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Energetic and Conformational Aspects of A:T Base‐Pair Opening within the DNA Double Helix
Author(s) -
Giudice Emmanuel,
Várnai Péter,
Lavery Richard
Publication year - 2001
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/1439-7641(20011119)2:11<673::aid-cphc673>3.0.co;2-s
Subject(s) - solvation , thymine , stacking , helix (gastropod) , chemistry , oligomer , hydrogen bond , base pair , crystallography , dna , groove (engineering) , solvation shell , chemical physics , stereochemistry , solvent , materials science , molecule , polymer chemistry , ecology , biochemistry , organic chemistry , snail , metallurgy , biology
Free energy profiles of opening of a centrally placed A:T pair within a DNA oligomer exhibits two regimes: Elastic deformation due to hydrogen bond rupture and a roughly linear region due to loss of stacking and solvation. Thymine opens equally easily into the minor and major grooves, while adenine favors the major groove direction. No significant variations from canonical backbone conformations were observed; however base opening induces considerable changes in surrounding solvent distribution, leading finally to a water channel which passes through the double helix.