DNA Dynamics in Nanoslits and Nanochannels : Roles of Semi-Flexibility and Hydrodynamic Screening

Classical polymer physics has been shown to be extremely successful in predicting flexible polymer conformation and dynamics in confined environments. Less is understood about the dynamics of confined semi-flexible chains. In sub-100nm channels, nano-fabrication has facilitated studies of DNA conformation and dynamics near and below the DNA persistence length ($\sim$50nm), which provides a good model for studying semi-flexible polymer dynamics. We investigate semi-flexible chain dynamics in nanochannels and nanoslits with Brownian dynamics simulations, Monte Carlo simulations, and optical microscopy. Our study explores how the bending energy, the conformational entropy, and the DNA-surface interactions affect the macromolecular conformation. The importance of intra-chain hydrodynamic interactions and how hydrodynamic screening affect chain dynamics is examined. Our study finds that the competition between chain semi-flexibility and confinement can lead to damping of low frequency chain relaxation modes.