Diffusion of polymer rings in linear polymer matrices

Strong effects of molecular topology on diffusion of entangled DNA molecules

When long polymers such as DNA are in a highly concentrated state they may become entangled, leading to restricted self-diffusion. Here, we investigate the effect of molecular topology on diffusion in concentrated DNA solutions and find surprisingly large effects, even with molecules of modest length and concentration. We measured the diffusion coefficients of linear and relaxed circular molecules by tracking the Brownian motion of single molecules with fluorescence microscopy. Four possible cases were compared: linear molecules surrounded by linear molecules, circular molecules surrounded by linear molecules, linear molecules surrounded by circles, and circles surrounded by circles. In measurements with 45-kbp DNA at 1 mg/ml, we found that circles diffused approximately 100 times slower when surrounded by linear molecules than when surrounded by circles. In contrast, linear and circular molecules diffused at nearly the same rate when surrounded by circles, and circles diffused approximately 10 times slower than linears when surrounded by linears. Thus, diffusion in entangled DNA solutions strongly depends on topology of both the diffusing molecule and the surrounding molecules. This effect also strongly depends on DNA concentration and length. The differences largely disappeared when the concentration was lowered to 0.1 mg/ml or when the DNA length was lowered to 6 kb. Present theories cannot fully explain these effects.

Diffusion of Single Star-Branched Dendrimer-like DNA

We report a single-molecule fluorescence study on the diffusion of star-branched polymer dendrimer-like DNA (DL-DNA). The DL-DNA molecules were synthesized from ligating Y-shaped DNA to the fourth generation. It was found through single particle tracking that the diffusion coefficient of DL-DNA changes in a nonmonotonic fashion with its increased concentration possibly due to arm arrest and arm retraction. The diffusion of DL-DNA in linear lambda DNA solution displayed a monotonic concentration dependence 1 order of magnitude greater than the diffusion of DL-DNA in DL-DNA solution. This difference is attributed to the different conformation of DL-DNA and lambda DNA and the entanglement of lambda DNA with a large radius of gyration. Our diffusion study facilitates DL-DNA transportation for drug delivery.