An ab initio molecular orbital study on the sequence-dependency of DNA conformation: an evaluation of intra- and inter-strand stacking interaction energy.
The various nearest neighbor stacking interaction energies of stacked base pairs in the DNA double helix are calculated for both A- and B-type conformations using an ab initio molecular orbital method. It is demonstrated that the sequence-dependent conformational preference for A- or B-type results from the stacking interaction. In particular, the base sequence showing the highest preference for an A-type conformation is revealed as GC/GC, and the one with the next highest preference, AT/AT; for a B-type conformation, the respective sequences are CG/CG and CA/TG. The overall conformation of a DNA fragment is not determined by these particular sequences only but is influenced by all base pair steps. An intrinsically favorable conformation is predicted from the constituent stacking interaction.
Biophysics Division, National Cancer Center Research Institute, Tokyo, Japan.
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Aida
D001482:Base Composition; D001483:Base Sequence; D004247:DNA; D009690:Nucleic Acid Conformation
D004247:DNA