Static and dynamic properties of DNA-based polymer structures under constraints and confinement

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The proposed project is a follow-up application for the second funding period of the Forschergruppe merging the main scientific activities of the currently running projects P1 and P2 into a joint project. The main objective of the joint project P2 is to explore the static and dynamic behaviour of complex, DNA-based polymer structures in liquid environment under simultaneous application of constraints and confinement.We will apply advanced optical methods in combination with force-sensitive (Seidel) techniques to study the local fluctuations of single molecules in one-dimensional confining geometries. We explore properties like internal friction in supercoiled molecules, while changing the degree of confinement systematically. The investigations in confined geometries will be carried out under both, equilibrium conditions, without applying external forces, and application of force fields like hydrodynamic drag and electrical fields. As polymers we will use linear, double-stranded DNA, plasmids and artificially designed DNA assemblies such as branched DNA structures. Implementing local optical probes (fluorescent dyes and/or quantum dots) in a site-specific manner into the molecular structures under investigation, will allow us to study the influence of such particular properties of the polymer like flexural rigidity and morphology on the statistical mechanical behaviour of the complex DNA structures in confined geometries. In particular, by controlling the degree of supercoiling of plasmids, we aim to investigate the direct relationship between topology, rigidity and morphology of the molecule in confinement. The planned studies are of importance from the physics as well as from the engineering perspective, because cognition of the Brownian dynamics of both constrained and confined molecules is also critical for the device design, potentially leading to new applications in nanoconfinement and singlemolecule detection. Here we will concentrate on restriction enzyme mapping and melting of single DNA molecules in nanochannels.