Universal scaling of crowding-induced DNA mobility is coupled with topology-dependent molecular compaction and elongation.

Using single-molecule fluorescence microscopy and particle-tracking techniques, we elucidate the role DNA topology plays in the diffusion and conformational dynamics of crowded DNA molecules. We focus on large (115 kbp), double-stranded ring and linear DNA crowded by varying concentrations (0-40%) of dextran (10, 500 kDa) that mimic cellular conditions. By tracking the center-of-mass and measuring the lengths of the major and minor axes of single DNA molecules, we characterize both DNA mobility reduction as well as crowding-induced conformational changes (from random spherical coils).

Crowding induces complex ergodic diffusion and dynamic elongation of large DNA molecules.

Despite the ubiquity of molecular crowding in living cells, the effects of crowding on the dynamics of genome-sized DNA are poorly understood. Here, we track single, fluorescent-labeled large DNA molecules (11, 115 kbp) diffusing in dextran solutions that mimic intracellular crowding conditions (0-40%), and determine the effects of crowding on both DNA mobility and conformation. Both DNAs exhibit ergodic Brownian motion and comparable mobility reduction in all conditions; however, crowder size (10 vs.

Nonlinear microrheology reveals entanglement-driven molecular-level viscoelasticity of concentrated DNA.

We optically drive a trapped microscale probe through entangled DNA at rates up to 100× the disentanglement rate (Wi≈100), then remove the trap and track subsequent probe recoil motion. We identify a unique crossover to the nonlinear regime at Wi≈20. Recoil dynamics display rate-dependent dilation and complex power-law healing of the reptation tube.