA-binding modes are sensitive to the position of the tethered peptide. A series of TO-peptide conjugates are described, demonstrating the utility of a solid-phase synthesis approach to their preparation and illustrating how the photophysical and DNA-binding properties of the compounds are influenced by chemical structure.},
	number = {4},
	journal = {Organic letters},
	author = {Carreon, Jay R and Mahon, Kerry P and Kelley, Shana O},
	month = mar,
	year = {2004},
	pmid = {14961612},
	keywords = {\#nosource, Amino Acid Sequence, Benzothiazoles, DNA, DNA: chemistry, Fluorescent Dyes, Fluorescent Dyes: chemistry, Models, Molecular, Molecular Structure, Peptides, Peptides: chemistry, Quinolines, Structure-Activity Relationship, Thiazoles, Thiazoles: chemistry},
	pages = {517--9},
}

Paper  doi  abstract   bibtex   

@article{Hoshika2004,
	title = {Synthesis and physical and physiological properties of 4'-{thioRNA}: application to post-modification of {RNA} aptamer toward {NF}-{kappaB}.},
	volume = {32},
	issn = {1362-4962},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=506795&tool=pmcentrez&rendertype=abstract},
	doi = {10.1093/nar/gkh705},
	abstract = {We report herein full details of the preparation of 4'-thiouridine, -cytidine, -adenosine and -guanosine phosphoramidites based on our synthetic protocol via the Pummerer reaction. Fully modified 4'-thioRNAs containing four kinds of 4'-thioribonucleoside units were prepared according to the standard RNA synthesis. The T(m) values and thermodynamic parameters of a series of duplexes were determined by UV melting and differential scanning calorimetry (DSC) measurements. The resulting overall order of thermal stabilities for the duplexes was 4'-thioRNA:4'-thioRNA ¿ 4'-thioRNA:RNA ¿ RNA:RNA ¿ RNA:DNA ¿ 4'-thioRNA:DNA. In addition, it was shown that the dominant factor in the stability of the duplexes consisting of 4'-thioRNA was enthalpic in character. The CD spectra of not only 4'-thioRNA:RNA and 4'-thioRNA:4'-thioRNA but also 4'-thioRNA:DNA were all similar to those of duplexes in the A-conformation. The stability of 4'-thioRNA in human serum was 600 times greater than that of natural RNA. Neither the RNA:RNA nor the 4'-thioRNA:4'-thioRNA duplexes were digested under the same conditions. The first example of a post-modification of an RNA aptamer by 4'-thioribonucleoside units was demonstrated. Full modification of the aptamer thioRNA3 resulted in complete loss of binding activity. In contrast, modifications at positions other than the binding site were tolerated without loss of binding activity. The post-modified RNA aptamer thioRNA5 was thermally stabilized and resistant toward nuclease digestion. The results presented in this paper will, it is hoped, contribute to the development of 4'-thioRNA as a new generation of artificial RNA.},
	number = {13},
	journal = {Nucleic acids research},
	author = {Hoshika, Shuichi and Minakawa, Noriaki and Matsuda, Akira},
	month = jan,
	year = {2004},
	pmid = {15263062},
	keywords = {\#nosource, Base Sequence, Binding, Binding Sites, Competitive, DNA, DNA: chemistry, DNA: metabolism, Double-Stranded, Double-Stranded: chemistry, Humans, NF-kappa B, NF-kappa B: metabolism, Organophosphorus Compounds, Organophosphorus Compounds: chemistry, RNA, RNA Stability, RNA: chemistry, Ribonucleotides, Ribonucleotides: chemical synthesis, Ribonucleotides: chemistry, Ribonucleotides: metabolism, Thionucleosides, Thionucleosides: chemistry, Thionucleosides: metabolism},
	pages = {3815--25},
}

Paper  doi  abstract   bibtex   

@article{Risitano2003,
	title = {Stability of intramolecular {DNA} quadruplexes: comparison with {DNA} duplexes.},
	volume = {42},
	issn = {0006-2960},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12767234},
	doi = {10.1021/bi026997v},
	abstract = {We have determined the stability of intramolecular quadruplexes that are formed by a variety of G-rich sequences, using oligonucleotides containing appropriately placed fluorophores and quenchers. The stability of these quadruplexes is compared with that of the DNA duplexes that are formed on addition of complementary C-rich oligonucleotides. We find that the linkers joining the G-tracts are not essential for folding and can be replaced with nonnucleosidic moieties, though their sequence composition profoundly affects quadruplex stability. Although the human telomere repeat sequence d[G(3)(TTAG(3))(3)] folds into a quadruplex structure, this forms a duplex in the presence of the complementary C-rich strand at physiological conditions. The Tetrahymena sequence d[G(4)(T(2)G(4))(3)], the sequence d[G(3)(T(2)G(3))(3)], and sequences related to regions of the c-myc promoter d(G(4)AG(4)T)(2) and d(G(4)AG(3)T)(2) preferentially adopt the quadruplex form in potassium-containing buffers, even in the presence of a 50-fold excess of their complementary C-rich strands, though the duplex predominates in the presence of sodium. The HIV integrase inhibitor d[G(3)(TG(3))(3)] forms an extremely stable quadruplex which is not affected by addition of a 50-fold excess of the complementary C-rich strand in both potassium- and sodium-containing buffers. Replacing the TTA loops of the human telomeric repeat with AAA causes a large decrease in quadruplex stability, though a sequence with AAA in the first loop and TTT in the second and third loops is slightly more stable.},
	number = {21},
	journal = {Biochemistry},
	author = {Risitano, Antonina and Fox, Keith R},
	month = jul,
	year = {2003},
	pmid = {12767234},
	keywords = {\#nosource, Animals, DNA, DNA: chemistry, Fluorescence, Genetic, HIV Integrase Inhibitors, HIV Integrase Inhibitors: chemistry, Humans, Nucleic Acid Conformation, Oligonucleotides, Oligonucleotides: chemistry, Promoter Regions, Protein Conformation, Protein Denaturation, Spectrometry, Telomere, Telomere: chemistry, Temperature, Tetrahymena, Tetrahymena: metabolism, Thermodynamics, Time Factors},
	pages = {6507--13},
}

@article{Weber2002,
  title = {Building an Asynchronous Web-Based Tool for Machine Learning Classification.},
  author = {Weber, Griffin and Vinterbo, Staal and {Ohno-Machado}, Lucila},
  year = {2002},
  journal = {JAMIA},
  volume = {Suppl. S},
  pages = {869--73},
  abstract = {Various unsupervised and supervised learning methods including support vector machines, classification trees, linear discriminant analysis and nearest neighbor classifiers have been used to classify high-throughput gene expression data. Simpler and more widely accepted statistical tools have not yet been used for this purpose, hence proper comparisons between classification methods have not been conducted. We developed free software that implements logistic regression with stepwise variable selection as a quick and simple method for initial exploration of important genetic markers in disease classification. To implement the algorithm and allow our collaborators in remote locations to evaluate and compare its results against those of other methods, we developed a user-friendly asynchronous web-based application with a minimal amount of programming using free, downloadable software tools. With this program, we show that classification using logistic regression can perform as well as other more sophisticated algorithms, and it has the advantages of being easy to interpret and reproduce. By making the tool freely and easily available, we hope to promote the comparison of classification methods. In addition, we believe our web application can be used as a model for other bioinformatics laboratories that need to develop web-based analysis tools in a short amount of time and on a limited budget.},
  copyright = {All rights reserved},
  pii = {D020001919},
  pubmedid = {12463949},
  keywords = {12463949,Algorithms,Anonymous Testing,Artificial Intelligence,Carcinoma,Child,Comparative Study,Computerized,Confidentiality,Databases,Diagnosis,Differential,Disclosure,DNA,Gene Expression,Gene Expression Profiling,Gene Expression Regulation,Genetic Markers,Humans,Internet,Logistic Models,Lung Neoplasms,Medical Records Systems,Multivariate Analysis,Neoplasm,Neoplasms,Neoplastic,Neural Networks (Computer),Non-U.S. Gov't,Oligonucleotide Array Sequence Analysis,P.H.S.,Privacy,Research Support,Rhabdomyosarcoma,Sarcoma,Small Cell,Software,U.S. Gov't},
  file = {/Users/staal/Documents/Zotero/storage/26TPF5RW/amia02-weber.pdf;/Users/staal/Documents/Zotero/storage/FRPABBPG/amia02-weber.pdf;/Users/staal/Documents/Zotero/storage/GME7HZA7/amia02-weber.pdf}
}

