Low-Frequency Intra-and Intermolecular Vibration Modes of H-Bonded Nucleobases in Oligonucleotide Double Helixes and Hydrated Nucleotide Duplex:Application of the PM3 Method

摘要

To understand the physical mechanisms of the structural-dynamic organization of the DNA double helix,it is important to investigate the spectrum of vibration modes of Watson-Crick base pairs with different models of H-bonding complexes.Using the PM3 technique,we calculate the energy of low-frequency intra-and inter-molecular vibration modes of isolated canonical nucleoside and nucleotide pairs and analyze the dependence on the elongation of oligonucleotide double helix.The vibration spectrum of hydrated duplex [d(ApA) (centre dot) d(TpT)]~(-2) (centre dot) 47H_2O was also calculated to elucidate the role of water in formation of the DNA spectrum.The results are compared with the available experimental data and analytical estimations.