Non-Ergodic Transport and Conformational Dynamics of DNA in Biomimetic Cytoskeleton Networks

Abstract

Macromolecular crowding is an increasingly relevant biophysical phenomenon affecting gene expression, drug delivery, protein function, and intracellular transport. Of particular interest is the influence that cytoskeletal filaments have on the transport and conformational dynamics of large DNA molecules -- two properties critical for processes such as transfection, viral infection, and gene therapy. Here, we use single-molecule conformational tracking (SMCT) to elucidate the transport properties and conformational dynamics of linear and relaxed circular (ring) DNA in in vitro composite networks of actin and microtubules with variable types of crosslinking. Specifically, we investigate the impact of crosslinking actin to actin, microtubules to microtubules, and actin to microtubules. While both linear and ring DNA undergo anomalous subdiffusion in all networks, the transport properties are heavily influenced by DNA topology (linear vs ring). Linear DNA chains are compacted and display a single mode of subdiffusion, while ring DNA polymers are swollen and exhibit biphasic subdiffusion suggestive of transient threading by the biomimetic cytoskeleton. These results are bolstered by the non-Gaussian nature of displacement probabilities and the non-ergodic behavior of both DNAs, with the relaxed circular DNA becoming less ergodic than their linear counterparts at long times.