Velocity fluctuation and force scaling during driven polymer transport through a nanopore

Abstract: Inspired by its central role in many biological processes, the transport of biopolymers across nanoscale pores is at the heart of a single-molecule sensing technology aimed at nucleic acid and protein sequencing, as well as biomarker detection. When electrophoretically driven through a pore by an electric potential gradient, a translocating polymer hinders the flow of ions, producing a transient current blockage signature that can be mapped to physicochemical properties of the polymer. Although investigated theoretically and by simulations, few experimental studies have attempted to validate the predicted transport properties, mainly due to the complex nature of the non-equilibrium translocation process. Here, we elucidate these fundamental concepts by constructing a patterned DNA nanostructure whose current signatures allow measurement of the instantaneous velocity throughout the translocation process. With simple physical insights from polymer and fluid dynamics, we show how the resulting molecular velocity profiles can be used to investigate the nanoscale forces at play and their dependence on experimental parameters such as polymer length, pore size and voltage. These results allow testing of theoretical models and outline their limitations. In addition to bridging experiment and theory, knowledge of the velocity fluctuation and force scaling during passage can assist researchers in designing nanopore experiments with optimized sensing performance.