Many-body effect for stacking interaction and hydrogen bonding between nucleobases

DOI
  • Hattori Nana
    Graduate School of Science, Hiroshima University, Center for Quantum Life Sciences, Hiroshima University
  • Aida Misako
    Graduate School of Science, Hiroshima University, Center for Quantum Life Sciences, Hiroshima University

Bibliographic Information

Other Title
  • 核酸塩基間のスタッキング相互作用と水素結合における多体効果

Description

The many-body interaction energies between nucleobases of DNA were calculated by means of ab initio MO method. We performed ab initio MO calculations for 2 and 3 base-pair steps in the conformation of B-DNA. To construct the stacking conformation for a base-pair in B-DNA, the geometry optimization was performed for each base-pair (A-T and G-C). All the stacked base-pairs were assumed to be parallel, with Rise 3.5 Å between them and Twist 36 degrees. Each many-body term in the interaction between nucleobases was obtained in the conformation of the stacked base-pairs. All the calculations were done with the theoretical level of MP2/6-31G(d). As for the interaction between bases, we found that the two-body term is dominant and each many-body term value depends on the base-sequence. The calculated interaction energies, the hydrogen bonding between the bases and the stacking interaction between the base-pairs, were used to estimate the stability of DNA oligomers (ΔE) with various base-sequences. Good correlation was found between the estimated ΔE values and the experimental ΔG values. This indicates that the internal energy of DNA oligomer can be estimated from summing-up of the constituent hydrogen bonding and the stacking interaction energies according to the base-sequence.

Journal

Keywords

Details 詳細情報について

  • CRID
    1390282680714704256
  • NII Article ID
    130005054526
  • DOI
    10.11545/ciqs.2010.0.jp16.0
  • Data Source
    • JaLC
    • CiNii Articles
  • Abstract License Flag
    Disallowed

Report a problem

Back to top