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 ∼ L -1 C -0.5 ). In contrast, with 25 and 45 kbp DNA topology had a strong influence. At 1 mg/mL we found D C - C > D L - C ≫ D L - L ≫ D C - 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 ∼ L -2 C -1.75 ) was observed at ∼6 times the molecular overlap concentration. In contrast, D C - L decreased much more steeply with concentration, indicating that a process much slower than reptation governs that case.