DNA in its biological active state is under negative torsional stress, which is influenced by processes such as transcription and replication and tightly regulated by the action of topoisomerases. More than a mere consequence of the biological activity of the cell, the internal tension leads to a global compaction of the DNA structure from a random coil state to a more ordered supercoiled state, in which two double strands are plectonemically wound around each other. The structural and dynamic properties of a supercoiled state result from a complex interplay between different physical factors: DNA bend and twist rigidity, coil entropy, electrostatic and hydrodynamic interactions between DNA segments, thermal fluctuations, global topological constrains and local "defects" in DNA structure, such as bent DNA sequences and inhomogeneities in DNA rigidity. These pose a fascinating set of problems concerning the statistics and dynamics of DNA in the supercoiled state and its transition into it, the formation and dynamics of plectonemic branches and the kinetics of DNA slithering motion within the branches. Understanding of the global structure and dynamics of superhelical DNA forms the indispensable fundament upon which more detailed studies can be based that are targeted towards specific biological questions. One important consequence of the global folding of the superhelix is that sites that are distant on the contour of the DNA chain can be brought together into close spatial proximity. This is of great biological significance because a timely juxtaposition of two (or more) distant DNA sites is a prerequisite for important processes such as gene regulation and DNA recombination. Supercoiling by itself is not specific in that it compacts the whole of DNA and may not necessarily bring two particular sites in proximity. The combination of DNA supercoiling and DNA bends may be very effective in bringing two specific sites together on DNA molecules.
We are interested in characterizing the conformational dynamics of superhelical DNA. The emphasis here lies on the interaction between global topological properties of DNA (superhelicity) with local inhomogeneities in DNA structure, such as variations in natural curvature and rigidity between different DNA sequences.
The analysis of the dynamics of internal structural rearrangements (branch extrusion, slithering) within DNA plectonemes is of particular interest. We have several techniques in our lab to study single molecule dynamics: Fluorescence Resonance Energy transfer (FRET), Fluorescence Corelation Spectroscopy (FCS), Fluorescence Cross Correlation Spectroscopy (FCCS) and FRET using Alternating Laser Excitaion (ALEX).