J. Phys. Chem. B 108, 3335-3341 (2004)

Doi: 10.1021/jp036901m

Modelling Protein-RNA interactions: An electron density study of the formamide and formic acid complexes with RNA Bases

The complexes formed by the double interaction established between the four RNA bases (adenine, cytosine, guanidine, and uracil) and formamide and formic acid as a model for the interacting groups of certain amino acid side chains have been theoretically studied. Density functional theory (B3LYP/6-31+G**) methods have been used for this study. The interaction energies obtained range between 10 and 19 kcal mol-1. The analysis of the electron density and the natural bond orbital analysis show that these complexes are bound by medium strength double hydrogen bonds established between the donor and acceptor groups of formamide and formic acid and those of the RNA bases. Comparisons are made with the results obtained in some experimental studies and the analysis of protein−RNA interactions databases.