title: Energetic and conformational aspects of A:T base-pair opening within the DNA double helix.
abstract: 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.
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France.
authors.forename: E
authors.initials: E
authors.lastname: Giudice
authors.forename: P
authors.initials: P
authors.lastname: Várnai
authors.forename: R
authors.initials: R
authors.lastname: Lavery
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*
chemical_list: D004247:DNA; D013941:Thymine