DNA Polymer Dynamics in Nanoconfinement

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CBET - 0852235 Doyle, Patrick S. This project studies the equilibrium and non-equilibrium dynamics of double stranded DNA in nanofluidic devices. The project will combine state-of-the-art nanofabrication, single molecule imaging and molecular modeling. The fundamental goal is to understand molecular transport in highly confined geometries with application to single molecule DNA mapping. The project has four primary objectives. 1) Measure transport coefficients and size of highly confined DNA. 2) Design and fabricate cross-slot devices to study electrophoretic stretching and relaxation of confined DNA. 3) Develop single molecule DNA mapping methods with stretching in cross-slot devices. 4) Develop scaling theories, Brownian dynamics simulations and other models to support the experimental studies. Confined DNA in nano-slits with heights smaller than the DNA's bulk radius of gyration is a relatively unexplored regime. DNA size and transport coefficients (diffusion coefficient, longest relaxation time, electrophoretic mobility) should be extremely sensitive to the local environment. The PI will construct experimental systems to study highly confined DNA with slit heights as small as 10nm. The PI will also build devices to electrophoretically stretch DNA in nanoslit cross-slot devices. Initial results point to the possibility of a new "2-step" coil-to-stretch transition that will be explored in detail both experimentally and theoretically. These nanoslit devices will not only allow for many fundamental polymer physics studies, but be excellent platforms for mapping single DNA molecules. To this end, the PI will develop means to selectively tag DNA at specific sites with quantum dots and then read off this barcoded molecule using the cross-slots. Simulations and scaling theories will lend support to the experiments. The single DNA mapping has clear impact on disease diagnostics, pathogen detection and drug discovery. The PI will engage undergraduate educators and students from other universities through the Research Experience for Teachers and Research Experience for Undergraduates programs and develop microfluidic modules they can take back to their universities. Videos for K-12 teachers will be developed for the Teacher's Domain repository maintained by Boston public radio. Web-based and short-course tutorials will be developed on topics of single molecule experiments and nano-scale transport.