Measurements of DNA-Loop Formation via Cre-Mediated Recombination

The Cre recombination system has become an important tool for genetic manipulation of higher organisms and a model for site-specific DNA-recombination mechanisms employed by the λ-Int superfamily of recombinases. We report a novel quantitative approach for characterizing the probability of DNA-loop formation in solution using time-dependent ensemble FRET measurements of intra- and intermolecular Cre-recombination kinetics. Our method uses an innovative technique for incorporating multiple covalent modifications at specific sites in covalently closed DNA. Because the mechanism of Cre recombinase does not conform to a simple kinetic scheme, we employ numerical methods to extract rate constants for fundamental steps that pertain to Cre-mediated loop closure. Cre recombination does not require accessory proteins, DNA supercoiling, or particular metal-ion cofactors and is thus a highly flexible system for quantitatively analyzing DNA-loop formation in vitro and in vivo.

Presented at the Discrete and Topological Models in Molecular Biology at the University of South Florida, March 12-14, 2012.
Cre Recombinase, DNA, DNA-loop formation
CC BY-NC 3.0 (Attribution-NonCommercial), ©2012 The Author(s).