Velocity Fluctuation and Force Scaling During Driven Polymer Transport through a Nanopore.

Abstract

Inspired by its central role in many biological processes, transport of biopolymers across nanoscale pores is at the heart of single-molecule sensing technologies 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 its physicochemical properties. Although investigated theoretically and through simulations, few experimental studies have attempted to validate predicted transport properties, mainly due to the complex nature of the nonequilibrium translocation process. Herein, we elucidate these fundamental concepts by constructing a patterned DNA nanostructure whose current signatures allow measurement of the instantaneous velocity throughout the translocation process and its dependence on experimental parameters such as polymer length, pore size, and voltage. With simple physical insights from polymer and fluid dynamics, we show how experimental molecular velocity profiles can be used to investigate the nanoscale forces at play and allow testing of the validity and limitations of theoretical concepts from Tension Propagation models. In addition to bridging experiments and theory, the knowledge of the velocity fluctuation and force scalings acquired from the extensive experimental data presented here can assist researchers in designing nanopore experiments with an optimized sensing performance.