Experimental investigation of the forces dictating polymer translocation through solid-state nanopores.

Abstract

After realizing direct long-read DNA and RNA sequencing, nanopores show also potential for decoding information on other polymers, including proteins and nanostructured DNA. Understanding the process by which these biopolymers are captured and traverse nanopores however remains a challenging task due to the complex nature of the non-equilibrium translocation dynamics which occur on multiple timescales and are dictated mainly by forces over which full experimental control is challenging. This unfortunately also makes verification of theoretical ideas difficult. In this work, we present solid-state nanopore data of DNA fragments for a wide range of experimental conditions in hopes of showcasing the various underlying forces and processes during capture and translocation. Namely, we specifically attempt to establish the absolute and relative magnitude of electrophoretic forces, and frictional contributions originating from hydrodynamic interactions both inside and outside nanopores. This is achieved by studying the dependence of translocation times on nanopore size (3-20 nm diameter) and DNA length (500-45,000 bp), and by measuring the time-dependent translocation velocity of DNA nanostructures, which consists of a linear DNA polymer with three helix-bundle (3HB) sub-structures patterned along its contour. The velocity profile of the patterned nanostructure is measured under different applied voltages (0.1-1 V), in different salt concentrations (0.5-4 M LiCl), and in different pore geometry. The data allow us to corroborate the predictions of tension propagation and consolidate previously published observations regarding measurements of electrophoretic pulling force and pore-polymer interactions in nanopore systems. In addition to bridging nanopore experiment and theory, these results can be used to inform and design several biosensing and digital storage applications.