Transcription-driven twin supercoiling of a DMA loop: A Brownian dynamics study

Steven P. Mielke; William H. Fink; Viswanathan V Krishnan; Niels Grønbech-Jensen; Craig J. Benham

doi:10.1063/1.1799613

Transcription-driven twin supercoiling of a DMA loop: A Brownian dynamics study

Steven P. Mielke, William H. Fink, Viswanathan V Krishnan, Niels Grønbech-Jensen, Craig J. Benham

Research output: Contribution to journal › Article

21 Scopus citations

Abstract

A computational model was developed for modeling the long-time conformational dynamics of extended regions of dsDNA in solution subjected to external and localized torques. The chain, linear when relaxed, was looped to form two open but topologicallly constrained subdomains. The 100 μs response of a 477-base pair B-DNA template was simulated by Brownian dynamics to the localized torque generated by the prokaryotic transcription ensemble. The results reveal the superhelicity to be simultaneously right handed in one subdomain and left handed in the other.

Original language	English (US)
Pages (from-to)	8104-8112
Number of pages	9
Journal	Journal of Chemical Physics
Volume	121
Issue number	16
DOIs	https://doi.org/10.1063/1.1799613
State	Published - Oct 22 2004
Externally published	Yes

ASJC Scopus subject areas

Atomic and Molecular Physics, and Optics

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title = "Transcription-driven twin supercoiling of a DMA loop: A Brownian dynamics study",

abstract = "A computational model was developed for modeling the long-time conformational dynamics of extended regions of dsDNA in solution subjected to external and localized torques. The chain, linear when relaxed, was looped to form two open but topologicallly constrained subdomains. The 100 μs response of a 477-base pair B-DNA template was simulated by Brownian dynamics to the localized torque generated by the prokaryotic transcription ensemble. The results reveal the superhelicity to be simultaneously right handed in one subdomain and left handed in the other.",

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AU - Fink, William H.

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AU - Grønbech-Jensen, Niels

AU - Benham, Craig J.

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AB - A computational model was developed for modeling the long-time conformational dynamics of extended regions of dsDNA in solution subjected to external and localized torques. The chain, linear when relaxed, was looped to form two open but topologicallly constrained subdomains. The 100 μs response of a 477-base pair B-DNA template was simulated by Brownian dynamics to the localized torque generated by the prokaryotic transcription ensemble. The results reveal the superhelicity to be simultaneously right handed in one subdomain and left handed in the other.

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