Acid–base properties of the nucleic-acid model 2′-deoxyguanylyl(5′→3′)-2′-deoxy-5′-guanylate, d(pGpG)3−, and of related guanine derivatives

Abstract

The dinucleotide d(pGpG) is an often employed DNA model to study various kinds of interactions between DNA and metal ions, but its acid–base properties were not yet described in detail. In this study the six deprotonation reactions of H₄[d(pGpG)]⁺ are quantified. The acidity constants for the release of the first proton from the terminal P(O)(OH)₂ group (pK_a = 0.65) and for one of the (N7)H⁺ sites (pK_a = 2.4) are estimated. The acidity constants of the remaining four deprotonation reactions were measured by potentiometric pH titrations in aqueous solution (25 °C; I = 0.1 M, NaNO₃): The pK_a values for the deprotonations of the second (N7)H⁺, the P(O)₂(OH)⁻, and the two (N1)H sites are 2.98, 6.56, 9.54 and 10.11, respectively. Based on these results we show how to estimate acidity constants for related systems that have not been studied, e.g. pGpG, which is involved in the initiation step of a rotavirus RNA polymerase. The relevance of our results for nucleic acids in general is briefly indicated.