Regulating DNA transport through solid-state nanopores to study non-canonical DNA structures and analyze gene synthesis reactions

Abstract

Voltage-driven transport of double-stranded DNA through nanopores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this dissertation, we show that this anomalous transport is the result of DNA self-interaction, a phenomenon which is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell time distributions that fit a simple drift-diffusion theory. This observation of smooth DNA translocation is then used to study the effect of epigenetic modifications on DNA transport dynamics and to analyze gene synthesis reactions. Additionally, a preliminary study is presented reporting on the detection of G-quadruplex structures using solid-state nanopores.