Paper  abstract   bibtex   

@article{Celik2002,
	title = {Selective targeting of zebrafish olfactory receptor neurons by the endogenous {OMP} promoter.},
	volume = {15},
	issn = {0953-816X},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11906521},
	abstract = {The olfactory nervous system of fish, in particular zebrafish, has become a valid model for that of higher vertebrates. However, no genetic markers for olfactory specific cell types, e.g. the olfactory receptor neurons, have been established in this species. Olfactory marker protein (OMP) is a reliable marker for olfactory receptor neurons in several other vertebrates. We have cloned zOMP, the zebrafish homologue of olfactory marker protein. During development, zOMP is expressed exclusively in the olfactory placode, presumably in olfactory receptor neurons, as shown by in situ hybridization. In the adult nasal epithelium zOMP is found restricted to the sensory region. zOMP appears to be a single gene, without close family members. The 5'-flanking region lacks most of the expected regulatory sequence motifs, both general and cell type-specific ones. Nevertheless, it drives reporter gene expression strongly and specifically in olfactory receptor neurons during the whole developmental period examined. Thus the zOMP promoter constitutes a powerful tool which should be useful to selectively introduce a wide variety of genetic modifications into olfactory receptor neurons.},
	number = {5},
	urldate = {2015-12-09},
	journal = {The European journal of neuroscience},
	author = {Celik, Arzu and Fuss, Stefan H and Korsching, S I},
	month = mar,
	year = {2002},
	pmid = {11906521},
	keywords = {\#nosource, Animals, Bacterial Proteins, Bacterial Proteins: diagnostic use, Bacterial Proteins: genetics, Cell Differentiation, Cell Differentiation: genetics, Cell Division, Cell Division: physiology, Cloning, Molecular, DNA, Complementary, DNA, Complementary: genetics, DNA, Complementary: isolation \& purification, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Gene Expression Regulation, Developmental: genetic, Gene Targeting, Gene Targeting: methods, Genetic Vectors, Genetic Vectors: genetics, Larva, Luminescent Proteins, Luminescent Proteins: diagnostic use, Luminescent Proteins: genetics, Models, Biological, Molecular Sequence Data, Nerve Tissue Proteins, Nerve Tissue Proteins: genetics, Nerve Tissue Proteins: metabolism, Olfactory Marker Protein, Olfactory Receptor Neurons, Olfactory Receptor Neurons: embryology, Olfactory Receptor Neurons: growth \& development, Olfactory Receptor Neurons: metabolism, Phylogeny, Promoter Regions, Genetic, Promoter Regions, Genetic: genetics, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, Stem Cells, Stem Cells: cytology, Stem Cells: metabolism, Transgenes, Transgenes: genetics, Zebrafish, Zebrafish Proteins, Zebrafish: embryology, Zebrafish: growth \& development, Zebrafish: metabolism, olfaction, zebrafish},
	pages = {798--806},
}

@article{Ohno-Machado2002,
  title = {Comparing Imperfect Measurements with the {{Bland-Altman}} Technique: Application in Gene Expression Analysis.},
  author = {{Ohno-Machado}, Lucila and Vinterbo, Staal and Dreiseitl, Stephen and Jenssen, Tor-Kristian and Kuo, Winston},
  year = {2002},
  journal = {JAMIA},
  volume = {Suppl. S},
  pages = {572--6},
  abstract = {Several problems in medicine and biology involve the comparison of two measurements made on the same set of cases. The problem differs from a calibration problem because no gold standard can be identified. Testing the null hypothesis of no relationship using measures of association is not optimal since the measurements are made on the same cases, and therefore correlation coefficients will tend to be significant. The descriptive Bland-Altman method can be used in exploratory analysis of this problem, allowing the visualization of gross systematic differences between the two sets of measurements. We utilize the method on three sets of matched observations and demonstrate its usefulness in detecting systematic variations between two measurement technologies to assess gene expression.},
  copyright = {All rights reserved},
  pii = {1833},
  pubmedid = {12463888},
  keywords = {12463888,Algorithms,Anonymous Testing,Artificial Intelligence,Bias (Epidemiology),Carcinoma,Child,Comparative Study,Computational Biology,Computerized,Confidentiality,Data Interpretation,Databases,Diagnosis,Differential,Disclosure,DNA,Gene Expression,Gene Expression Profiling,Gene Expression Regulation,Genetic Markers,Humans,Internet,Logistic Models,Lung Neoplasms,Medical Records Systems,Messenger,Multivariate Analysis,Neoplasm,Neoplasms,Neoplastic,Neural Networks (Computer),Non-U.S. Gov't,Oligonucleotide Array Sequence Analysis,P.H.S.,Privacy,Research Support,Rhabdomyosarcoma,RNA,Sarcoma,Small Cell,Software,Statistical,U.S. Gov't}
}

Paper  doi  abstract   bibtex   

@article{sandstrom_-tract_2002,
	title = {A-tract {DNA} disfavours triplex formation.},
	volume = {315},
	issn = {0022-2836},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11812143},
	doi = {10.1006/jmbi.2001.5249},
	abstract = {Optimisation of DNA triplex stability is of fundamental importance in the anti-gene strategy. In the present work, thermal denaturation studies by UV-spectrophotometry and structural and dynamical characterizations by NMR spectroscopy have been used systematically to investigate the effects on triplex stability of isolated insertions of different base triplets into an otherwise homogeneous 15-mer dT x dA-dT oligo-triplex. It is found that insertion of a single central C(+) x G-C or T x D-T triplet (D=2,6-diaminopurine) leads to a pronounced stabilization (up to 20 deg. C if the cytosine base is C5 methylated) at acidic as well as neutral pH. To a smaller degree, this is the case also for a C(+) x I-C triplet insertion. Using imino proton exchange measurements, it is shown that insertion of a DT base-pair in the underlying duplex perturbs the intrinsic A-tract structure in the same way as has been shown for a GC insert. We propose that the intrinsic properties of A-tract duplex DNA (e. g. high propeller twist and rigidity) are unfavourable for triplex formation and that GC- or DT-inserts stabilize the triplex by interfering with the A-tract features of the underlying duplex. The C(+) x I-C triplet without the N2 amino group in the minor groove is readily accommodated within the typical, highly propeller-twisted A-tract structure. This might be related to its smaller effect on the stability of the corresponding triplex. These results may be valuable for understanding DNA triplex formation in vivo as well as for the design of efficient triplex-forming oligonucleotides and in choosing suitable target sequences in the anti-gene strategy.},
	number = {4},
	journal = {Journal of molecular biology},
	author = {Sandström, Karin and Wärmländer, Sebastian and Gräslund, Astrid and Leijon, Mikael},
	month = jan,
	year = {2002},
	pmid = {11812143},
	keywords = {\#nosource, Base Composition, Base Pairing, Base Pairing: drug effects, Base Sequence, DNA, DNA: chemistry, DNA: genetics, DNA: metabolism, Kinetics, Magnesium Chloride, Magnesium Chloride: pharmacology, Magnetic Resonance Spectroscopy, Mutation, Mutation: genetics, Nucleic Acid Conformation, Nucleic Acid Conformation: drug effects, Nucleic Acid Denaturation, Nucleic Acid Denaturation: drug effects, Poly A, Poly A: genetics, Sodium Chloride, Sodium Chloride: pharmacology, Spectrophotometry, Structure-Activity Relationship, Temperature, Ultraviolet},
	pages = {737--48},
}

Website  abstract   bibtex   

@article{
 title = {Single molecule detection of double-stranded DNA in poly(methylmethacrylate) and polycarbonate microfluidic devices.},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {Bacteriophage lambda,Bacteriophage lambda: chemistry,DNA, Viral,DNA, Viral: analysis,Electrophoresis, Capillary,Electrophoresis, Capillary: instrumentation,Equipment Design,Fluorescent Dyes,Fluorescent Dyes: analysis,Fluorescent Dyes: chemistry,Fluorometry,Fluorometry: instrumentation,Intercalating Agents,Intercalating Agents: analysis,Intercalating Agents: chemistry,Lasers,Microchemistry,Microchemistry: instrumentation,Molecular Weight,Polycarboxylate Cement,Polycarboxylate Cement: chemistry,Polymethyl Methacrylate,Polymethyl Methacrylate: chemistry,Quinolines,Quinolines: analysis,Quinolines: chemistry,Rheology,Sensitivity and Specificity,Thiazoles,Thiazoles: analysis,Thiazoles: chemistry,Time Factors},
 pages = {3939-48},
 volume = {22},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/11700724},
 month = {10},
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 created = {2016-06-24T20:49:59.000Z},
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 last_modified = {2016-06-24T20:49:59.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wabuyele2001},
 abstract = {Single photon burst techniques were used to detect double-stranded DNA molecules in poly(methylmethacrylate) (PM MA) and polycarbonate (PC) microfluidic devices. A confocal epi-illumination detection system was constructed to monitor the fluorescence signature from single DNA molecules that were multiply labeled with the mono-intercalating dye, TOPRO-5, which possessed an absorption maximum at 765 nm allowing excitation with a solid-state diode laser and fluorescence monitoring in the near-infrared (IR). Near-IR excitation minimized autofluorescence produced from the polymer substrate, which was found to be significantly greater when excitation was provided in the visible range (488 nm). A solution containing lambda-DNA (48.5 kbp) was electrokinetically transported through the microfluidic devices at different applied voltages and solution pH values to investigate the effects of polymer substrate on the transport rate and detection efficiency of single molecular events. By applying an autocorrelation analysis to the data, we were able to obtain the molecular transit time of the individual molecules as they passed through the 7 microm laser beam. It was observed that the applied voltage for both devices affected the transport rate. However, solution pH did not alter the transit time for PM MA-based devices since the electroosmotic flow of PMMA was independent of solution pH. In addition, efforts were directed toward optimizing the sampling efficiency (number of molecules passing through the probe volume) by using either hydrodynamically focused flows from a sheath generated by electrokinetic pumping from side channels or reducing the channel width of the microfluidic device. Due to the low electroosmotic flows generated by both PMMA and PC, tight focusing of the sample stream was not possible. However, in PMMA devices, flow gating was observed by applying field strengths > -120 V/cm to the sheath flow channels. By narrowing the microchannel width, the number of molecular events detected per unit time was found to be four times higher in channels with 10 microm widths compared to those of 50 microm, indicating improved sampling efficiency for the narrower channels without significantly deteriorating detection efficiency. Attempts were made to do single molecule sizing of lambda-DNA, M13 (7.2 kbp) and pUC19 (2.7 kbp) using photon burst detection. While the average number of photons for each DNA type were different, the standard deviations were large due to the Gaussian intensity profile of the excitation beam. To demonstrate the sensitivity of single molecule analysis in the near-IR using polymer microfluidic devices, the near-IR chromophore, NN382, wasanalyzed using ourconfocal imager. A detection efficiency of 94% for single NN382 molecules was observed in the PC devices.},
 bibtype = {article},
 author = {Wabuyele, M B and Ford, S M and Stryjewski, W and Barrow, J and Soper, S a},
 journal = {Electrophoresis},
 number = {18}
}

Paper  doi  abstract   bibtex   

@article{Yang2001,
	title = {Counterion-dye staining method for {DNA} in agarose gels using crystal violet and methyl orange.},
	volume = {22},
	issn = {0173-0835},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11332752},
	doi = {10.1002/1522-2683()22:5<855::AID-ELPS855>3.0.CO;2-Y},
	abstract = {Sensitive and safe methods for visualization of DNA in agarose gels are described. 0.001\% crystal violet dissolved in distilled water was used for DNA staining on agarose gels and it could detect as little as 16 ng of DNA (3 kb, pGem-7Zf/EcoRI) without destaining procedure. The detection limit is four times lower than that of ethidium bromide. To improve the sensitivity, we studied a counterion-dye staining method using methyl orange as a counterion-dye which contributes to reduce excessive background staining by crystal violet. Dye concentration, pH of staining solution, mixing molar ratio of two dyes, and staining times were optimized for the counterion-dye staining. By the staining with a mixed solution of 0.0025\% crystal violet and 0.0005\% methyl orange in distilled water, 8 ng of the 3 kb DNA in an agarose gel was detected within 30 min.},
	number = {5},
	journal = {Electrophoresis},
	author = {Yang, Y and Jung, D W and Bai, D G and Yoo, G S and Choi, J K},
	month = mar,
	year = {2001},
	pmid = {11332752},
	keywords = {\#nosource, Agar Gel, Azo Compounds, DNA, DNA: analysis, Electrophoresis, Ethidium, Gentian Violet, Hydrogen-Ion Concentration, Indicators and Reagents, Sensitivity and Specificity, Solutions, Staining and Labeling, Staining and Labeling: methods, Water},
	pages = {855--9},
}

Paper  doi  abstract   bibtex   

@article{Schaffitzel2001,
	title = {In vitro generated antibodies specific for telomeric guanine-quadruplex {DNA} react with {Stylonychia} lemnae macronuclei},
	volume = {98},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=37477&tool=pmcentrez&rendertype=abstract},
	doi = {10.1073/pnas.141229498},
	abstract = {Most eukaryotic telomeres contain a repeating motif with stretches of guanine residues that form a 3-terminal overhang extending beyond the telomeric duplex region. The telomeric repeat of hypotrichous ciliates, d(T4G4), forms a 16-nucleotide 3-overhang. Such sequences can adopt parallel-stranded as well as antiparallel-stranded quadruplex conformations in vitro. Although it has been proposed that guanine-quadruplex conformations may have important cellular roles including telomere function, recombination, and transcription, evidence for the existence of this DNA structure in vivo has been elusive to date. We have generated high-affinity single-chain antibody fragment (scFv) probes for the guanine-quadruplex formed by the Stylonychia telomeric repeat, by ribosome display from the Human Combinatorial Antibody Library. Of the scFvs selected, one (Sty3) had an affinity of K d = 125 pM for the parallel-stranded guanine-quadruplex and could discriminate with at least 1,000-fold specificity between parallel or antiparallel quadruplex conformations formed by the same sequence motif. A second scFv (Sty49) bound both the parallel and antiparallel quadruplex with similar (K d = 35 nM) affinity. Indirect immunofluorescence studies show that Sty49 reacts specifically with the macronucleus but not the micronucleus of Stylonychia lemnae. The replication band, the region where replication and telomere elongation take place, was also not stained, suggesting that the guanine-quadruplex is resolved during replication. Our results provide experimental evidence that the telomeres of Stylonychia macronuclei adopt in vivo a guanine-quadruplex structure, indicating that this structure may have an important role for telomere functioning.},
	number = {15},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Schaffitzel, Christiane and Berger, Imre and Postberg, Jan and Hanes, Jozef and Lipps, Hans J and Plückthun, Andreas},
	year = {2001},
	note = {Publisher: Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
Publisher: The National Academy of Sciences},
	keywords = {\#nosource, animals, antibodies, dna, dna immunology, g quadruplexes, guanine, humans, hypotrichida, hypotrichida genetics, immunoglobulin fragments, immunoglobulin fragments biosynthesis, immunoglobulin fragments immunology, immunoglobulin variable region, immunoglobulin variable region biosynthesis, immunoglobulin variable region immunology, nucleic acid, protozoan, protozoan biosynthesis, protozoan immunology, repetitive sequences, telomere},
	pages = {8572--8577},
}

