Structure, energetics, vibrational frequencies and charge transfer of basepairs, nucleoside pairs, nucleotide pairs and B-DNA pairs of trinucleotides: ab initio HF/MINI-1 and empirical force field study

Geometries, interaction energies and vibrational frequencies of base pairs, nucleoside pairs and nucleotide pairs were studied by ab initio Hartree-Fo ck (HF) method using MINI-1 basis set and empirical Cornell ee al. force fi eld (AMBER 4.1). A good agreement was found between HF/MINI-1 and AMBER res ults. In addition, both methods provide reasonable agreement with available high-level ab initio data. Finally, AMBER potential was used to determine the structure, energetics and vibrational frequencies of B-DNA pairs of tri nucleotides. Stabilization energies of clusters are lowered when passing fr om base pairs to nucleoside pairs, nucleotide pairs and to pairs of trinucl eotides. The lowest vibrations of base pairs and nucleoside pairs correspon d to intermolecular motions of bases, specifically to buckle and propeller motions. In the case of pairs of larger subunits the lowest vibrations are of intramolecular nature (rotation around glycosidic bond, sugar and phosph ate vibration). The spectra of these clusters became more complicated and q uasi-degenerate. Intermolecular charge transfer between bases in H-bonded a nd stacked pairs is negligible, while a significant intramolecular charge t ransfer was observed.