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 | |
| State | Published - Oct 22 2004 |
| Externally published | Yes |
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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 journal › Article
}
TY - JOUR
T1 - Transcription-driven twin supercoiling of a DMA loop
T2 - A Brownian dynamics study
AU - Mielke, Steven P.
AU - Fink, William H.
AU - Krishnan, Viswanathan V
AU - Grønbech-Jensen, Niels
AU - Benham, Craig J.
PY - 2004/10/22
Y1 - 2004/10/22
N2 - 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.
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.
UR - http://www.scopus.com/inward/record.url?scp=8344267602&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=8344267602&partnerID=8YFLogxK
U2 - 10.1063/1.1799613
DO - 10.1063/1.1799613
M3 - Article
C2 - 15485274
AN - SCOPUS:8344267602
VL - 121
SP - 8104
EP - 8112
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 16
ER -