title: DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations.
abstract: The intrinsic curvature of seven 98 bp DNA molecules containing up to four centrally located A6-tracts has been measured by gel and capillary electrophoresis as a function of the number and arrangement of the A-tracts. At low cation concentrations, the electrophoretic mobility observed in polyacrylamide gels and in free solution decreases progressively with the increasing number of phased A-tracts, as expected for DNA molecules with increasingly curved backbone structures. Anomalously slow electrophoretic mobilities are also observed for DNA molecules containing two pairs of phased A-tracts that are out of phase with each other, suggesting that out-of-phase distortions of the helix backbone do not cancel each other out. The mobility decreases observed for the A-tract samples are due to curvature, not cation binding in the A-tract minor groove, because identical free solution mobilities are observed for a molecule with four out-of-phase A-tracts and one with no A-tracts. Surprisingly, the curvature of DNA A-tracts is gradually lost when the monovalent cation concentration is increased to ∼200 mM, regardless of whether the cation is a hydrophilic ion like Na+, NH4+, or Tris+ or a hydrophobic ion like tetrabutylammonium. The decrease in A-tract curvature with increasing ionic strength, along with the known decrease in A-tract curvature with increasing temperature, suggests that DNA A-tracts are not significantly curved under physiological conditions.
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA.
authors.forename: Earle
authors.initials: E
authors.lastname: Stellwagen
authors.forename: Justin P
authors.initials: JP
authors.lastname: Peters
authors.forename: L James
authors.initials: LJ
authors.lastname: Maher
authors.forename: Nancy C
authors.initials: NC
authors.lastname: Stellwagen
mesh_terms: D001483:Base Sequence; D002414:Cations, Monovalent / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D019075:Electrophoresis, Capillary; D057927:Hydrophobic and Hydrophilic Interactions; D007477:Ions; D008969:Molecular Sequence Data; D016011:Normal Distribution; D009690:Nucleic Acid Conformation; D012996:Solutions
chemical_list: D002414:Cations, Monovalent; D007477:Ions; D012996:Solutions; D004247:DNA