Paper  abstract   bibtex   

@article{Tendian2000,
	title = {Interaction of deoxyguanosine nucleotide analogs with human telomerase.},
	volume = {57},
	issn = {0026-895X},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10727514},
	abstract = {To maintain the telomeres at the ends of the chromosomes, telomerase in human cells adds a repeating sequence of nucleotides (TTAGGG) to the 3'-end of each chromosome using an RNA component of the enzyme as the template for DNA synthesis. Because of the selective expression of this enzyme in cancer cells, we have evaluated the interaction of human telomerase with several deoxyguanosine nucleotides of clinical importance. 2',3'-dideoxyguanosine 5'-triphosphate, 6-thio-2'-deoxyguanosine 5'-triphosphate (T-dGTP), carbovir 5'-triphosphate, and D-carbocyclic-2'-deoxyguanosine 5'-triphosphate (D-CdG-TP) inhibited telomerase activity by 50\% when these analogs were present at only 2 to 9 times the dGTP concentration. The L-enantiomer of CdG-TP was far less inhibitory, thereby demonstrating the stereoselectivity of telomerase for nucleotide substrates. T-dGTP was incorporated into the DNA by telomerase in the absence of dGTP, but unlike dGTP there was little extension of the DNA chain after its incorporation. These results indicate that the metabolites of three clinically useful agents (6-mercaptopurine, 6-thioguanine, and Abacavir) can inhibit human telomerase activity, and it is possible that the effect of these nucleotides on telomerase activity or telomere function could contribute to the mechanism of action of these agents.},
	number = {4},
	journal = {Molecular pharmacology},
	author = {Tendian, S W and Parker, W B},
	month = apr,
	year = {2000},
	pmid = {10727514},
	keywords = {\#nosource, Cell Division, Cell Division: drug effects, Cell Extracts, DNA, DNA: metabolism, Deoxyguanine Nucleotides, Deoxyguanine Nucleotides: chemistry, Deoxyguanine Nucleotides: metabolism, Deoxyguanine Nucleotides: pharmacology, HeLa Cells, Humans, Telomerase, Telomerase: metabolism},
	pages = {695--9},
}

@article{jilani_molecular_1999,
	title = {Molecular cloning of the human gene, {PNKP}, encoding a polynucleotide kinase 3'-phosphatase and evidence for its role in repair of {DNA} strand breaks caused by oxidative damage},
	volume = {274},
	issn = {0021-9258},
	abstract = {Mammalian polynucleotide kinases catalyze the 5'-phosphorylation of nucleic acids and can have associated 3'-phosphatase activity, predictive of an important function in DNA repair following ionizing radiation or oxidative damage. The sequences of three tryptic peptides from a bovine 60-kDa polypeptide that correlated with 5'-DNA kinase and 3'-phosphatase activities identified human and murine dbEST clones. The 57.1-kDa conceptual translation product of this gene, polynucleotide kinase 3'-phosphatase (PNKP), contained a putative ATP binding site and a potential 3'-phosphatase domain with similarity to L-2-haloacid dehalogenases. BLAST searches identified possible homologs in Caenorhabditis elegans, Schizosaccharomyces pombe, and Drosophila melanogaster. The gene was localized to chromosome 19q13.3-13.4. Northern analysis indicated a 2-kilobase mRNA in eight human tissues. A glutathione S-transferase-PNKP fusion protein displayed 5'-DNA kinase and 3'-phosphatase activities. PNKP is the first gene for a DNA-specific kinase from any organism. PNKP expression partially rescued the sensitivity to oxidative damaging agents of the Escherichia coli DNA repair-deficient xth nfo double mutant. PNKP gene function restored termini suitable for DNA polymerase, consistent with in vivo removal of 3'-phosphate groups, facilitating DNA repair.},
	language = {eng},
	number = {34},
	journal = {The Journal of Biological Chemistry},
	author = {Jilani, A. and Ramotar, D. and Slack, C. and Ong, C. and Yang, X. M. and Scherer, S. W. and Lasko, D. D.},
	month = aug,
	year = {1999},
	keywords = {Amino Acid Sequence, Animals, Base Sequence, Blotting, Southern, Cattle, Chromosome Mapping, Cloning, Molecular, DNA Damage, DNA Repair, DNA, Complementary, Humans, Hydrogen Peroxide, Molecular Sequence Data, Oxidation-Reduction, Phosphoric Monoester Hydrolases, Polynucleotide 5'-Hydroxyl-Kinase},
	pages = {24176--24186},
}

Paper  abstract   bibtex   

@article{Srivastava1999,
	title = {Effect of sulphur crosslinking on the stability and transition of triple helical {DNA}.},
	volume = {36},
	issn = {0301-1208},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10650716},
	abstract = {In continuation to our work on order-order and order-disorder transition in triple stranded DNA when it is bounded to netropsin, we report in this communication the stabilizing/destabilizing effect of disulphide linkage on the phase dynamics of the triplex using the amended Zimm-Bragg theory. It is observed that in contrast to the sequential triplex–¿duplex –¿single strand melting of the uncrosslinked triplex, crosslinking causes the triplex state to melt directly to the single stranded state, with no apparent intermediary of a duplex state. Since there is no overall difference in the enthalpy of crosslinked and uncrosslinked triplexes, the transition is entropy driven.},
	number = {3},
	journal = {Indian journal of biochemistry \& biophysics},
	author = {Srivastava, Seema and Gupta, Vishwambhar Dayal and Singh, Shyam},
	month = jun,
	year = {1999},
	pmid = {10650716},
	keywords = {\#nosource, Base Sequence, Cross-Linking Reagents, Cross-Linking Reagents: chemistry, DNA, DNA: chemistry, Disulfides, Disulfides: chemistry, Molecular Sequence Data, Nucleic Acid Conformation, Thermodynamics},
	pages = {177--87},
}

Paper  doi  abstract   bibtex   

@article{schmid_programmed_1999,
	title = {Programmed cell death in castor bean endosperm is associated with the accumulation and release of a cysteine endopeptidase from ricinosomes},
	volume = {96},
	copyright = {Copyright © 1999, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/96/24/14159},
	doi = {10/fwpzcr},
	abstract = {The cells of the endosperm of castor bean seeds (Ricinus communis) undergo programmed cell death during germination, after their oil and protein reserves have been mobilized. Nuclear DNA fragmentation first was observed at day 3 in the endosperm cells immediately adjacent to the cotyledons and progressed across to the outermost cell layers by day 5. We also detected the accumulation of small organelles known as ricinosomes, by using an antibody against a cysteine endoprotease. By the time the nuclear DNA was susceptible to heavy label by terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling, the ricinosomes had released into the cytoplasm their content of cysteine endoprotease, which became activated because of the cleavage of its propeptide. The cysteine endoprotease is distinguished by a C-terminal KDEL sequence, although it is not retained in the lumen of the endoplasmic reticulum and is a marker for ricinosomes. Homologous proteases are found in the senescing tissues of other plants, including the petals of the daylily. Ricinosomes were identified in this tissue by electron microscopy and immunocytochemistry. It seems that ricinosomes are not unique to Ricinus and play an important role in the degradation of plant cell contents during programmed cell death.},
	language = {en},
	number = {24},
	urldate = {2021-11-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Schmid, Markus and Simpson, David and Gietl, Christine},
	month = nov,
	year = {1999},
	pmid = {10570215},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {Apoptosis, Castor Bean, Cell Nucleus, Cysteine Endopeptidases, DNA Fragmentation, DNA, Plant, Germination, Hemerocallis sp., In Situ Hybridization, Organelles, Plants, Toxic, Ricinus communis, Seeds, papain-type KDEL peptidase},
	pages = {14159--14164},
}

