Deoxyribonucleic acid (DNA) is an essential molecule that enables the storage and retrieval of genetic information. In its role during cellular processes, this long flexible molecule is significantly bent and twisted. Previously, we developed an elastodynamic rod approximation to study DNA deformed into a loop by a gene regulatory protein (lac repressor) and predicted the energetics and topology of the loops. Although adequate for DNA looping, our model neglected electrostatic interactions, which are essential when considering processes that result in highly supercoiled DNA including plectonemes. Herein, we extend the rod approximation to account for electrostatic interactions and present strategies that improve computational efficiency. Our calculations for the stability for a circularly bent rod and for an initially straight rod compare favorably to existing equilibrium models. With this new capability, we are now well-positioned to study the dynamics of transcription and other dynamic processes that result in DNA supercoiling.
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e-mail: todd.lillian@ttu.edu
e-mail: ncp@umich.edu
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January 2011
Research Papers
Electrostatics and Self-Contact in an Elastic Rod Approximation for DNA
Todd D. Lillian,
Todd D. Lillian
Assistant Professor
Department of Mechanical Engineering,
e-mail: todd.lillian@ttu.edu
Texas Tech University
, Lubbock, TX 79409
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N. C. Perkins
N. C. Perkins
Professor
Fellow ASME
Department of Mechanical Engineering,
e-mail: ncp@umich.edu
University of Michigan
, Ann Arbor, MI 48109
Search for other works by this author on:
Todd D. Lillian
Assistant Professor
Department of Mechanical Engineering,
Texas Tech University
, Lubbock, TX 79409e-mail: todd.lillian@ttu.edu
N. C. Perkins
Professor
Fellow ASME
Department of Mechanical Engineering,
University of Michigan
, Ann Arbor, MI 48109e-mail: ncp@umich.edu
J. Comput. Nonlinear Dynam. Jan 2011, 6(1): 011008 (6 pages)
Published Online: October 4, 2010
Article history
Received:
June 9, 2009
Revised:
June 21, 2010
Online:
October 4, 2010
Published:
October 4, 2010
Citation
Lillian, T. D., and Perkins, N. C. (October 4, 2010). "Electrostatics and Self-Contact in an Elastic Rod Approximation for DNA." ASME. J. Comput. Nonlinear Dynam. January 2011; 6(1): 011008. https://doi.org/10.1115/1.4002267
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