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. Examples of “sequence-dependent” material properties include the stress-free curvature and the stiffness for bending and torsion. Quantifying and separating 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.
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e-mail: ncp@umich.edu
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January 2008
Research Papers
Resolving the Sequence-Dependent Stiffness of DNA Using Cyclization Experiments and a Computational Rod Model
Noel C. Perkins,
Noel C. Perkins
Fellow ASME
Mechanical Engineering, 2350 Hayward,
e-mail: ncp@umich.edu
University of Michigan
, Ann Arbor, MI 48109-2125
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Jens-Christian Meiners
Jens-Christian Meiners
Physics (Biophysics Research Division), 930 North University Avenue,
e-mail: meiners@umich.edu
University of Michigan
, Ann Arbor, MI 48109-1055
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Sachin Goyal
Noel C. Perkins
Fellow ASME
Mechanical Engineering, 2350 Hayward,
University of Michigan
, Ann Arbor, MI 48109-2125e-mail: ncp@umich.edu
Jens-Christian Meiners
Physics (Biophysics Research Division), 930 North University Avenue,
University of Michigan
, Ann Arbor, MI 48109-1055e-mail: meiners@umich.edu
J. Comput. Nonlinear Dynam. Jan 2008, 3(1): 011003 (6 pages)
Published Online: November 2, 2007
Article history
Received:
May 6, 2007
Revised:
July 12, 2007
Published:
November 2, 2007
Citation
Goyal, S., Perkins, N. C., and Meiners, J. (November 2, 2007). "Resolving the Sequence-Dependent Stiffness of DNA Using Cyclization Experiments and a Computational Rod Model." ASME. J. Comput. Nonlinear Dynam. January 2008; 3(1): 011003. https://doi.org/10.1115/1.2802582
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