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Sequence dependence of the B‐A conformational transition of DNA
Author(s) -
Mazur J.,
Sarai A.,
Jernigan R. L.
Publication year - 1989
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360280704
Subject(s) - chemistry , van der waals force , intramolecular force , sequence (biology) , crystallography , base (topology) , base pair , electrostatics , conformational change , dna , stereochemistry , chemical physics , molecule , mathematical analysis , biochemistry , mathematics , organic chemistry
We have studied, by conformational analysis, the sequence dependence of DNA conformational transition between B‐ and A‐forms. We have considered intramolecular interactions between base pairs, without backbone, to examine their role in the conformational transition between B‐ and A‐forms, and found that base pairs themselves usually have intrinsic conformational preferences for the B‐ or A‐form. Calculation of all ten possible base steps shows that the base combinations, CC (or GG), GC, AT, and TA, have tendencies to assume the A‐conformation. Results show that it is particularly easy to slide along the long axis of the base pair for these steps, with AT and CC showing especially flat energies. These calculations show that a preference for the B‐ or A‐conformation depends on the electrostatic energy parameters, in particular, on dielectric and shielding constants; the A‐conformations are mainly stabilized by electrostatic interactions between favorably juxtaposed atomic charges on base pairs; however, the B‐conformation generally has more favorable van der Waals interactions than the A‐form. These sequence‐dependent conformational preference and environmental effects agree roughly with experimental observations, suggesting that the origin of the conformational polymorphism is attributable to the intrinsic conformational preference of base pairs.