2007/02/23 by Sachin Goyal, Goyal, Sachin, Noel C. Perkins +1
Biochemistry, Genetics and Molecular Biology · Environmental Science · Physics and Astronomy · #Bacteriophages and microbial interactions #Biological Physics (physics.bio-ph) #Chemical Physics (physics.chem-ph) #Computational Physics (physics.comp-ph) #DNA and Nucleic Acid Chemistry #FOS: Physical sciences #RNA and protein synthesis mechanisms #physics.bio-ph #physics.chem-ph #physics.comp-ph
paper · pdf · doi:10.48550/arxiv.physics/0702200
2 pages, 2 figures, Nonlinear Vibrations, Aug 13-17, 2006, Blacksburg, VA
arxiv created 2007/02/23 · openalex publication_date 2007/02/23 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial step in many gene regulatory mechanisms. We use the mechanical rod model of DNA molecules to simulate its structural interactions with proteins (enzymes) during gene expression. Our rod model can simulate the nonlinear dynamics of loop and supercoil formation in DNA on long length scales. The formulation accounts for the structural stiffness of the DNA strand, its intrinsic curvature, chiral (right-handed helical) construction and its physical interactions with the surrounding medium. The simulations of protein-mediated DNA looping illustrate how the mechanical properties of DNA may affect the chemical kinetics of DNA-protein interactions and thereby regulate gene expression.