TY - JOUR
T1 - Protonation of Nucleobases in Single- and Double-Stranded DNA
AU - González-Olvera, Julio C.
AU - Durec, Matúš
AU - Marek, Radek
AU - Fiala, Radovan
AU - Morales-García, María del Rosario J.
AU - González-Jasso, Eva
AU - Pless, Reynaldo C.
N1 - Publisher Copyright:
© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
PY - 2018/10/4
Y1 - 2018/10/4
N2 - 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 N3 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 O2 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.
AB - 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 N3 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 O2 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.
KW - DNA methylation
KW - methylcytosine
KW - nucleobases
KW - oligonucleotides
KW - protonation
UR - http://www.scopus.com/inward/record.url?scp=85052403102&partnerID=8YFLogxK
U2 - 10.1002/cbic.201800310
DO - 10.1002/cbic.201800310
M3 - Artículo
C2 - 30073767
SN - 1439-4227
VL - 19
SP - 2088
EP - 2098
JO - ChemBioChem
JF - ChemBioChem
IS - 19
ER -