This document summarizes a study modeling DNA unzipping in the presence of DNA binding proteins using single molecule experimental techniques. The study aims to determine the minimum binding energy and distance between proteins that can be detected using these techniques. The model partitions the DNA-protein system and uses statistical mechanics to calculate force-extension curves for different protein binding energies and distances. The results show a minimum detectable binding energy of 10 kJ/mol and a minimum resolvable distance between proteins of up to 50 base pairs depending on relative protein strengths. Future work could consider the kinetics of the unzipping process.

1. Modeling DNA unzipping in the presence of DNA binding proteins Farhat Habib, Dr. Ralf Bundschuh Department of Physics, The Ohio State University

11. Minimum resolvable distance between two proteins 1400 1500 1700 1800 50 40 20 10 12 14 16 18 20 22 30 1600 R(nm) Protein separation (bp) Force (pN)