title: Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies.
abstract: Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC)_{n} repeats or (TG)_{n} repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC)_{n} sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG)_{n} sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.
authors.affiliation: Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, Korea.
authors.forename: Ah-Young
authors.initials: AY
authors.lastname: Kwon
authors.affiliation: Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA.
authors.forename: Gi-Moon
authors.initials: GM
authors.lastname: Nam
authors.affiliation: Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, Korea.|Institute Charles Sadron, Université de Strasbourg, CNRS UPR22, 23 rue du Loess 67034, Strasbourg cedex 2, France.
authors.forename: Albert
authors.initials: A
authors.lastname: Johner
authors.affiliation: Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, Korea.
authors.forename: Seyong
authors.initials: S
authors.lastname: Kim
authors.affiliation: Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea.|Department of Physics, Korea University, Seoul 02841, Korea.
authors.forename: Seok-Cheol
authors.initials: SC
authors.lastname: Hong
authors.affiliation: Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, Korea.|Institute Charles Sadron, Université de Strasbourg, CNRS UPR22, 23 rue du Loess 67034, Strasbourg cedex 2, France.
authors.forename: Nam-Kyung
authors.initials: NK
authors.lastname: Lee
mesh_terms: D059371:DNA, B-Form / Q000737:chemistry* / Q000235:genetics; D043542:DNA, Z-Form / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D059371:DNA, B-Form; D043542:DNA, Z-Form