287859 Intrachain Hydrodynamic Interactions for DNA in Slits

Monday, October 29, 2012
Hall B (Convention Center )
Jeremy J. Jones1, Johan van der Maarel2 and Patrick S. Doyle1, (1)Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, (2)Department of Physics, National University of Singapore, Singapore, Singapore

Advancements in nanofabrication techniques have given rise to a new generation of micro and nanodevices for use in biological assays. These devices are also ideal platforms to study fundamental issues regarding DNA polymer conformations and dynamics in confinement. Over the past decade there has been extensive work by our group and others in examining DNA in slits. Despite this body of work, there is still not agreement about concepts such as "complete" screening of hydrodynamics or whether one can assume blobs in a DNA chain are non-draining. Here we use an intrachain density-density         correlation function to extract information about the dynamic correlations at different length and time scales within single DNA chains.  Using this technique we are able to measure long-time correlated intrachain dynamics that would otherwise be masked by translational diffusion of the DNA center of mass.  This affords us opportunity to explicitly examine the effects of hydrodynamics on DNA segmental motion across different length scales.  Our results resolve outstanding issues raised in prior studies regarding intrachain hydrodynamic interactions and their effects on chain dynamics.

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