Theoretical study of the hydration of RNA

Abstract

The hydration phenomena of A-RNA double helix and the anticodon loop of transfer RNA have been theoretically investigated using the empirical potential energy functions. In the first step, the hydration schemes of a model compound of A-RNA and a polynucleotide which has the structure of the anticodon loop of yeast $tRNA^{phe}$ have been determined and the results for A-RNA have been shown to be in good agreement with other theoretical and experimental values. In the second step, the stabilization energy produced by the introduction of water in the first hydration shell was calculated by considering the hydrated one as a supermolecule. The results indicate that hydration scheme of A-RNA considerably differs from that of B-DNA and stabilization energy due to hydration of A-RNA is not so great as B-DNA. In the anticodon loop structure, however, stabilizing effect of the hydrated water molecules upon the structure is significant. From the results, the reason why the structure of RNA remains unchanged with the change of hydration degree while that of DNA is altered was studied.