Unfolding dynamics of single collapsed DNA molecules

Abstract

We observed elastic responses of single DNA molecules and visualized them during the collapsing transition induced by trivalent cation, spermidine (SPD). The force-extension curves show worm-like behavior, force plateau, and stick-release responses depending on SPD concentration. The periodic stick-release responses may reflect the unraveling of toroidal condensates. At much higher SPD concentration, we observed re-elongation of a single collapsed DNA. For the visualization, a fluorescent dye, YOYO, was used. We observed bright spots in the fluorescence intensity profile of a collapsed DNA during stretching, which may correspond to the collapsed parts within the single DNA. The decrease of the intensity of the spots in stretching implies the mechanical unfolding of collapsed parts. Towards achieving a microscopic understanding of these experimental results, we also investigate the elastic properties of a highly charged polyelectrolyte (PE) chain by Brownian dynamics simulation method. In our dynamic simulation, a PE has a small intrinsic stiffness (i.e., the PE is semiflexible) to model the stiffness of DNA chain, and added multivalent counterions are explicitly taken into account. As the electrostatic coupling parameter (proportional to counterion valency) is increased, counterion condensation is observed, leading finally to the PE collapse through the discontinuous transition for a sufficiently large coupling parameter. Mechanical unfolding of a PE globule reveals its molecular elasticities including force plateau, in agreement with the experimental observations. A numerically deduced electrostatic condensation energy is compared to the experimental value. Charge ordering in the PE-counterion complex and its deformation by the external forcing are elucidated in conjunction with the PE elastic responses. Other dynamic effects such as the effect of a pulling speed are also discussed.