dorsal/arxiv
View SchemaStructural Modeling of DNA Loops in Lactose-Repressor
| Authors | Sachin Goyal, Noel C. Perkins |
|---|---|
| Categories | |
| ArXiv ID | physics/0702200 |
| URL | https://arxiv.org/abs/physics/0702200 |
Abstract
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.
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"abstract": "It is well known that the structural deformations (stressed states) of DNA\nmolecule play a crucial role in its biological functions including gene\nexpression. For instance, looping in DNA (often mediated by protein binding) is\na crucial step in many gene regulatory mechanisms. We use the mechanical rod\nmodel of DNA molecules to simulate its structural interactions with proteins\n(enzymes) during gene expression. Our rod model can simulate the nonlinear\ndynamics of loop and supercoil formation in DNA on long length scales. The\nformulation accounts for the structural stiffness of the DNA strand, its\nintrinsic curvature, chiral (right-handed helical) construction and its\nphysical interactions with the surrounding medium. The simulations of\nprotein-mediated DNA looping illustrate how the mechanical properties of DNA\nmay affect the chemical kinetics of DNA-protein interactions and thereby\nregulate gene expression.",
"arxiv_id": "physics/0702200",
"authors": [
"Sachin Goyal",
"Noel C. Perkins"
],
"categories": [
"physics.bio-ph",
"physics.chem-ph",
"physics.comp-ph"
],
"title": "Structural Modeling of DNA Loops in Lactose-Repressor",
"url": "https://arxiv.org/abs/physics/0702200"
},
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