Fundamental Applications of Nanopores: Controlled DNA Translocations to Nanofluidics

Nanopores are nanometer sized openings that are the connection between two electrolyte filled reservoirs. The measurement of the ion transport flowing through such a pore allows to probe physically or biologically interesting phenomena. These range from the passage of biological molecules, to the modulation of current due to multiple physical effects when the nanopore undergoes mechanical strain or pressure induced flow. Many types of nanopores exist: biological protein pores engineered to be able to sequence DNA, glass nanocapillaries easily interfaced with optical tools, or silicon nitride membrane pores which are a standard tool of recent nanotechnology.

This thesis is split into two parts. The first focuses on the use of glass nanocapillaries which allow the facile combination of nanopore experiments with optical tweezers. Optical tweezers are a well established single molecule tool that allow precise force measurement on biologically relevant scales. They are used here for the control of DNA passing through the nanopore. Their ability to measure small scale forces allows the detailed investigation of DNA binding proteins, and attempts to measure the force of DNA passage through biological pores. Extensions of these experiments to the elastic behaviour of DNA during its passage through a nanopore reveal the effects of flow generated by the charged surface of nanopores themselves. This motivates attempts to control such flows as well as the second part of the thesis.

The second part of the thesis focuses on nanofluidics, the role of fluid flow and ion transport at the nanoscale. Using a setup combining pressure with nanopores it is possible to probe, via precise measurements of the conduction of the nanopore, the wetting state of the pore. Contamination phenomena are shown to be abundant with such small systems and a description of their effects on standard measurements such as direct current current-voltage curves is given. Following this, pressure is applied to perfectly filled pores and, thanks to a new alternating current detection method, is shown to be able to discern the effect of pressure induced strain at the pore as well as the coupling of hydraulic flow with electrical properties of the pore. Finally, extensions beyond aqueous solvents are explored in both nanocapillaries and silicon nitride pores. For this, room-temperature ionic liquids are used. These liquids are known from previous studies to behave differently at surfaces and in nano-confinement. The nanopore system both with and without added pressure is shown to be a good tool for investigating such phenomena.