title: Sequence sensitivity of breathing dynamics in heteropolymer DNA.
abstract: We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy is demonstrated.
authors.affiliation: NORDITA, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark.
authors.forename: Tobias
authors.initials: T
authors.lastname: Ambjörnsson
authors.forename: Suman K
authors.initials: SK
authors.lastname: Banik
authors.forename: Oleg
authors.initials: O
authors.lastname: Krichevsky
authors.forename: Ralf
authors.initials: R
authors.lastname: Metzler
mesh_terms: D017123:Bacteriophage T7 / Q000737:chemistry*; D001483:Base Sequence; D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D015233:Models, Statistical; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D011108:Polymers / Q000737:chemistry*; D011401:Promoter Regions, Genetic; D012965:Sodium Chloride / Q000494:pharmacology; D013050:Spectrometry, Fluorescence; D013269:Stochastic Processes
chemical_list: D011108:Polymers; D012965:Sodium Chloride; D004247:DNA