title: Conformational preferences of DNA in reduced dielectric environments.
abstract: The effect of reduced dielectric environments on the conformational sampling of DNA was examined through molecular dynamics simulations. Different dielectric environments were used to model one aspect of cellular environments. Implicit solvent based on the Generalized Born methodology was used to reflect different dielectric environments in the simulations. The simulation results show a tendency of DNA structures to favor noncanonical A-like conformations rather than canonical A- and B-forms as a result of the reduced dielectric environments. The results suggest that the reduced dielectric response in cellular environments may be sufficient to enhance the sampling of A-like DNA structures compared to dilute solvent conditions.
authors.affiliation: Department of Chemistry and ‡Department of Biochemistry & Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States.
authors.forename: Asli
authors.initials: A
authors.lastname: Yildirim
authors.forename: Monika
authors.initials: M
authors.lastname: Sharma
authors.forename: Bradley Michael
authors.initials: BM
authors.lastname: Varner
authors.forename: Liang
authors.initials: L
authors.lastname: Fang
authors.forename: Michael
authors.initials: M
authors.lastname: Feig
mesh_terms: D044704:DNA, A-Form / Q000737:chemistry* / Q000378:metabolism; D059371:DNA, B-Form / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D044704:DNA, A-Form; D059371:DNA, B-Form; D012997:Solvents