title: Dynamics of curved DNA molecules: prediction and experiment.
abstract: We have developed a quantitative predictive model capable of describing the dynamics of migration of intrinsically curved DNA fragments on polyacrylamide gels. The model takes into account structural features of DNA, end-to-end distance, screening of hydrodynamic interactions, ionic strength of buffer, electrostatic persistence length, structural fluctuations of the macromolecule, counter condensation, and variation of dielectric constant and viscosity of water with MPD. In doing so, we have also addressed a decade old issue on the effect of the organic solvent 2-methyl-2,4-pentanediol on gel migration of phased A-tracts. We show here that A-tract-solvent interactions are less favored compared with A-tract-A-tract and solvent-solvent interactions.
authors.affiliation: Department of Biology, Technion, Technion City, Haifa 32000, Israel.
authors.forename: Tali E
authors.initials: TE
authors.lastname: Haran
authors.forename: Ilana
authors.initials: I
authors.lastname: Cohen
authors.forename: Alexander
authors.initials: A
authors.lastname: Spasic
authors.forename: Kevin
authors.initials: K
authors.lastname: Yang
authors.forename: Udayan
authors.initials: U
authors.lastname: Mohanty
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D015180:Electrophoresis, Gel, Two-Dimensional; D008956:Models, Chemical; D015394:Molecular Structure; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA