Journal
CHEMBIOCHEM
Volume 19, Issue 19, Pages 2088-2098Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/cbic.201800310
Keywords
methylcytosine; DNA methylation; nucleobases; oligonucleotides; protonation
Funding
- CEITEC 2020 [LQ1601]
- CEITEC-Central European Institute of Technology-under CEITEC [LM2011020]
- Ministry of Education, Youth and Sports of the Czech Republic
- CONACYT (Consejo Nacional de Ciencia y Tecnologia, in Mexico) [37678, 1295273]
- Instituto Politecnico Nacional [SIP20121522, SIP20144138]
- CONACYT [61322]
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Single-stranded model oligodeoxyribonucleotides, each containing a single protonatable base-cytosine, adenine, guanine, or 5-methylcytosine-centrally located in a background of non-protonatable thymine residues, were acid-titrated in aqueous solution, with UV monitoring. The basicity of the central base was shown to depend on the type of the central base and its nearest neighbours and to rise with increasing oligonucleotide length and decreasing ionic strength of the solution. More complex model oligonucleotides, each containing a centrally located 5-methylcytosine base, were comparatively evaluated in single-stranded and double-stranded form, by UV spectroscopy and high-field NMR. The N-3 protonation of the 5-methylcytosine moiety in the double-stranded case occurred at much lower pH, at which the duplex was already experiencing general dissociation, than in the single-stranded case. The central guanine:5-methylcytosine base pair remained intact up to this point, possibly due to an unusual alternative protonation on O-2 of the 5-methylcytosine moiety, already taking place at neutral or weakly basic pH, as indicated by UV spectroscopy, thus suggesting that 5-methylcytosine sites in double-stranded DNA might be protonated to a significant extent under physiological conditions.
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