title: Helix untwisting and bubble formation in circular DNA.
abstract: The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as a function of temperature. The method can predict helical repeat, openings loci, and bubble sizes for specific sequences in a broad temperature range. Some results are presented for a short DNA circle recently identified in mammalian cells.
authors.affiliation: School of Science and Technology, CNISM, Università di Camerino, I-62032 Camerino, Italy. marco.zoli@unicam.it
authors.forename: Marco
authors.initials: M
authors.lastname: Zoli
mesh_terms: D004270:DNA, Circular / Q000138:chemical synthesis* / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D013696:Temperature
chemical_list: D004270:DNA, Circular