New experimental concepts to study DNA dynamics in confined microstructures

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Our project aims at experimental studies on the motion and internal dynamics of single DNA molecules in small channels, pores or slits. The geometrical confinements will be introduced by microfabricated polymer elements as well as by patterned aqueous wetting as layers. To precisely quantify both mass and confinement-dependent self-diffusion as well as characteristic time scales of internal structural relaxation of DNA biopolymers, various sophisticated modes of fluorescence correlation spectroscopy (FCS) combined with smart labeling procedures based on fluorescence energy transfer (FRET) will be employed. These spectroscopic techniques provide unparalleled sensitivity, minimal invasiveness, and access to dynamic time scales between several hundred nanoseconds and seconds, and can be easily combined with optically transparent micro- and nanostructures. In the first funding phase of the project, mobility and flexibility of DNA molecules in specifically designed nanopatterns will be primarily investigated, to test several theoretical models for their applicabilitiy. The perspective of testing biological function of DNA under these conditions is further outlined. This work will contribute to a fundamental qualitative and quantitative understanding of how local confinement of macromolecules alters their mobility, internal dynamics, and finally their (biological) activity. However, there is also practical relevance as the precise control of molecular motion of complex molecules is a prerequisite to establish new micro- and nanofluidic components suitable for molecular separation processes, based on macro-molecular flow properties.