Publication details

Protonation of Guanine:5-Methylcytosine and Guanine:Cytosine Base Pairs in Duplex Oligodeoxyribonucleotides



Year of publication 2022
Type Article in Periodical
Magazine / Source ChemistrySelect
MU Faculty or unit

Central European Institute of Technology

Keywords nucleobases; protonation; duplex DNA; oligonucleotides; basicity
Description NMR- and UV-monitored acid titrations conducted on short model oligodeoxyribonucleotide duplexes demonstrate the protonation of guanine:5-methylcytosine and guanine:cytosine base pairs at the O-2 position of the cytosine base, at pH values close to 7, without disruption of the general duplex structure. In the NMR technique, this protonation transition is most clearly observed by monitoring the 5-methylcytosine-H6 resonance, while pH effects on the 5-methylcytosine methyl group, on guanine-H8, and on the cytosine-H5 and -H6 resonances are small. The local sequences G(Me)CG, (TCT)-C-Me, and TCT show decreasing basicity, in this order. The basicity of the G:C-Me base pair is almost unaffected by ionic strength. Under more acidic conditions, adenine:thymine base pairs may be similarly protonated at the adenine base. Hydrogens on thymine bases contained in single-stranded oligonucleotides are strongly affected by the protonation of near-by bases. The results posit that canonical double-stranded DNA is protonated to a significant extent at certain sites under physiological conditions.
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