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 journalArticle

19 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)8104-8112
Number of pages9
JournalJournal of Chemical Physics
Volume121
Issue number16
DOIs
StatePublished - Oct 22 2004
Externally publishedYes

Fingerprint

Dynamic mechanical analysis
Transcription
torque
Torque
B-Form DNA
templates
deoxyribonucleic acid

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Transcription-driven twin supercoiling of a DMA loop : A Brownian dynamics study. / Mielke, Steven P.; Fink, William H.; Krishnan, Viswanathan V; Grønbech-Jensen, Niels; Benham, Craig J.

In: Journal of Chemical Physics, Vol. 121, No. 16, 22.10.2004, p. 8104-8112.

Research output: Contribution to journalArticle

Mielke, Steven P. ; Fink, William H. ; Krishnan, Viswanathan V ; Grønbech-Jensen, Niels ; Benham, Craig J. / Transcription-driven twin supercoiling of a DMA loop : A Brownian dynamics study. In: Journal of Chemical Physics. 2004 ; Vol. 121, No. 16. pp. 8104-8112.
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