Base-pairing energies of proton-bound heterodimers of cytosine and modified cytosines: Implications for the stability of DNA i-motif conformations. Yang, B. & Rodgers, M. T Journal of the American Chemical Society, December, 2013. ![Base-pairing energies of proton-bound heterodimers of cytosine and modified cytosines: Implications for the stability of DNA i-motif conformations. [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex The DNA i-motif conformation was discovered in (CCG)•(CGG)n trinucleotide repeats, which are associated with fragile-X syndrome, the most widespread inherited cause of mental retardation in humans. The DNA i-motif is a four-stranded structure whose strands are held together by proton-bound dimers of cytosine (C(+)•C). The stronger base-pairing interactions in C(+)•C proton-bound dimers as compared to Watson-Crick G•C base pairs are the major forces responsible for stabilization of the i-motif conformations. Methylation of cytosine results in silencing of the FMR1 gene and causes fragile-X syndrome. However, the influence of methylation or other modifications such as halogenation of cytosine on the base-pairing energies (BPEs) in the i-motif remains elusive. To address this, proton-bound heterodimers of cytosine and 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, and 5-iodocytosine are probed in detail. Experimentally, the BPEs of proton-bound heterodimers of cytosine and modified cytosines are determined using threshold collision-induced dissociation (TCID) techniques. All modifications at the 5-position of cytosine are found to lower the BPE, and therefore would tend to destabilize DNA i-motif conformations. However, the BPEs in these proton-bound heterodimers still significantly exceed those of the Watson-Crick G•C and neutral C•C base pairs, suggesting that C(+)•C mismatches are still energetically favored such that i-motif conformations are preserved. Excellent agreement between TCID measured BPEs and B3LYP calculated values is found with the def2-TZVPPD and 6-311+G(2d,2p) bases sets, suggesting that calculations at these levels of theory can be employed to provide reliable energetic predictions for related systems.
@article{Yang2013,
title = {Base-pairing energies of proton-bound heterodimers of cytosine and modified cytosines: {Implications} for the stability of {DNA} i-motif conformations.},
issn = {1520-5126},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24320604},
doi = {10.1021/ja409515v},
abstract = {The DNA i-motif conformation was discovered in (CCG)•(CGG)n trinucleotide repeats, which are associated with fragile-X syndrome, the most widespread inherited cause of mental retardation in humans. The DNA i-motif is a four-stranded structure whose strands are held together by proton-bound dimers of cytosine (C(+)•C). The stronger base-pairing interactions in C(+)•C proton-bound dimers as compared to Watson-Crick G•C base pairs are the major forces responsible for stabilization of the i-motif conformations. Methylation of cytosine results in silencing of the FMR1 gene and causes fragile-X syndrome. However, the influence of methylation or other modifications such as halogenation of cytosine on the base-pairing energies (BPEs) in the i-motif remains elusive. To address this, proton-bound heterodimers of cytosine and 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, and 5-iodocytosine are probed in detail. Experimentally, the BPEs of proton-bound heterodimers of cytosine and modified cytosines are determined using threshold collision-induced dissociation (TCID) techniques. All modifications at the 5-position of cytosine are found to lower the BPE, and therefore would tend to destabilize DNA i-motif conformations. However, the BPEs in these proton-bound heterodimers still significantly exceed those of the Watson-Crick G•C and neutral C•C base pairs, suggesting that C(+)•C mismatches are still energetically favored such that i-motif conformations are preserved. Excellent agreement between TCID measured BPEs and B3LYP calculated values is found with the def2-TZVPPD and 6-311+G(2d,2p) bases sets, suggesting that calculations at these levels of theory can be employed to provide reliable energetic predictions for related systems.},
journal = {Journal of the American Chemical Society},
author = {Yang, Bo and Rodgers, Mary T},
month = dec,
year = {2013},
pmid = {24320604},
keywords = {\#nosource},
}
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The stronger base-pairing interactions in C(+)•C proton-bound dimers as compared to Watson-Crick G•C base pairs are the major forces responsible for stabilization of the i-motif conformations. Methylation of cytosine results in silencing of the FMR1 gene and causes fragile-X syndrome. However, the influence of methylation or other modifications such as halogenation of cytosine on the base-pairing energies (BPEs) in the i-motif remains elusive. To address this, proton-bound heterodimers of cytosine and 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, and 5-iodocytosine are probed in detail. Experimentally, the BPEs of proton-bound heterodimers of cytosine and modified cytosines are determined using threshold collision-induced dissociation (TCID) techniques. All modifications at the 5-position of cytosine are found to lower the BPE, and therefore would tend to destabilize DNA i-motif conformations. 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