title: Supercoiling and denaturation of DNA loops.
abstract: We study the statistical mechanics of small DNA loops emphasizing the competition between elasticity, supercoiling, and denaturation. Motivated by recent experiments and atomistic molecular dynamics simulation, we propose a new coarse-grained phenomenological model of DNA. We extend the classical elastic rod models to include the possibility of denaturation and nonlinear twist elasticity. Using this coarse-grained model, we obtain a phase diagram in terms of fractional overtwist and loop size that can be used to rationalize a number of experimental results which have also been confirmed by atomistic simulations.
authors.affiliation: Department of Mathematics, University of Bristol, University Walk, Bristol, UK. t.liverpool@bristol.ac.uk
authors.forename: T B
authors.initials: TB
authors.lastname: Liverpool
authors.forename: S A
authors.initials: SA
authors.lastname: Harris
authors.forename: C A
authors.initials: CA
authors.lastname: Laughton
mesh_terms: D016475:3T3 Cells; D000818:Animals; D001696:Biomechanical Phenomena; D048429:Cell Size; D004278:DNA, Superhelical / Q000737:chemistry*; D004548:Elasticity; D005347:Fibroblasts / Q000166:cytology*; D051379:Mice; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012212:Rheology; D014783:Viscosity
chemical_list: D004278:DNA, Superhelical