Diffusion dynamics of circular DNA mini-rings in solution
Seminar Room 1, Newton Institute
In gel electrophoresis it was observed in Ref.  that underwound DNA mini-rings migrate slower than overwound DNA mini-rings in EDTA solution. Motivated with the novel observation we have evaluated the diffusion constant of a closed ladder-shaped polymer in solution via Brownian dynamics with hydrodynamic interaction. It gives a model of a supercoiled DNA mini-ring consisting of DNA double strands. Here, the topology of the whole molecule such as the linking number (Lk) of the double DNA strands is conserved in time. By introducing the bending rigidity, we have found that the diffusion constant of a ladder-shaped molecule with base flipping becomes smaller and much more dependent on the linking number, Lk . We thus suggest that the numerical observations should explain the different migration sppeds between the underwound and overwound DNA mini-rings. Here we also recall an interesting observation that for knotted DNAs the migration speeds in gel are proportional to th e diffusion constants in a good solvent.
 J.M. Fogg, D.J. Catanese, Jr., G.L. Randall, M.C. Swick, and L. Zechiedrich, Proc. Institute Math. App. Vol. 150 (2009), 73-121.  N. Kanaeda, T. Deguchi and L. Zechiedrich, Bussei-Kenkyu Vol. 92 (2009) pp. 145-146.