Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures. Gray, R. D & Chaires, J. B Nucleic acids research, 36(12):4191–203, July, 2008. ![Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures. [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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.
@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},
}
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{"_id":"4HFWj4xJ4ffhejkFC","bibbaseid":"gray-chaires-kineticsandmechanismofkandnainducedfoldingofmodelsofhumantelomericdnaintogquadruplexstructures-2008","author_short":["Gray, R. D","Chaires, J. B"],"bibdata":{"bibtype":"article","type":"article","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":[{"propositions":[],"lastnames":["Gray"],"firstnames":["Robert","D"],"suffixes":[]},{"propositions":[],"lastnames":["Chaires"],"firstnames":["Jonathan","B"],"suffixes":[]}],"month":"July","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","bibtex":"@article{Gray2008,\n\ttitle = {Kinetics and mechanism of {K}+- and {Na}+-induced folding of models of human telomeric {DNA} into {G}-quadruplex structures.},\n\tvolume = {36},\n\tissn = {1362-4962},\n\turl = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2475619&tool=pmcentrez&rendertype=abstract},\n\tdoi = {10.1093/nar/gkn379},\n\tabstract = {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.},\n\tnumber = {12},\n\tjournal = {Nucleic acids research},\n\tauthor = {Gray, Robert D and Chaires, Jonathan B},\n\tmonth = jul,\n\tyear = {2008},\n\tpmid = {18567908},\n\tkeywords = {\\#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},\n\tpages = {4191--203},\n}\n\n","author_short":["Gray, R. D","Chaires, J. 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