(266a) Direct Observation of Flexible Polymer Chain Dynamics Using ssDNA

Authors: 
Schroeder, C. M., University of Illinois at Urbana-Champaign
Brockman, C., University of Illinois at Urbana-Champaign
Kim, S. J., University of Illinois at Urbana-Champaign
Latinwo, F., University of Illinois at Urbana-Champaign


In this work, we introduce a new experimental system for single molecule investigation of flexible polymer chains based on single stranded DNA (ssDNA). Traditional experimental techniques including ?bulk? viscometry and light scattering measurements have revealed a wealth of information regarding polymer dynamics. Single molecule tools allow for the direct observation of polymer backbone dynamics, thereby enabling characterization of real-time dynamic information and distributions in molecular behavior, including ?molecular individualism? and molecular subpopulations. However, the vast majority of single molecule polymer studies has focused on double stranded DNA (dsDNA), a semi-flexible polymer. Here, we present a generalized platform for biochemical synthesis of long ssDNA of arbitrary sequence with concomitant labeling of the polymer backbone with a fluorescent dye, which serves as a new model system for molecular studies of flexible polymer chains. The bare persistence length of ssDNA (l≈0.6 nm) is similar to synthetic flexible polymer molecules such as polystyrene (l≈0.7 nm), whereas dsDNA exhibits a large persistence length (l≈53 nm) due to the structural rigidity of the double helix. Using the new experimental system for ssDNA, we present results from an initial set of dynamical studies, including polymer chain relaxation from high stretch. In addition to fluorescence measurements of polymer chain dynamics, we are currently measuring the force-extension relation of single polymer chains using magnetic tweezers and bifocal imaging with an inverted microscope. Finally, we present Brownian dynamics simulations to model ssDNA dynamics in order to predict dynamic behaviors, such as polymer relaxation, under varying solvent conditions. Using computational and experimental tools, we seek to elucidate the fundamental dynamical differences between ?real? and ?ideal? polymer chains and explore the impact of enhanced chain flexibility on dynamical phenomena. Overall, a molecular-based understanding of non-equilibrium flexible chain dynamics will aid in processing control and provide insight for molecular self-assembly processes.