Theoretical Study of 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. The hydration schemes of a model compound of A-RNA and a polynucleotide which has the structure of the anticodon loop of yeast tRNAPhe have been determined, and their stabilization energies produced by the introduction of water in the first hydration shell were calculated by considering the hydrated ones as supermolecules. 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 bound 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.