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Related Experiment Video

Updated: Jun 1, 2026

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

Single-Molecule Measurement of Protein Interaction Dynamics Within Biomolecular Condensates

Published on: January 5, 2024

Discrete persistent-chain model for protein binding on DNA.

Pui-Man Lam¹, Yi Zhen

¹Physics Department, Southern University, Baton Rouge, Louisiana 70813, USA. puiman_lam@subr.edu

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|May 24, 2011

Summary

We developed a model for protein binding on DNA, calculating how force affects binding and DNA extension. This helps analyze experimental data to understand protein-DNA interactions.

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Area of Science:

Biophysics
Molecular Biology
Computational Biology

Background:

Protein-DNA interactions are crucial for biological processes.
Understanding these interactions at a molecular level is essential.
Quantifying binding dynamics under force is experimentally challenging.

Purpose of the Study:

To develop a discrete persistent-chain model for protein binding on DNA.
To derive analytical and numerical solutions for force-extension curves.
To provide a method for analyzing experimental data and deducing binding parameters.

Main Methods:

Developed a discrete persistent-chain model incorporating protein binding sites and energy costs.
Derived analytic expressions for force-extension curves and protein fraction at low forces.
Employed numerical methods to solve the model for higher forces.

Main Results:

Obtained analytic solutions for force-extension curves and bound protein fractions under small forces.
Achieved numerical solutions for force-extension curves and average bound protein fractions at higher forces.
The model successfully relates applied force to DNA extension and binding status.

Conclusions:

The developed model provides a framework for understanding protein-DNA binding under mechanical force.
It enables the analysis of experimental force-extension curves.
The model can deduce the number of bound proteins, particularly in cases of non-specific binding.