Topology-Dependent Dynamics Of Single Dna Molecules

We present the data on the conformational dynamics of circular DNA molecules with defined levels of topological complexity, characterized by the knot type K and linking number Lk. Covalently closed DNAs covalently conjugated to specific fluorophores were investigated using fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) measurements. We investigate in detail the respective effects of supercoiling and DNA knotting using Lk-topoisomer pools and specific DNA-knot types that were respectively generated by topoisomerase-I relaxation and Cre site-specific recombination. Previous Brownian-dynamics simulations by Langowski et al. (1994) suggest that increasing superhelicity leads to progressively faster dynamics on long time scales, corresponding to translational diffusion, but also on short time scales, corresponding to segmental motions within supercoiled DNA. We investigate here whether DNA knotting similarly affects translational and internal motions. The acceleration of DNA dynamics with increased supercoiling may have implications for processes in cells, such as transcriptional regulation and DNA recombination, both of which are dependent on the dynamics of juxtaposition involving multiple DNA sites.