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Updated: Aug 2, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
A model for protein-DNA interaction dynamics
1The Blackett Laboratory, Imperial College of Science, Technology, and Medicine, Prince Consort Road, SW7 2BZ, London, U.K. p.etchegoin@ic.ac.uk
Abstract:
We map a simplified version of the protein-DNA interaction problem into an Ising-model in a random magnetic field. The model includes a "head" which moves along the chain while interacting with the underlying spins. The head moves by using the statistical fluctuations of base openings. A Monte Carlo (MC) simulation of this model reveals the possibility of biased diffusion in one direction, followed by sequence identification and binding. The model provides some insight into the mechanisms used by some repressor proteins to diffuse and bind to specific DNA-binding sites.
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