  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.
