SINGLE BIOMOLECULE SENSING AND CHARACTERIZATION USING SOLID-STATE NANOPORES

Abstract

Solid-state nanopores are an important tool for statistically significant detection and analysis of individual biomolecules. In this work, we demonstrated a method for detection of >100,000 DNA translocation events per nanopore. Detection of single molecules in such high numbers allowed for statistically relevant sampling of rare conformations and structures of DNA molecules, including knots. Knots are self-entanglements of long DNA molecules, important in biological processes and DNA sequencing technology. Using nanopores, we investigated equilibrium structures of DNA knots and showed the occurrence of both large and small knots in DNA, as well as different modes of knot translocation dynamics. Using the large statistics in concert with simulations, we investigated complexity of knotting in different solutions, and occurrence of rare composite knots. We showed that knot sliding and tightening is relevant only to small nanopores. Insights into DNA-DNA interactions and the appropriate nanopore configurations for controlling them are also presented.