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Computational Elastic Rod Model Applied to DNA Looping

[+] Author Affiliations
Todd D. Lillian, N. C. Perkins

University of Michigan, Ann Arbor, MI

S. Goyal

Woods Hole Oceanographic Institution, Woods Hole, MA

Paper No. DETC2007-34956, pp. 1449-1456; 8 pages
doi:10.1115/DETC2007-34956
From:
  • ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 5: 6th International Conference on Multibody Systems, Nonlinear Dynamics, and Control, Parts A, B, and C
  • Las Vegas, Nevada, USA, September 4–7, 2007
  • Conference Sponsors: Design Engineering Division and Computers and Information in Engineering Division
  • ISBN: 0-7918-4806-X | eISBN: 0-7918-3806-4
  • Copyright © 2007 by ASME

abstract

DNA is a long flexible biopolymer containing genetic information. Proteins often take advantage of DNA’s inherent flexibility to perform their cellular functions. Here we present selected results from our computational studies of the mechanical looping of DNA by the Lactose repressor protein. The Lactose repressor resides in the bacterium E. coli and deforms DNA into a loop as a means of controlling the production of enzymes necessary for digesting lactose. We examine this looping process using a computational rod model [1–3] to understand the strain energy and geometry for the resultant DNA loops. Our model captures the multiple looped conformations of the molecule arising from both multiple boundary conditions and geometric nonlinearities. In addition, the model captures the periodic variation of strain energy with base-pair length as suggested by repression experiments (see, for example, [4, 5]).

Copyright © 2007 by ASME
Topics: DNA

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