Single Molecule Studies in Polymer Physics and Biology

Charles Schroeder

Harvard University, Deparment of Chemistry and Chemical Biology

Single Molecule Studies of DNA Replication and Polymer Physics

Single molecule techniques offer a powerful approach to investigate complex physical and biological processes. In this work, we present two topics in polymer physics: polymer conformation hysteresis and characteristic periodic motion in shear flow. In the first experiment, we directly visualize long chain DNA molecules in planar extensional flow using fluorescence microscopy and observe that the conformation of a single polymer is strongly dependent on its deformation history. Conformation hysteresis arises due to intramolecular hydrodynamic interactions. In a separate experiment, we observe a characteristic periodic motion for both free and surface-tethered DNA molecules in shear flow, and we present scaling analyses for this behavior. Experimental results are complemented by results from Brownian dynamics simulation. We also study biological systems using single molecule tools. In one research area, we study DNA replication by direct observation of single DNA polymerase molecules on DNA strands in vitro. A flow-stretched DNA assay allows for characterization of enzymatic rate, processivity, and pausing during DNA synthesis as a function of base pair content.