title: Plectoneme tip bubbles: coupled denaturation and writhing in supercoiled DNA.
abstract: We predict a novel conformational regime for DNA, where denaturation bubbles form at the tips of plectonemes, and study its properties using coarse-grained simulations. For negative supercoiling, this regime lies between bubble-dominated and plectoneme-dominated phases, and explains the broad transition between the two observed in experiment. Tip bubbles cause localisation of plectonemes within thermodynamically weaker AT-rich sequences, and can greatly suppress plectoneme diffusion by a pinning mechanism. They occur for supercoiling densities and forces that are typically encountered for DNA in vivo, and may be exploited for biological control of genomic processes.
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, United Kingdom.
authors.forename: Christian
authors.initials: C
authors.lastname: Matek
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, United Kingdom.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ouldridge
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, United Kingdom.
authors.forename: Jonathan P K
authors.initials: JP
authors.lastname: Doye
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, United Kingdom.
authors.forename: Ard A
authors.initials: AA
authors.lastname: Louis
mesh_terms: D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010957:Plasmids / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D004278:DNA, Superhelical