Protonation of nucleobases in single- and double-stranded DNA

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Authors

GONZÁLEZ-OLVERA Julio C. DUREC Matúš MAREK Radek FIALA Radovan MORALES-GARCÍA María del Rosario J. GONZÁLEZ-JASSO Eva PLESS Reynaldo Carlos

Year of publication 2018
Type Article in Periodical
Magazine / Source ChemBioChem
MU Faculty or unit

Central European Institute of Technology

Citation
Web DOI: 10.1002/cbic.201800310
Doi http://dx.doi.org/10.1002/cbic.201800310
Keywords oligonucleotide; DNA; strand; NMR; UV; protonation; cytosine; 5-methyl cytosine
Attached files
Description Single-stranded model oligodeoxyribonucleotides containing a single protonable base: cytosine, adenine, guanine, or 5-methylcytosine, centrally located in a background of non-protonable thymines 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 containing a centrally located 5-methylcytosine base were comparatively evaluated in single-stranded and double-stranded form, by UV-spectroscopy and high-field NMR. Compared to the single-stranded case, the N3-protonation of the 5-methylcytosine moiety in the double-stranded case occurred at much lower pH, where the duplex already suffered general dissociation. The central guanine:5-methylcytosine base pair remained intact up to this point, possibly due to an unusual alternative protonation on O2 of the 5-methylcytosine moiety already taking place at neutral or weakly basic pH, as indicated by UV spectroscopy, suggesting that in double-stranded DNA, 5-methylcytosine sites may be protonated to a significant extent under physiological conditions.
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