Nanopore Resistive Sensing: Bridging Theory and Experiments

Abstract

Nanopore sensing is a single molecule technique which consists in detecting molecules as they pass through a nanopore, i.e. a nanoscale hole, driven by an electric potential gradient applied across the pore. When in conductive aqueous solutions, the passage of a biomolecule is detected as a transient ionic current blockade, due to translocating molecules momentarily hindering the movement of ions across the pore. The characteristics of the blockade signals (e.g. average or maximum current blockage amplitude, signal duration, sequence of blockade sublevels, etc.) can contain rich information related to the physical and chemical properties of the passing biomolecule. The simplicity by which nanopore sensing operates has resulted in highly successful applications and exciting research endeavors including nucleic acid sequencing. The application-driven nature of the nanopore sensing field has resulted in a separation between nanopore sensing theory and experiments. The rich physics of the polymer capture and translocation through nanopores has yet to be extensively characterized experimentally. As such, the work in this thesis aims to bridge the gap existing between nanopore theory and experiments by providing new mathematical frameworks by which to analyze and interpret complex nanopore signals, or by providing clear experimental demonstrations of the forces underlying nanopore capture and translocation. Namely, the subjects covered in this thesis either attempt to characterize the electric field inside nanopores and in their vicinity, or attempt to characterize the response of polymers to this field, whether confined inside nanopore during translocation or outside the pore during capture. More precisely, in Chapter 2 a novel framework by which to model the blocked-state access region contributions is introduced. Chapter 3 studies the capture and translocation kinetics in the presence of salt concentration gradients across the nanopore membrane, conditions which allow the non-uniform modulation of the electric field in the nanopore system. Chapter 4 introduces a patterned nanostructure whose blockade signal allows estimating its instantaneous translocation velocity which, accompanied by simple physical insights, allows probing the underlying forces driving and opposing translocation. Lastly, Chapter 5 investigates the folding kinetics of a rigid DNA nanostructure, providing interesting insights into the structure’s composition and the role of rigidity on translocation dynamics. The work presented was highly motivated by the core idea that a clearly presented description of the physical principles of nanopore sensing will be greatly beneficial for assisting researchers in designing better experiments, thus enabling the development of more applications.