@article{
 title = {Which of our genes makes us human?},
 type = {article},
 year = {1998},
 keywords = {*Chromosomes, Human,*Genome,*Genome, Human,*Human Characteristics,*Sequence Analysis, DNA,Animal,Chromosome Mapping,Gene Expression,Human,Mutation,Pan troglodytes/genetics,Pongidae/*genetics,Sialic Acids/chemistry/physiology,Species Specificity},
 pages = {1432-1434},
 volume = {281},
 id = {85b008be-1b1d-3c94-bd62-2d641fa111cc},
 created = {2017-06-19T13:42:20.922Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:21.018Z},
 tags = {03/11/21},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>News</m:note>},
 bibtype = {article},
 author = {Gibbons, A},
 journal = {Science},
 number = {5382}
}

Paper  abstract   bibtex   

@article{Allawi1998,
	title = {Thermodynamics of internal {C}.{T} mismatches in {DNA}.},
	volume = {26},
	issn = {0305-1048},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10090733},
	abstract = {Thermodynamics of 23 oligonucleotides with internal single C.T mismatches were obtained by measuring UV absorbance as a function of temperature. Results from these 23 duplexes were combined with three measurements from the literature to derive nearest-neighbor thermodynamic parameters for seven linearly independent trimer sequences with internal C.T mismatches. The data show that the nearest-neighbor model is adequate for predicting thermodynamics of oligonucleotides with internal C.T with average deviations for Delta G degrees37, Delta H degrees, Delta S degrees and T m of 6.4\%, 9.9\%, 10.6\%, and 1.9 degreesC respectively. C.T mismatches destabilize the duplex in all sequence contexts. The thermodynamic contribution of C. T mismatches to duplex stability varies weakly depending on the orientation of the mismatch and its context and ranges from +1.02 kcal/mol for GCG/CTC and CCG/GTC to +1.95 kcal/mol for TCC/ATG.},
	number = {11},
	journal = {Nucleic acids research},
	author = {Allawi, H T and SantaLucia, J},
	month = jun,
	year = {1998},
	pmid = {9592156},
	note = {ISBN: 1058110594},
	keywords = {\#nosource, Biomolecular, Cytidine, DNA, DNA: chemistry, Hydrogen-Ion Concentration, Nuclear Magnetic Resonance, Nucleic Acid Heteroduplexes, Thermodynamics, Thymidine},
	pages = {2694--701},
}

@article{rogakou_dna_1998,
	title = {{DNA} double-stranded breaks induce histone {H2AX} phosphorylation on serine 139},
	volume = {273},
	issn = {0021-9258},
	abstract = {When mammalian cell cultures or mice are exposed to ionizing radiation in survivable or lethal amounts, novel mass components are found in the histone H2A region of two-dimensional gels. Collectively referred to as gamma, these components are formed in vivo by several procedures that introduce double-stranded breaks into DNA. gamma-Components, which appeared to be the only major novel components detected by mass or 32PO4 incorporation on acetic acid-urea-Triton X-100-acetic acid-urea-cetyltrimethylammonium bromide or SDS-acetic acid-urea-cetyltrimethylammonium bromide gels after exposure of cells to ionizing radiation, are shown to be histone H2AX species that have been phosphorylated specifically at serine 139. gamma-H2AX appears rapidly after exposure of cell cultures to ionizing radiation; half-maximal amounts are reached by 1 min and maximal amounts by 10 min. At the maximum, approximately 1\% of the H2AX becomes gamma-phosphorylated per gray of ionizing radiation, a finding that indicates that 35 DNA double-stranded breaks, the number introduced by each gray into the 6 x 10(9) base pairs of a mammalian G1 genome, leads to the gamma-phosphorylation of H2AX distributed over 1\% of the chromatin. Thus, about 0.03\% of the chromatin appears to be involved per DNA double-stranded break. This value, which corresponds to about 2 x 10(6) base pairs of DNA per double-stranded break, indicates that large amounts of chromatin are involved with each DNA double-stranded break. Thus, gamma-H2AX formation is a rapid and sensitive cellular response to the presence of DNA double-stranded breaks, a response that may provide insight into higher order chromatin structures.},
	language = {eng},
	number = {10},
	journal = {The Journal of Biological Chemistry},
	author = {Rogakou, E. P. and Pilch, D. R. and Orr, A. H. and Ivanova, V. S. and Bonner, W. M.},
	month = mar,
	year = {1998},
	keywords = {Amino Acid Sequence, Animals, Cells, Cultured, Chromatin, DNA, Electrophoresis, Gel, Two-Dimensional, Gamma Rays, Histones, Mice, Mice, Inbred Strains, Molecular Sequence Data, Nuclear Proteins, Peptide Fragments, Phosphorylation, Phosphoserine, Protein Kinases, Recombinant Proteins, Whole-Body Irradiation},
	pages = {5858--5868},
}

@article{
 title = {The genetical archaeology of the human genome},
 type = {article},
 year = {1996},
 identifiers = {[object Object]},
 keywords = {*Gene Pool,*Genome, Human,DNA, Mitochondrial/genetics,Evolution, Molecular,Female,Human,Male,Models, Genetic,Phylogeny,Support, Non-U.S. Gov't,Variation (Genetics)/*genetics},
 pages = {135-140},
 volume = {14},
 id = {da42c725-f648-32fa-a720-c48d07c5c47c},
 created = {2017-06-19T13:46:05.495Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:46:05.676Z},
 tags = {03/09/17},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
 abstract = {Palaentology and archaeology are disciplines that traditionally deal with the reconstruction of human origins and history. Recently, however, molecular genetics has come to make increasing contributions to this area. In particular, several data sets indicate that variation of the human gene pool originated in Africa within the last 200,000 years. Furthermore, the study of DNA sequences allows the detection of expansions in population size. Here we briefly summarize and exemplify how DNA sequences can be used to reconstruct the history of populations.},
 bibtype = {article},
 author = {von Haeseler, A and Sajantila, A and Paabo, S},
 journal = {Nat Genet},
 number = {2}
}

@article{
 title = {Parthenogenesis and apospory in the Laminariales: A flow cytometry analysis},
 type = {article},
 year = {1996},
 keywords = {CELL-WALL,CULTURE,DNA,GENETICS,JAPONICA,LIFE-HISTORY,PHAEOPHYTA,SACCHARINA,SBR_Phyto,SEAWEEDS,SPOROPHYTES},
 pages = {369-380},
 volume = {31},
 id = {b1cac542-699e-33d5-b6c6-d73c1d9d1e03},
 created = {2015-11-02T11:41:35.000Z},
 file_attached = {false},
 profile_id = {9e8929f8-811d-3561-b42b-6003aef71c7c},
 group_id = {98cf6291-ef58-3f8a-a4b6-c8754044662f},
 last_modified = {2016-06-16T13:22:52.000Z},
 tags = {1996,sbr_phyto},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 abstract = {Tissue explants and unisexual cultures of Macrocystis pyrifera, Laminaria saccharina and L. Digitata regenerated into various forms, including gametophyte-like filaments, callus-like structures. Stipe-like structures and either abnormal or normal sporophytes. The ploidy of the various forms of growth was assessed using flow cytometry analysis of isolated nuclei. Unisexual cultures of female gametophytes of L. Digitata gave rise to abnormal parthenogenetic sporophytes, with nuclei exhibiting 2C, 4C and 8C ploidy levels. Aposporous gametophyte-like filaments grown from the tissue explants of M. Pyrifera developed into abnormal sporophytes and both forms were diploid. Development of stipe medullary explants of L. Saccharina led to the complete regeneration of functional sporophytes, involving the outgrowth of aposporous gametophytes. The regenerated sporophytes were either diploid or tetraploid but only diploid sporophytes were found to be fertile. The developmental and biotechnological significance of these results is discussed.},
 bibtype = {article},
 author = {Gall, E A and Asensi, A and Marie, D and Kloareg, B},
 journal = {European Journal of Phycology},
 number = {4}
}

