DNA Hairpin Dynamics under Molecular Crowding Conditions

Abstract

We are interested in the effects of the cellular environment on the behaviour of DNA. We have studied diffusing and immobilised DNA hairpins, which are excellent model systems for studying DNA hybridization, under molecular crowding conditions. We used two complementary single-molecule fluorescence methods to probe the structure and dynamics of the hairpins. The hairpins followed two-state folding dynamics with a closing rate increasing by 4-fold and the opening rate decreasing 2-fold, for only modest concentrations of crowder [10% w/w polyethylene glycol (PEG)]. We interpret the enhanced base pairing in terms of excluded volume effects and increased ion activity. The demonstration of large changes in the base-pairing thermodynamics and kinetics for a simple DNA molecule under relatively dilute crowding conditions suggests that crowding may be even more important for controlling cellular processes than first thought.