Polymer dynamics in crowded environment via single-molecule imaging

Single-molecule optical imaging is performed of entangled chain dynamics in crowded environments, for cases of both Brownian diffusion and driven transport. The molecules of lambda-DNA are tracked while entangled in networks of both crosslinked gel and entangled actin filaments, and the stochasticity of dynamics is explored by acquiring millions of data points with nm resolution. Brownian diffusion displays pronounced intermittency, long-lived pausing states interrupted by transient swift hopping that couples with large-scale chain shape fluctuation. This trend persists when lambda-DNA chains are driven in a preferred direction by electric fields, the chains migrating in discrete steps with strong coupling between chain motion and shape fluctuation. These trends contrast with commonly-accepted models of the chain mobility. Selective labeling of chain ends reveals a novel mode of gel electrophoresis: one end of the chain tends to stretch and pull slack from the quiescent remainder of the chain until the other end snaps forward and the cycle repeats. Methodologies developed during the course of this study, especially automated image analysis to track chain contours and modular assembly of fragments into catenated chains to track locally-labeled fluorescent regions of chain molecules, could be adapted to other related systems to resolve fundamental questions of polymer chain dynamics at the single-molecule and single-segment level with other chain architectures. A related study on diffusion in crowded hard-sphere colloid suspensions is also summarized and included in this thesis