Paper  abstract   bibtex   

@article{greene_spo0a_1996,
	title = {The {Spo}0A protein of {Bacillus} subtilis inhibits transcription of the {abrB} gene without preventing binding of the polymerase to the promoter},
	volume = {271},
	issn = {0021-9258},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8626703},
	abstract = {Repression of transcription of the abrB gene is essential to expression of many of the postexponential genes in Bacillus. The repression is due to the activity of the response regulator protein Spo0A. We have used in vitro transcription and DNase I and hydroxyl radical footprinting to explore the mechanism of transcription inhibition. Spo0A binds to specific DNA sequences (0A boxes), and two such boxes are found downstream of the tandem promoters for the abrB gene. The data indicate that both RNA polymerase and Spo0A bind simultaneously to a DNA fragment containing the promoters and the 0A boxes. The Spo0A prevents the polymerase from inducing DNA strand denaturation at the promoter for the abrB gene.},
	number = {19},
	urldate = {2009-05-03TZ},
	journal = {The Journal of Biological Chemistry},
	author = {Greene, E A and Spiegelman, G B},
	month = may,
	year = {1996},
	pmid = {8626703},
	keywords = {Bacillus subtilis, Bacterial Proteins, Base Sequence, Binding Sites, DNA Footprinting, DNA, Bacterial, DNA-Binding Proteins, DNA-Directed RNA Polymerases, Deoxyribonuclease I, Escherichia coli, Gene Expression Regulation, Bacterial, Genes, Bacterial, Hydroxyl Radical, Kinetics, Molecular Sequence Data, Promoter Regions, Genetic, Transcription Factors, Transcription, Genetic},
	pages = {11455--11461}
}

Paper  doi  abstract   bibtex   

@article{frank-kamenetskii_triplex_1995,
	title = {Triplex {DNA} structures.},
	volume = {64},
	issn = {0066-4154},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7574496},
	doi = {10.1146/annurev.bi.64.070195.000433},
	abstract = {A DNA triplex is formed when pyrimidine or purine bases occupy the major groove of the DNA double Helix forming Hoogsteen pairs with purines of the Watson-Crick basepairs. Intermolecular triplexes are formed between triplex forming oligonucleotides (TFO) and target sequences on duplex DNA. Intramolecular triplexes are the major elements of H-DNAs, unusual DNA structures, which are formed in homopurine-homopyrimidine regions of supercoiled DNAs. TFOs are promising gene-drugs, which can be used in an anti-gene strategy, that attempt to modulate gene activity in vivo. Numerous chemical modifications of TFO are known. In peptide nucleic acid (PNA), the sugar-phosphate backbone is replaced with a protein-like backbone. PNAs form P-loops while interacting with duplex DNA forming triplex with one of DNA strands leaving the other strand displaced. Very unusual recombination or parallel triplexes, or R-DNA, have been assumed to form under RecA protein in the course of homologous recombination.},
	journal = {Annual review of biochemistry},
	author = {Frank-Kamenetskii, M D and Mirkin, S M},
	month = jan,
	year = {1995},
	pmid = {7574496},
	note = {tex.ids= frank-kamenetskiiTriplexDNAStructure, frank-kamenetskiiTriplexDNAStructures, frank-kamenetskiiTriplexDNAStructuresa},
	keywords = {Animals, DNA, DNA: chemistry, DNA: genetics, Drug Stability, Genetic, Humans, Molecular Structure, Nucleic Acid Conformation, Nucleic Acids, Nucleic Acids: chemistry, Peptides, Peptides: chemistry, Recombination},
	pages = {65--95},
}

Paper  abstract   bibtex   

@article{gilbert_protein_1995,
	title = {Protein {Hpn}: cloning and characterization of a histidine-rich metal-binding polypeptide in {Helicobacter} pylori and {Helicobacter} mustelae},
	volume = {63},
	issn = {0019-9567},
	shorttitle = {Protein {Hpn}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7790085},
	abstract = {Helicobacter pylori is a human gastrointestinal pathogen involved in gastritis, duodenal ulcers, and gastric neoplasia. This microorganism produces large amounts of a urease which, like all known ureases, has nickel in the active site. We have identified a protein in clinical isolates of H. pylori and an identical protein in the ferret pathogen Helicobacter mustelae that strongly binds Ni2+ and Zn2+. This protein has been named Hpn to emphasize its origins in H. pylori and its affinity for nickel. The encoding hpn gene, cloned and expressed in Escherichia coli ER1793, has an open reading frame (180 bp) that specifies a protein with a calculated molecular mass of 7,077 Da and with the same amino-terminal sequence as that of wild-type Hpn. The deduced sequence of Hpn consists of 60 amino acids, of which 28 (47\%) are histidines. The hpn gene does not map with the urease gene cluster on the H. pylori chromosome. An Hpn-negative, isogenic H. pylori strain, generated by hpn gene deletion and grown on blood agar, had the same urease activity that wild-type cells did. Thus, the role of Hpn in helicobacters is unknown.},
	number = {7},
	urldate = {2009-11-20TZ},
	journal = {Infection and Immunity},
	author = {Gilbert, J V and Ramakrishna, J and Sunderman, F W and Wright, A and Plaut, A G},
	month = jul,
	year = {1995},
	pmid = {7790085},
	keywords = {Amino Acid Sequence, Base Sequence, Cloning, Molecular, DNA, Bacterial, Genes, Bacterial, Helicobacter, Helicobacter pylori, Molecular Sequence Data, Nickel, Oligonucleotide Probes, Proteins, Restriction Mapping, Urease},
	pages = {2682--2688}
}

@article{Venczel1993,
  title = {Parallel and Antiparallel {{G-DNA}} Structures from a Complex Telomeric Sequence.},
  author = {a Venczel, E and Sen, D},
  year = {1993},
  month = jun,
  journal = {Biochemistry},
  volume = {32},
  number = {24},
  eprint = {8512932},
  eprinttype = {pubmed},
  pages = {6220--8},
  issn = {0006-2960},
  abstract = {We investigated the formation in vitro of higher order structures by a DNA oligomer containing the terminal motif TGTG3TGTGTGTG3, derived from the Saccharomyces telomeric consensus, in order to (a) understand why certain cations favor the formation of parallel-stranded (G4 and G8) G-DNA structures, while others favor foldback, antiparallel structures (G'2) and (b) probe the structures of G-DNAs formed by this telomeric sequence, which is more complex than its well-studied counterparts from the protozoans oxytricha and tetrahymena. We find that dramatic switches in the formation of G4 versus G'2 structures occur in solutions of not only the group Ia cations, Li(+)-Cs+, but also in those of the group IIa cations, Mg(2+)-Ba2+. These data and the temperature-dependent formation and destruction of the different structures lend support to the kinetic scheme of Sen and Gilbert (1990), by which rapidly forming G'2 structures accumulate in highly stabilizing potassium (and strontium) solutions at the expense of the thermodynamically more stable G4 structures. Both the G4 and the G'2 complexes formed by the Saccharomyces sequence show novel structural features. Protection and interference experiments with dimethyl sulfate and potassium permanganate reveal that the core of alternating thymines and guanines within the telomeric motif plays a critical role in the stabilization of the parallel G4 structure, but not of the antiparallel G'2. Very likely, in the G4 complex, this GT core forms a novel higher order arrangement of alternating G and T quartets, the latter possibly comparable to the U quartets described by Cheong and Moore (1992) in their NMR study of the higher order structure formed by rUG4U.},
  pmid = {8512932},
  keywords = {\#nosource,Base Sequence,Cations,Divalent,DNA,Fungal,Fungal: chemistry,Methylation,Molecular Sequence Data,Monovalent,Nucleic Acid Conformation,Osmolar Concentration,Potassium Permanganate,Potassium Permanganate: chemistry,Saccharomyces,Saccharomyces: genetics,Telomere,Temperature,Thymine,Thymine: chemistry}
}

