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Updated: Jun 1, 2026

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates
Published on: January 5, 2024
Discrete persistent-chain model for protein binding on DNA
1Physics Department, Southern University, Baton Rouge, Louisiana 70813, USA. puiman_lam@subr.edu
Abstract:
We describe and solve a discrete persistent-chain model of protein binding on DNA, involving an extra σ(i) at a site i of the DNA. This variable takes the value 1 or 0, depending on whether or not the site is occupied by a protein. In addition, if the site is occupied by a protein, there is an extra energy cost ɛ. For a small force, we obtain analytic expressions for the force-extension curve and the fraction of bound protein on the DNA. For higher forces, the model can be solved numerically to obtain force-extension curves and the average fraction of bound proteins as a function of applied force. Our model can be used to analyze experimental force-extension curves of protein binding on DNA, and hence deduce the number of bound proteins in the case of nonspecific binding.
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