Energetic and conformational aspects of A : T base-pair opening within theDNA double helix

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 ru pture and a roughly linear region due to loss of stacking and solvation. Th ymine 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 conside rable changes in surrounding solvent distribution, leading finally to a wat er channel which passes through the double helix.