@article{
 title = {Transfer-Rna Genes in the Mitochondrial Genome from a Liverwort, Marchantia-Polymorpha - the Absence of Chloroplast-Like Transfer-Rnas},
 type = {article},
 year = {1992},
 identifiers = {[object Object]},
 keywords = {dna,maize,methionine transfer rna,nucleotide sequence,organization},
 pages = {3773-3777},
 volume = {20},
 id = {5d61099c-c2ba-3093-b010-5cad4d29f8f5},
 created = {2011-05-20T17:26:09.000Z},
 file_attached = {false},
 profile_id = {b6c31fe8-61c6-3818-89a8-62873f3171f3},
 group_id = {7bdcaa0c-1528-351f-a09a-f8da52223946},
 last_modified = {2011-05-20T17:26:09.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Twenty-nine genes for 27 species of tRNAs were deduced from the complete nucleotide sequence of the mitochondrial genome from a liverwort, Marchantia Polymorpha. One to three species of tRNA genes corresponded to each of 20 amino acids including three species for leucine and arginine, two species for serine and glycine, and one for the rest of the amino acids. Interestingly, all tRNA genes were located in the semicircle of the liverwort mitochondrial genome except for the trnY and trnR genes. The region containing these tRNA genes was originally duplicated, and two trnR genes have diverged from each other. On the other hand, trnY and trnfM are present as two identical copies. The G:U and U:N wobbling between the first nucleotide of the anticodon and the third nucleotide of the codon permit the 27 tRNA identified species to translate almost all codons. However, at least two additional tRNA genes, trnI-GAU for AUY codon and trnT-UGU for ACR codon, are required to read all codons used in the liverwort mitochondrial genome. All of the identified tRNA genes are 'native' in liverwort mitochondria, not 'chloroplast-like' tRNAs as are found in the mitochondria of higher plants. This result implies that the tRNA gene transfer from chloroplast to mitochondrial genome in higher plants has occurred after the divergence from bryophytes.},
 bibtype = {article},
 author = {Oda, K and Yamato, K and Ohta, E and Nakamura, Y and Takemura, M and Nozato, N and Akashi, K and Ohyama, K},
 journal = {Nucleic Acids Research},
 number = {14}
}

@article{yamamoto_ubiquitous_1992,
	title = {Ubiquitous presence in mammalian cells of enzymatic activity specifically cleaving 8-hydroxyguanine-containing {DNA}},
	volume = {83},
	issn = {0910-5050},
	doi = {10.1111/j.1349-7006.1992.tb00114.x},
	abstract = {Here we report the finding of enzymatic activity that specifically cleaves DNA containing 8-hydroxyguanine (oh8Gua) residues in various mammalian cells. To detect this activity, we used a synthetic double-stranded DNA containing a single oh8Gua at a defined position as the substrate, and analyzed the products of enzymatic digestion by polyacrylamide gel electrophoresis. Two cleavage sites near the oh8Gua residue were detected with partially purified fractions from cow brain and rat liver, and also with preparations from all mammalian tissues examined. These results suggest that enzymatic activity for the removal of oh8Gua from DNA is widely distributed in mammalian cells.},
	language = {eng},
	number = {4},
	journal = {Japanese Journal of Cancer Research: Gann},
	author = {Yamamoto, F. and Kasai, H. and Bessho, T. and Chung, M. H. and Inoue, H. and Ohtsuka, E. and Hori, T. and Nishimura, S.},
	month = apr,
	year = {1992},
	pmid = {1506269},
	pmcid = {PMC5918833},
	keywords = {Animals, Base Sequence, Brain, Cattle, DNA, DNA Repair, DNA-Formamidopyrimidine Glycosylase, Escherichia coli, Escherichia coli Proteins, Liver, Mammals, Molecular Sequence Data, N-Glycosyl Hydrolases, Oligodeoxyribonucleotides, Organ Specificity, Rats, Species Specificity, Substrate Specificity},
	pages = {351--357},
}

Paper  abstract   bibtex   

@article{Zuo1990,
	title = {Effect of base-pair sequence on the conformations and thermally induced transitions in oligodeoxyribonucleotides containing only {AT} base pairs.},
	volume = {29},
	issn = {0006-2960},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/2350548},
	abstract = {Tm curves, CD spectra, and kinetics results of the self-complementary DNA dodecamers d(A6T6), d(A3T3A3T3), d(A2T2A2T2A2T2), d(ATATATATATAT), and d(T6A6) demonstrate that the thermal transitions of these oligomers at low salt concentration involve a hairpin intermediate. At high salt concentrations (greater than 0.1 M Na+) only a duplex to denatured-strand transition appears to occur. The temperature and salt-concentration regions of the transitions are very sequence dependent. Alternating-type AT sequences have a lower duplex stability and a greater tendency to form hairpins than sequences containing more nonalternating AT base pairs. Of the two nonalternating sequences, d(T6A6) is significantly less stable than d(A6T6). Both oligomers have CD curves that are very similar to the unusual CD spectrum of poly(dA).poly(dT). The Raman spectra of these two oligomers are also quite similar, but at low temperature, small intensity differences in two backbone modes and three nucleoside vibrations are obtained. The hairpin to duplex transition for the AT dodecamers was examined by salt-jump kinetics measurements. The transition is faster than transitions for palindromic-sequence oligomers containing terminal GC base pairs. Stopped-flow kinetics studies indicate that the transition is second order and has a relatively low activation energy. The reaction rate increases with increasing ionic strength. These results are consistent with a three-step mechanism for the hairpin to duplex reaction: (i) fraying of the hairpin oligomers' terminal base pairs, (ii) a rate-determining bimolecular step involving formation of a cruciform-type intermediate from two hairpin oligomers with open terminal base pairs, and (iii) base-pair migration and formation in the intermediate to give the duplex.},
	number = {18},
	journal = {Biochemistry},
	author = {Zuo, E T and Tanious, F a and Wilson, W D and Zon, G and Tan, G S and Wartell, R M},
	month = may,
	year = {1990},
	pmid = {2350548},
	keywords = {\#nosource, Adenine, Base Composition, Base Sequence, Circular Dichroism, DNA, Kinetics, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Denaturation, Oligodeoxyribonucleotides, Raman, Spectrophotometry, Spectrum Analysis, Thymine, Ultraviolet},
	pages = {4446--56},
}

