NDLI: Comparison of the Acid–Base Properties of Ribose and 2′-Deoxyribose Nucleotides

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Comparison of the Acid–Base Properties of Ribose and 2′-Deoxyribose Nucleotides

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Jezowska-bojczuk, Malgorzata Kozlowski, Henryk Knobloch, Bernd Sigel, Roland K. O. Mucha, Ariel
Description	Author Affiliation: Mucha A ( Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland.)
Abstract	The extent to which the replacement of a ribose unit by a 2′-deoxyribose unit influences the acid–base properties of nucleotides has not hitherto been determined in detail. In this study, by potentiometric pH titrations in aqueous solution, we have measured the acidity constants of the 5′-di- and 5′-triphosphates of 2′-deoxyguanosine [i.e., of $H_{2}(dGDP)^{−}$ and $H_{2}(dGTP)^{2−}]$ as well as of the 5′-mono-, 5′-di-, and 5′-triphosphates of 2′-deoxyadenosine [i.e., of $H_{2}(dAMP)^{±},$ $H_{2}(dADP)^{−},$ and $H_{2}(dATP)^{2−}].$ These 12 acidity constants (of the 56 that are listed) are compared with those of the corresponding ribose derivatives (published data) measured under the same experimental conditions. The results show that all protonation sites in the 2′-deoxynucleotides are more basic than those in their ribose counterparts. The influence of the 2′-OH group is 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 (by about 0.2 pK units), while the effect on the phosphate groups and the N1H or $N1H^{+}$ sites is less pronounced but clearly present. In addition, $^{1}H NMR$ chemical shift change studies in dependence on pD in $D_{2}O$ have been carried out for the dAMP, dADP, and dATP systems, which confirmed the results from the potentiometric pH titrations and showed the nucleotides to be in their anti conformations. 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 $pK_{a}$ values in DNAzymes and ribozymes, as needed for the delineation of acid–base mechanisms in catalysis.
ISSN	09476539
e-ISSN	15213765
Journal	Chemistry - A European Journal
Issue Number	22
Volume Number	14
Language	English
Publisher	Wiley-VCH;ChemPubSoc Europe
Publisher Date	2008-01-01
Publisher Place	Germany
Access Restriction	Open
Subject Keyword	Acids Chemistry Alkalies Deoxyribose Nucleotides Ribose Hydrogen-Ion Concentration Magnetic Resonance Spectroscopy Comparative Study Research Support, Non-U.S. Gov't
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Catalysis

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