Investigating Classic Lac Repressor-Dna Looping Experiments Using a Computational Rod Model

Abstract

Protein mediated DNA looping is a well known gene regulatory mechanism. A commonly studied system that controls gene expression is lactose repressor (LacI) induced DNA looping. In two in vitro studies, the Muller-Hill group investigates how the lac repressor protein in E. coli forms loops with linear and cyclized DNA. Their experiments analyzed LacI induced looping on linear DNA over a wide range of interoperator lengths (6-21 helical turns) and on supercoiled DNA minicircles of 452 base pairs. In these experiments, electron microscopy, non-denaturing polyacrylamide gel elecrophoresis, and DNase I protection experiments were used to detect loop formation, estimate loop size, quantify loop stability, and for supercoiled DNA to detect loop topology (ΔLk). In our study, we exercise our computational rod model to make side-by-side comparisons of our predictions with their experimental observations. By making comparisons, we look to understand the energetic cost of loop formation and the resulting topology of the looped complex.