Abstract
The Gibbs free energy of formation of metallo-base pair was calculated for the base pairs composed of T, U, F, CN, C and I nucleosides and HgII and AgI metals. The effect of particular metal and the effect of pH on relative stabilization of metallo-base pairs were studied with calculated Gibbs free energies. The stability of Hg-mediated base pairs gradually decreased owing to the F and CN chemical modification of thymine at carbon C5 and owing to the imino to imidazole change of N3 nitrogen atom linked with HgII. The prevalence of AgI-stabilization versus HgII-stabilization was calculated for the metallo-base pairs composed of T, U, F, CN, C and I nucleosides where nucleophilicity of N3 nitrogen atom gradually decreased. The calculated relative stabilizations of metallo-base pairs agreed qualitatively with the increase in melting temperatures measured previously for respective duplexes upon adding HgII and AgI metals (Okamoto et al., 2009). The absolute magnitude of 1J(Hg,N) and 2J(N,N) coupling constants across metal-mediated linkage increased owing to F and CN modification of T and further increase of magnitudes of J-couplings was calculated for imino to imidazole change of metal-bound nitrogen.
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