title: Comparative bending dynamics in DNA with and without regularly repeated adenine tracts.
abstract: The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of DNA structure. The paper reports on comparative theoretical and experimental studies of bending dynamics in 35-mer DNA fragments. This length appears large enough for the curvature to be distinguished by gel electrophoresis. Two DNA fragments, with identical base pair composition but different sequences, are compared. In the first one, a single A-tract motif is four times repeated in phase with the helical screw whereas the second sequence is "random." Both calculations and experiments indicate that the A-tract DNA is distinguished by large static curvature and characteristic bending dynamics, suggesting that the computed effect corresponds to the experimental phenomenon. The results agree poorly with the view that DNA bending is caused by the specific local geometry of base pair stacking or binding of solvent counterions, but lend additional support to the hypothesis of a compressed frustrated state of the backbone as the principal physical cause of the static curvature. Possible ways of experimental verification of this hypothesis are discussed.
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13, Rue Pierre et Marie Curie, Paris, 75005, France. aleyey@ibpc.fr
authors.forename: Alexey K
authors.initials: AK
authors.lastname: Mazur
authors.forename: Dimitri E
authors.initials: DE
authors.lastname: Kamashev
mesh_terms: D000225:Adenine / Q000737:chemistry; D020029:Base Pairing; D001483:Base Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012091:Repetitive Sequences, Nucleic Acid; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D004247:DNA; D000225:Adenine