Paper  abstract   bibtex   

@article{Dervan1986,
	title = {Design of sequence-specific {DNA}-binding molecules.},
	volume = {232},
	issn = {0036-8075},
	url = {http://ww2.chemistry.gatech.edu/~lw26/bCourse_Information/nucleic_acid_biochem/articles/dervan_science_1986.pdf http://www.ncbi.nlm.nih.gov/pubmed/2421408},
	abstract = {Base sequence information can be stored in the local structure of right-handed double-helical DNA (B-DNA). The question arises as to whether a set of rules for the three-dimensional readout of the B-DNA helix can be developed. This would allow the design of synthetic molecules that bind DNA of any specific sequence and site size. There are four stages of development for each new synthetic sequence-specific DNA-binding molecule: design, synthesis, testing for sequence specificity, and reevaluation of the design. This approach has produced bis(distamycin)fumaramide, a synthetic, crescent-shaped oligopeptide that binds nine contiguous adenine-thymine base pairs in the minor groove of double-helical DNA.},
	number = {4749},
	journal = {Science (New York, N.Y.)},
	author = {Dervan, P B},
	month = apr,
	year = {1986},
	pmid = {2421408},
	keywords = {\#nosource, Base Sequence, Bisbenzimidazole, Bisbenzimidazole: metabolism, Chemical, DNA, DNA: genetics, DNA: metabolism, Dactinomycin, Dactinomycin: metabolism, Distamycins, Distamycins: metabolism, Edetic Acid, Edetic Acid: analogs \& derivatives, Edetic Acid: metabolism, Iron, Iron: metabolism, Models, Netropsin, Netropsin: metabolism, Organometallic Compounds, Pyrroles, Pyrroles: metabolism, Structure-Activity Relationship},
	pages = {464--71},
}

Paper  doi  bibtex   

@article{shapiro_differentiation_1976,
	title = {Differentiation in the {Caulobacter} cell cycle},
	volume = {30},
	issn = {0066-4227},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/185940},
	doi = {10.1146/annurev.mi.30.100176.002113},
	urldate = {2009-05-03TZ},
	journal = {Annual Review of Microbiology},
	author = {Shapiro, L},
	year = {1976},
	pmid = {185940},
	keywords = {Bacteria, Bacteriophages, Carbohydrate Metabolism, Cell Division, Cell Wall, Cyclic GMP, DNA, Bacterial, Enzyme Repression, Flagella, Morphogenesis, Mutation, Nucleotides, Cyclic, Protein Biosynthesis, Transcription, Genetic, Transduction, Genetic},
	pages = {377--407}
}

Paper  doi  bibtex   

@article{Patel1974,
	title = {Assignment of the proton {Nmr} chemical shifts of the {T}-{N3H} and {G}-{N1H} proton resonances in isolated {AT} and {GC} {Watson}-{Crick} base pairs in double-stranded deoxy oligonucleotides in aqueous solution.},
	volume = {13},
	issn = {0006-3525},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/4433696},
	doi = {10.1002/bip.1974.360131003},
	number = {10},
	journal = {Biopolymers},
	author = {Patel, D J and Tonelli, A E},
	month = jan,
	year = {1974},
	pmid = {4433696},
	keywords = {\#nosource, Base Sequence, DNA, Deoxyribonucleotides, Magnetic Resonance Spectroscopy, Oligonucleotides, Protons, RNA, Temperature},
	pages = {1943--64},
}

Paper  abstract   bibtex   

@article{haars_stalk_1974,
	title = {Stalk formation and its inhibition in {Caulobacter} crescentus},
	volume = {120},
	issn = {0021-9193},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/4436259},
	abstract = {Estimates of average rates of stalk formation over several generations of growth in Caulobacter crescentus showed that long-stalked Sk1 mutant and phosphate-starved wild-type cultures produce stalk material at about twice the rate of wild-type C. crescentus grown with adequate nutrients. Thus, the long stalks of Sk1 or phosphate-starved caulobacters are not merely a function of their longer doubling times. Inhibition of cell division of Sk1 418 with mitomycin C (MC) caused production of cellular filaments and resulted in inhibition of stalk formation. There was no appreciable decrease in total cell mass or in rates of ribonucleic acid and protein synthesis in the MC-treated cultures as compared with controls, but stalk formation, which is normally dependent on these processes, was severely retarded. Average stalk lengths in MC-treated Sk1 cultures were 30\% of those found in control cultures. MC-produced cellular filaments were also subjected to deoxyribonucleic acid analysis and ultrastructural examination. The deoxyribonucleic acid content of MC-treated bacteria was about 50 to 60\% that of untreated bacteria. Hydroxyurea also was found to produce some cellular filaments and shorter stalks, but with accompanying decreases in growth rate and yield.},
	number = {3},
	urldate = {2009-05-03TZ},
	journal = {Journal of Bacteriology},
	author = {Haars, E G and Schmidt, J M},
	month = dec,
	year = {1974},
	pmid = {4436259},
	keywords = {Adenosine Triphosphate, Bacteria, Bacterial Proteins, Carbon Radioisotopes, Cell Division, DNA, Bacterial, Hydroxyurea, Leucine, Mitomycins, Morphogenesis, Mutation, Phosphates, RNA, Bacterial, Thymidine, Tritium, Uridine},
	pages = {1409--1416}
}

Paper  bibtex   

@article{Lezius1967,
	title = {Enzymatic synthesis of {DNA} with 4-thio-thymidine triphosphate as substitute for {dTTP}.},
	volume = {3},
	issn = {0014-2956},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/4295053},
	number = {1},
	journal = {European journal of biochemistry / FEBS},
	author = {Lezius, a G and Scheit, K H},
	month = dec,
	year = {1967},
	pmid = {4295053},
	keywords = {\#nosource, Animals, Carbon Isotopes, Catalysis, Cattle, Cellulose, Centrifugation, Chromatography, DNA, DNA Nucleotidyltransferases, Density Gradient, Deoxyribonucleases, Escherichia coli, Escherichia coli: enzymology, Genetic, Glass, Nucleotides, Pancreas, Pancreas: enzymology, Paper, Phosphoric Monoester Hydrolases, Phosphorus Isotopes, Polymers, Snakes, Spectrophotometry, Sulfhydryl Compounds, Templates, Thymidine, Thymus Gland, Thymus Gland: enzymology, Tritium, Venoms},
	pages = {85--94},
}

@article{della_fera_persistent_2021,
	title = {Persistent Human Papillomavirus Infection},
	volume = {13},
	issn = {1999-4915},
	doi = {10.3390/v13020321},
	abstract = {Persistent infection with oncogenic human papillomavirus ({HPV}) types is responsible for {\textasciitilde}5\% of human cancers. The {HPV} infectious cycle can sustain long-term infection in stratified epithelia because viral {DNA} is maintained as low copy number extrachromosomal plasmids in the dividing basal cells of a lesion, while progeny viral genomes are amplified to large numbers in differentiated superficial cells. The viral E1 and E2 proteins initiate viral {DNA} replication and maintain and partition viral genomes, in concert with the cellular replication machinery. Additionally, the E5, E6, and E7 proteins are required to evade host immune responses and to produce a cellular environment that supports viral {DNA} replication. An unfortunate consequence of the manipulation of cellular proliferation and differentiation is that cells become at high risk for carcinogenesis.},
	pages = {321},
	number = {2},
	journaltitle = {Viruses},
	shortjournal = {Viruses},
	author = {Della Fera, Ashley N. and Warburton, Alix and Coursey, Tami L. and Khurana, Simran and {McBride}, Alison A.},
	date = {2021-02-20},
	pmid = {33672465},
	pmcid = {PMC7923415},
	keywords = {cancer, papillomavirus, {HPV}, Humans, Papillomavirus Infections, Virus Replication, latency, Papillomaviridae, persistence, {DNA}, Viral, Animals, epithelium, extrachromosomal replication, Genome, Viral, immune evasion, tethering},
	file = {Plný text:C\:\\Users\\Miroslava Kuderavá\\Zotero\\storage\\PG4QMPJY\\Della Fera et al. - 2021 - Persistent Human Papillomavirus Infection.pdf:application/pdf},
}