280516 Single Molecule Polymer Dynamic Measurements in an Automated Hydrodynamic Trap
For nearly two decades, fluorescently-labeled double stranded DNA (dsDNA) has been the model system for studying single molecule polymer dynamics in non-equilibrium conditions. Single polymer molecule studies utilizing double stranded DNA (dsDNA) have provided a treasure trove of information regarding polymer dynamics; however, dsDNA is a semi-flexible polymer with markedly different local molecular properties and a large persistence length (l≈53 nm) compared to flexible polymer chains, such as polystyrene (l≈0.7 nm) and ssDNA (l≈0.6 nm). Recently, we developed a biochemical synthesis platform for producing long strands of fluorescently-labeled single stranded DNA (ssDNA). In addition, our lab has also developed a microfluidic-based, automated hydrodynamic trap to confine individual particles in free solution at the stagnation point in planar extensional flow. In this work, we extend the use of the automated hydrodynamic trap to study chain dynamics of both dsDNA and ssDNA in extensional flow.
As a proof of principle, we trapped single molecules of dsDNA for up to 10 minutes enabling a host of experiments, including repeated relaxation time measurement an individual molecule and chain behavior for both randomly varying and oscillating strain rates. We then used the automated trap to measure ssDNA relaxation for chains with varying molecular weights and compared the results to our dsDNA measurements to elucidate the differences between relaxation time scaling for “real” and “ideal” chains. Overall, we seek a molecular-based understanding of the non-equilibrium dynamics of flexible polymer chains, which is crucial for control in processing and molecular self-assembly.
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