Self-diffusion of entangled linear and circular DNA molecules: Dependence on length and concentration

Self-diffusion coefficients (D) of DNA molecules of varying length and concentration were measured by tracking the Brownian motion of individual fluorescently labeled tracer molecules. Four possible cases were examined: linear tracer molecules surrounded by linear molecules (L-L), circular tracers surrounded by linears (C-L), linear tracers surrounded by circles (L-C), and circles surrounded by circles (C-C). With 6 and 11 kilobasepair (kbp) DNA D was largely insensitive to topology and varied consistent with Rouse scaling (D similar to L-1C-0.5). In contrast, with 25 and 45 kbp DNA topology had a strong influence. At 1 mg/mL we found DC-C > DL-C > DL-L > DC-L. In the L-L, L-C, and C-C cases a crossover from scaling consistent with the Rouse model to scaling consistent with the reptation model (D similar to L-2C-1.75) was observed at similar to 6 times the molecular overlap concentration. In contrast, DC-L decreased much more steeply with concentration, indicating that a process much slower than reptation governs that case.