Nanopore Translocation of Entangled DNA and RNA Filaments

Explore the complex dynamics of polymer translocation through nanopores in this specialized lecture focusing on DNA and RNA filaments with altered structures. Delve into the statistical mechanics of out-of-equilibrium systems as they relate to DNA sequencing and biological processes, examining cases where polymer structure is fundamentally changed during translocation. Learn about DNA unzipping mechanisms where one strand is pulled through a nanopore while the other remains outside, and discover the unique properties of xrRNAs - short, highly pseudoknotted RNA structures that resist degradation by exonucleases. Understand how native-centric atomistic models and translocation simulations reveal the mechanistic basis of xrRNA resistance, demonstrating its dependence on entangled architecture. Examine recent findings on long DNA pore translocation, where experimental and simulation data show how solvent flow-induced torque leads to plectoneme formation. Gain insights into nonequilibrium thermodynamics applications in nanopore systems and the role of secondary and tertiary RNA elements in translocation processes, supported by cutting-edge research findings and computational modeling approaches.