Variation of stacking interactions along with twist parameter in DNA and RNA: DFT-D studies

Abstract

In this study the structural features of dinucleotide sequences are quantitatively described in terms of the important orientation parameters of the bases and Watson-Crick base pairs using quantum chemical calculations. Variation of twist parameter in DNA and canonical RNA reveals the most probable value for each sequence. However, all the dinucleotide steps do not show the minima corresponding to specific twist value. All the quantum chemical calculations are done using DFT-D with ωB97X-D functional and 6-31G (2d,2p) basis set. In order to completely understand behavior of the base paired dinucleotide step, we have adopted Metropolis Monte Carlo simulation in 18 dimensional phase space using classical force-field. The results agree in general with the results obtained from DFT-D studies as well as experimental observations. We believe that Monte Carlo simulation with energy from DFT-D would better predict structural features of non-canonical base pairs, which appear frequently in RNA and lacks experimental details.