ISBN: 978-83-60043-10-3 - eurobic9

Eurobic9, 2-6 September, 2008, Wrocław, Poland
P131. Acid-Base Properties of 2'-Deoxyribose versus Ribose Nucleotides
A. Mucha a , B. Knobloch a , M. Jeżowska-Bojczuk b , H. Kozłowski b , R.K.O. Sigel a
a Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland,
b Faculty of Chemistry, University of Wrocław, F. Joliot Curie 14, 50-383, Wrocław, Poland
e-mail: ariel@eto.wchuwr.pl
The extent of the influence of the exchange of a ribose by a 2'-deoxyribose on the acid-base properties of
nucleotides has so far not yet been determined in detail. In this study, we have measured by potentiometric pH
titrations in aqueous solution the acidity constants of the 5'-mono-, 5'-di- and 5'-triphosphates of 2'deoxyadenosine
[i.e., of H2(dAMP) ± , H2(dADP) – and H2(dATP) 2– ] as well as of the 5'-di- and 5'-triphosphates of
2'-deoxyguanosine [i.e., of H2(dGDP) – and H2(dGTP) 2– ] (see Fig.1). These in total 12 acidity constants are
compared with the corresponding ribose derivatives, which have been measured under the same experimental
conditions (published data). The results show that all protonation sites in the 2'-deoxynucleotides are more basic
than in their ribose counterparts. The influence of the 2'-OH group is thereby dependent on the number of 5'phosphate
groups as well as on the nature of the purine nucleobase. The basicity of N7 in guanine nucleotides is
most significantly enhanced (about 0.2 pK units), the effect on the phosphate groups and the N1H or (N1H) +
sites is less pronounced but clearly present. In addition, for the dAMP, dADP and dATP systems 1 H-NMR
chemical shift change studies in D2O in dependence on pD were carried out confirming the results from the
potentiometric pH titrations and showing that the nucleotides are in their anti conformation. [1] Overall, our
results are not only of relevance for metal ion binding to nucleotides or nucleic acids, but also constitute an exact
basis for the calculation, determination, and understanding of perturbed pKa values in DNAzymes and ribozymes
needed for an acid-base mechanism in catalysis.
Figure 1. The chemical structures of the investigated nucleotides.
Acknowledgements: Financial support from the Swiss National Science Foundation (SNF-Förderungsprofessur
to R.K.O.S., PP002-114759/1), the Polish State Committee for Scientific Research (KBN Grant No. N.204 029
32/0791), the Universities of Zürich and Wrocław, and within the COST D39 programme from the Swiss State
Secretariat for Education and Research is gratefully acknowledged, as are the International Relations Office of
the University of Zürich (fellowship to A.M.) and helpful hints by Prof. Dr. H. Sigel (University of Basel).
References:
[1] A. Mucha, B. Knobloch, M. Jeżowska-Bojczuk, H. Kozłowski, R.K.O. Sigel, Comparison of the Acid-Base
Properties of Ribose and 2'-Deoxyribose Nucleotides, Chem. Eur. J., 2008, DOI: 10.1002/chem.200800496
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