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.
Skip Nav Destination
e-mail: ncp@umich.edu
e-mail: meiners@umich.edu
Article navigation
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
Search for other works by this author on:
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
Search for other works by this author on:
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
Download citation file:
Get Email Alerts
An Efficient Analysis of Amplitude and Phase Dynamics in Networked MEMS-Colpitts Oscillators
J. Comput. Nonlinear Dynam
Influences of Tooth Crack on Dynamic Characteristics of a Multi-Stage Gear Transmission System Considering the Flash Temperature
J. Comput. Nonlinear Dynam (December 2024)
Data-Driven Modeling of Tire–Soil Interaction With Proper Orthogonal Decomposition-Based Model Order Reduction
J. Comput. Nonlinear Dynam (December 2024)
Related Articles
Biomechanical Measurements of Torsion-Tension Coupling in Human Cadaveric Femurs
J Biomech Eng (January,2011)
A New Three-Dimensional Exponential Material Model of the Coronary Arterial Wall to Include Shear Stress Due to Torsion
J Biomech Eng (October,2008)
On Modeling Morphogenesis of the Looping Heart Following Mechanical Perturbations
J Biomech Eng (December,2008)
Biomechanical Evaluation of a Novel Lumbosacral Axial Fixation Device
J Biomech Eng (November,2005)
Related Proceedings Papers
Related Chapters
Basic Concepts
Design & Analysis of ASME Boiler and Pressure Vessel Components in the Creep Range
Flexibility Analysis
Process Piping: The Complete Guide to ASME B31.3, Third Edition
Side Friction Mobilization Rates for Laterally Loaded Piles from the Pressuremeter
The Pressuremeter and its Marine Applications: Second International Symposium