Sequence sensitivity of breathing dynamics in heteropolymer DNA

Tobias Ambjörnsson; Suman K. Banik; Oleg Krichevsky; Ralf Metzler

doi:10.1103/PhysRevLett.97.128105

Sequence sensitivity of breathing dynamics in heteropolymer DNA

Tobias Ambjörnsson, Suman K. Banik, Oleg Krichevsky, Ralf Metzler

Department of Physics

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68 Scopus citations

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.

Original language	English
Article number	128105
Journal	Physical Review Letters
Volume	97
Issue number	12
DOIs	https://doi.org/10.1103/PhysRevLett.97.128105
State	Published - 29 Sep 2006

ASJC Scopus subject areas

General Physics and Astronomy

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10.1103/PhysRevLett.97.128105

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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.",

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AU - Ambjörnsson, Tobias

AU - Banik, Suman K.

AU - Krichevsky, Oleg

AU - Metzler, Ralf

PY - 2006/9/29

Y1 - 2006/9/29

N2 - 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.

AB - 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.

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DO - 10.1103/PhysRevLett.97.128105

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VL - 97

JO - Physical Review Letters

JF - Physical Review Letters

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Sequence sensitivity of breathing dynamics in heteropolymer DNA

Abstract

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