Computational Elastic Rod Model Applied to DNA Looping

DNA is a long flexible biopolymer containing genetic information. Proteins often take advantage of DNA’s inherent flexibility to perform their cellular functions. Here we present selected results from our computational studies of the mechanical looping of DNA by the Lactose repressor protein. The Lactose repressor resides in the bacterium E. coli and deforms DNA into a loop as a means of controlling the production of enzymes necessary for digesting lactose. We examine this looping process using a computational rod model [1–3] to understand the strain energy and geometry for the resultant DNA loops. Our model captures the multiple looped conformations of the molecule arising from both multiple boundary conditions and geometric nonlinearities. In addition, the model captures the periodic variation of strain energy with base-pair length as suggested by repression experiments (see, for example, [4, 5]).