Deoxyribonucleic acid (DNA) is a long and flexible biopolymer that contains genetic information. Building upon the discovery of the iconic double helix over 50 years ago, subsequent studies have emphasized how its biological function is related to the mechanical properties of the molecule. A remarkable system which highlights the role of DNA bending and twisting is the packing and ejection of DNA into and from viral capsids. A recent 3D reconstruction of bacteriophage reveals a novel toroidal structure of highly bent/twisted DNA contained in a small cavity below the viral capsid. Here, we extend an elastic rod model for DNA to enable simulation of the toroid as it is compacted and subsequently ejected from a small volume. We compute biologically-relevant forces required to form the toroid and predict ejection times of several nanoseconds.
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July 2013
Research-Article
A Model for Highly Strained DNA Compressed Inside a Protein Cavity
Andrew D. Hirsh,
Andrew D. Hirsh
1
Graduate Student
Research Assistant
University of Michigan,
e-mail: adhirsh@umich.edu
Research Assistant
Department of Mechanical Engineering
,University of Michigan,
Ann Arbor, MI 48109
e-mail: adhirsh@umich.edu
1Corresponding author.
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Todd D. Lillian,
Todd D. Lillian
Assistant Professor
Texas Tech University,
e-mail: todd.lillian@ttu.edu
Department of Mechanical Engineering
,Texas Tech University,
Lubbock, TX 79409
e-mail: todd.lillian@ttu.edu
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Troy A. Lionberger,
Troy A. Lionberger
Postdoctoral Research Associate
Department of Physics,
University of California,
e-mail: talionberger@gmail.com
Howard Hughes Medical Institute
,Department of Physics,
University of California,
Berkeley, Berkeley, CA 94720
e-mail: talionberger@gmail.com
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Ioan Andricioaei,
Ioan Andricioaei
Associate Professor
e-mail: andricio@uci.edu
University of California,
e-mail: andricio@uci.edu
Department of Chemistry
,University of California,
Irvine, Irvine, CA 92697
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N. C. Perkins
N. C. Perkins
Professor
Fellow ASME
University of Michigan,
e-mail: ncp@umich.edu
Fellow ASME
Department of Mechanical Engineering
,University of Michigan,
Ann Arbor, MI 48109
e-mail: ncp@umich.edu
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Andrew D. Hirsh
Graduate Student
Research Assistant
University of Michigan,
e-mail: adhirsh@umich.edu
Research Assistant
Department of Mechanical Engineering
,University of Michigan,
Ann Arbor, MI 48109
e-mail: adhirsh@umich.edu
Todd D. Lillian
Assistant Professor
Texas Tech University,
e-mail: todd.lillian@ttu.edu
Department of Mechanical Engineering
,Texas Tech University,
Lubbock, TX 79409
e-mail: todd.lillian@ttu.edu
Troy A. Lionberger
Postdoctoral Research Associate
Department of Physics,
University of California,
e-mail: talionberger@gmail.com
Howard Hughes Medical Institute
,Department of Physics,
University of California,
Berkeley, Berkeley, CA 94720
e-mail: talionberger@gmail.com
Maryna Taranova
Ioan Andricioaei
Associate Professor
e-mail: andricio@uci.edu
University of California,
e-mail: andricio@uci.edu
Department of Chemistry
,University of California,
Irvine, Irvine, CA 92697
N. C. Perkins
Professor
Fellow ASME
University of Michigan,
e-mail: ncp@umich.edu
Fellow ASME
Department of Mechanical Engineering
,University of Michigan,
Ann Arbor, MI 48109
e-mail: ncp@umich.edu
1Corresponding author.
Contributed by the Design Engineering Division of ASME for publication in the JOURNAL OF COMPUTATIONAL AND NONLINEAR DYNAMICS. Manuscript received July 31, 2011; final manuscript received March 9, 2012; published online October 30, 2012. Assoc. Editor: Aki Mikkola.
J. Comput. Nonlinear Dynam. Jul 2013, 8(3): 031001 (8 pages)
Published Online: October 30, 2012
Article history
Received:
July 31, 2011
Revision Received:
March 9, 2012
Citation
Hirsh, A. D., Lillian, T. D., Lionberger, T. A., Taranova, M., Andricioaei, I., and Perkins, N. C. (October 30, 2012). "A Model for Highly Strained DNA Compressed Inside a Protein Cavity." ASME. J. Comput. Nonlinear Dynam. July 2013; 8(3): 031001. https://doi.org/10.1115/1.4007535
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