Re-Interpretation of Müller-Hill Experiments on the LacR-DNA Complex Using a Computational Model

Abstract

The looping of DNA by proteins such as the Lac repressor (LacR) is a fundamental gene regulatory mechanism. While our understanding of looping has certainly grown from advances in experimental and theoretical techniques, fundamental questions remain concerning the energetic cost of the reaction and the topology of the looped complex. In this study, we return to the well-established in vitro studies from the Müller-Hill lab concerning the LacR-induced looping of both linear and supercoiled DNA over a broad range of inter-operator lengths (6-21 helical turns). In these studies, gel electrophoresis was used to detect loop formation, to estimate loop size, and to quantify loop stability. For supercoiled DNA, gel electrophoresis also detected loop topology (Lk). Both DNase I protection experiments and electron microscopy further probed loop topologies. In returning to these experimental results, we use a new computational model to explore the experimental observations and to add new interpretations.