Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA.

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

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

The topological state of DNA in vivo is dynamically regulated by a number of processes that involve interactions with bound proteins. In one such process, the tracking of RNA polymerase along the double helix during transcription, restriction of rotational motion of the polymerase and associated structures, generates waves of overtwist downstream and undertwist upstream from the site of transcription. The resulting superhelical stress is often sufficient to drive double-stranded DNA into a denatured state at locations such as promoters and origins of replication, where sequence-specific duplex opening is a prerequisite for biological function. In this way, transcription and other events that actively supercoil the DNA provide a mechanism for dynamically coupling genetic activity with regulatory and other cellular processes. Although computer modeling has provided insight into the equilibrium dynamics of DNA supercoiling, to date no model has appeared for simulating sequence-dependent DNA strand separation under the nonequilibrium conditions imposed by the dynamic introduction of torsional stress. Here, we introduce such a model and present results from an initial set of computer simulations in which the sequences of dynamically superhelical, 147 base pair DNA circles were systematically altered in order to probe the accuracy with which the model can predict location, extent, and time of stress-induced duplex denaturation. The results agree both with well-tested statistical mechanical calculations and with available experimental information. Additionally, we find that sites susceptible to denaturation show a propensity for localizing to supercoil apices, suggesting that base sequence determines locations of strand separation not only through the energetics of interstrand interactions, but also by influencing the geometry of supercoiling.

Original languageEnglish (US)
Pages (from-to)124911
Number of pages1
JournalThe Journal of Chemical Physics
Volume123
Issue number12
DOIs
StatePublished - Sep 22 2005
Externally publishedYes

Fingerprint

Superhelical DNA
Denaturation
biopolymer denaturation
deoxyribonucleic acid
DNA
Computer simulation
Transcription
simulation
strands
torsional stress
nonequilibrium conditions
Replication Origin
DNA-Directed RNA Polymerases
Torsional stress
helices
upstream
constrictions
apexes
computerized simulation
interactions

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA. / Mielke, Steven P.; Grønbech-Jensen, Niels; Krishnan, Viswanathan V; Fink, William H.; Benham, Craig J.

In: The Journal of Chemical Physics, Vol. 123, No. 12, 22.09.2005, p. 124911.

Research output: Contribution to journalArticle

Mielke, Steven P. ; Grønbech-Jensen, Niels ; Krishnan, Viswanathan V ; Fink, William H. ; Benham, Craig J. / Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA. In: The Journal of Chemical Physics. 2005 ; Vol. 123, No. 12. pp. 124911.
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