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J Theor Biol. 1988 Feb 7;130(3):327-35.

An ab initio molecular orbital study on the sequence-dependency of DNA conformation: an evaluation of intra- and inter-strand stacking interaction energy.

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  • Biophysics Division, National Cancer Center Research Institute, Tokyo, Japan.


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.

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