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Resolving the Sequence-Dependent Stiffness of DNA Using Cyclization Experiments and a Computational Rod Model

[+] Author Affiliations
Sachin Goyal

Woods Hole Oceanographic Institution, Woods Hole, MA

Noel C. Perkins, Jens-Christian Meiners

University of Michigan, Ann Arbor, MI

Paper No. DETC2007-35141, pp. 1457-1465; 9 pages
doi:10.1115/DETC2007-35141
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

Structural deformations of DNA play a central role in many biological processes including gene expression. The structural deformations are sensitive to the material properties of the molecule and these, in turn, vary along the molecule’s length according to its base-pair sequence. Example ‘sequence-dependent’ material properties include the stress-free curvature and the stiffness for bending and torsion. Separating and quantifying these sequence-dependent properties from experimental data remains a significant challenge as they often work in unison in nature. In this paper, we offer a method for resolving and quantifying the sequence-dependent stiffness of DNA from cyclization (loop closure) experiments using a computational rod model of the molecule.

Copyright © 2007 by ASME
Topics: Stiffness , DNA

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