Direct Observation of Flexible Polymer Chain Relaxation Using ssDNA

We report the direct observation of chain relaxation for single flexible polymers at the molecular level. Recently, we developed a new experimental system for single molecule studies of flexible polymers based on single stranded DNA (ssDNA). We developed a biochemical synthesis platform for producing long strands of fluorescently-labeled ssDNA suitable for single polymer experiments. ssDNA molecules are synthesized to contain “designer” sequences, which avoids intrachain base pairing interactions. Using this system, we directly observe the relaxation process for single ssDNA polymer chains, thereby extending experimental studies of single polymer dynamics to a new class of molecules. Indeed, the vast majority of previous single polymer studies have relied on double stranded DNA, a semi-flexible polymer with markedly different molecular properties compared to flexible polymer chains (dsDNA persistence length ≈66 nm; ssDNA persistence length ≈0.6 nm). In this work, we present results from initial studies of ssDNA relaxation dynamics, which effectively highlights the differences in dynamics between “real” flexible polymers and “ideal” chains. We use fluorescence microscopy to characterize polymer chain relaxation from high stretch in free solution within a microfluidic device, and we present results for ssDNA chain relaxation as a function of polymer molecular weight and salt concentration. We compare results from single polymer experiments of chain relaxation to Brownian dynamics simulations incorporating force-extension elastic relations appropriate for flexible polymers. Using a combined experimental and computational approach, we explore the importance of backbone flexibility and solvent quality on chain relaxation, and we determine dynamical scaling laws for ssDNA chain relaxation. Overall, we seek a molecular-based understanding of the non-equilibrium dynamics of flexible polymer chains, which is crucial for control of polymer processing and molecular self-assembly.

 

1. C. Brockman, S. J. Kim and C. M. Schroeder, Soft Matter, in press (2011).
2. F. Latinwo and C. M. Schroeder, Soft Matter, in press (2011).