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Title: Is ab initio DFT method useful in analyzing sequence specificity of bases in nucleic acid?
Authors: Parajuli, Raghab
Kalita, Rituraj
Medhi, C
Keywords: Sequences;Ab initio;Stacked model;DNA
Issue Date: Mar-2006
Publisher: NISCAIR-CSIR, India
IPC Code: Int. CI.7 C 07 D
Abstract: The stacking interaction of base pairs in DNA has been studied by using DFT method. The results obtained from DFT study are complementary to those of ab initio and semi-quantitative studies, and subsequently useful for analyzing sequence specificity among various sequences in DNA, The interaction energies of optimum stacked base pairs are higher than those of ab initio and semi-quantitative results, but significant variation of interaction energies of different sequence combination is observed. The stacked models, AT-AT, AT-TA, GC-GC, GC-CG, AT-GC and AT-CG combinations indicate some stabilization at different twist angles. The results obtained from DFT method clearly show some electrostatic interaction energies associated in each stacked model, although provide small interaction energies due to the exclusion of dispersion interaction.
Page(s): 782-791
ISSN: 0975-0983(Online); 0376-4699(Print)
Appears in Collections:IJC-B Vol.45B(03) [March 2006]

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