Localization of denaturation bubbles in random DNA sequences

Terence Hwa; Enzo Marinari; Kim Sneppen; Lei han Tang

doi:10.1073/pnas.0736291100

Localization of denaturation bubbles in random DNA sequences

Terence Hwa^*
, Enzo Marinari
, Kim Sneppen
, Lei han Tang

^*Corresponding author for this work

Department of Physics

Research output: Contribution to journal › Journal article › peer-review

83 Citations (Scopus)

Abstract

We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to AT-rich segments. In the localized regime, the bubbles exhibit "aging" and move around subdiffusively with continuously varying dynamic exponents. These properties are derived by using results of large-deviation theory together with scaling arguments and are verified by Monte Carlo simulations.

Original language	English
Pages (from-to)	4411-4416
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	100
Issue number	8
DOIs	https://doi.org/10.1073/pnas.0736291100
Publication status	Published - 15 Apr 2003

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title = "Localization of denaturation bubbles in random DNA sequences",

abstract = "We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to AT-rich segments. In the localized regime, the bubbles exhibit {"}aging{"} and move around subdiffusively with continuously varying dynamic exponents. These properties are derived by using results of large-deviation theory together with scaling arguments and are verified by Monte Carlo simulations.",

author = "Terence Hwa and Enzo Marinari and Kim Sneppen and Tang, \{Lei han\}",

note = "T.H. is supported by National Science Foundation Grant 0211308 and a Burroughs-Wellcome functional genomics award.",

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T1 - Localization of denaturation bubbles in random DNA sequences

AU - Hwa, Terence

AU - Marinari, Enzo

AU - Sneppen, Kim

AU - Tang, Lei han

N1 - T.H. is supported by National Science Foundation Grant 0211308 and a Burroughs-Wellcome functional genomics award.

PY - 2003/4/15

Y1 - 2003/4/15

N2 - We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to AT-rich segments. In the localized regime, the bubbles exhibit "aging" and move around subdiffusively with continuously varying dynamic exponents. These properties are derived by using results of large-deviation theory together with scaling arguments and are verified by Monte Carlo simulations.

AB - We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to AT-rich segments. In the localized regime, the bubbles exhibit "aging" and move around subdiffusively with continuously varying dynamic exponents. These properties are derived by using results of large-deviation theory together with scaling arguments and are verified by Monte Carlo simulations.

UR - https://www.scopus.com/pages/publications/0037447270

U2 - 10.1073/pnas.0736291100

DO - 10.1073/pnas.0736291100

M3 - Journal article

C2 - 12672955

AN - SCOPUS:0037447270

SN - 0027-8424

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SP - 4411

EP - 4416

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 8

ER -

Localization of denaturation bubbles in random DNA sequences

Abstract

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