Dynamics of Large DNA Loops

Abstract

Dynamics of Large DNA Loops Long range interactions between genetically distant regions of DNA (>10 kbp) are not governed by the elastic energies of bending and twisting of DNA, but rather by entropic forces. Furthermore, such large scale interactions are mediated strongly by the excluded volume interactions of DNA and proteins of the cellular environment. It is not clear how these interactions locally couple to variables such as temperature, salt strength, pH, etc. in nanoconfined volumes where the monomer density of DNA is comparable to that in the cell nucleus. Using a nanofluidic device, we manipulate fluid flow to drive DNA into large loops, on the order of kilobasepairs, in a range of buffer concentrations and protein backgrounds. By analyzing the dynamics of the loop formation, steady state fluctuations, and deformation, we quantify an energy landscape. We can use this energy landscape to characterize activation barriers for proteins to form DNA loops. Once these activation barriers are overcome, we can test for enhancements in the loop elongation rate due to proteins. In addition, we can test for arrested states caused by proteins binding to specific sequences.