P2

P2: Static and Dynamic Properties of DNA-Based Polymer Structures under Constraints and Confinement

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The main objective of project P2 is to explore the static and dynamical behaviour of complex, DNAbased polymer structures in liquid environment under simultaneous application of constraints and confinement, which both alter the statistical mechanical properties of DNA, and thus, DNA manipulation in and DNA transport through micro- and nanometer-sized geometries. Therefore, the understanding of the Brownian dynamics of constrained and confined molecular structures will have a considerable impact on bridging both bottom-up approaches, based on advanced structural DNA nanotechnology, and top-down methods, designed for single-molecule detection and large-scale manipulation, together. To this aim, we will apply a novel approach of single-molecule detection based on the specific attachment of a single quantum dot, which will – in distinction to all previous studies of DNA in confined geometries – not change the mechanical properties of the investigated molecule in an unpredictable manner. The local fluctuations of single-tethered molecules in one- and two-dimensionally confined geometries will be studied whilst the degree of confinement is systematically changed. The investigations 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 (dsDNA) and artificially designed DNA structures such as linear chains of double-cross-over elements, DNA tubes, and branched DNA structures, which 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.