Nanopore Based Single-molecule Sensors

Abstract

In the past two decades nanopores have been used as highly sensitive detection systems for exploring the properties of analytes at single molecule resolution. The small dimensions of a nanopore permit the molecule of interest to be confined within it, allowing for the extraction of valuable information relating to its physical and chemical properties. Single molecule analysis, as opposed to bulk measurements does not involve ensemble averaging. Hence, short-lived states such as an intermediate configuration during a conformational change can be observed directly, while such states would be masked in the bulk assay. The main project described in this thesis involves the design and fabrication of a hybrid silicon nitride-DNA origami nanopore system for use in biosensing of proteins. We used the nanopore system to experimentally observe the effect of forces between the translocating molecule and nanopore with a focus on the electro kinetics inside the pore and escape rate problem. These are further verified by finite element simulations and MATLAB simulations which enables us to investigate the physics behind the different types of events that we observe. The key findings from this work can be summarized as follows. We report on an operating regime of this nanopore sensor, characterized by attractive interactions between the nanoparticle and the pore, where the dwell time is exponentially sensitive to the target-pore interaction. We used negatively and positively charged gold nanoparticles to control the strength of their interaction with the negatively charged silicon nitride pore. Our experiments revealed how this modulation of the electrostatic force greatly affects the ionic current with an exponential dependance of dwell times. A stochastic model is developed for analyzing this analyte-pore interaction based on the well-known Kramer’s problem of escape from a barrier.Finally, the nitride nanopore was functionalized using DNA origami with thrombin binding aptamer (TBA15), a well studied 15-mer aptamer DNA sequence that binds selectively with thrombin protein. Consistent with our previous experiment, we observed current traces with large dwell time blockades for thrombin whereas for another protein the trace contained minimal dwell time current enhancements. The presence of TBA15 aptamer increased the interaction energy between the thrombin and the nanopore resulting in a blockage with comparatively larger dwell time and enabled us in sensing thrombin at concentrations as low as 20nM. Nanopore technology will remain an important field of science in the 21st century. We believe equipped with our understanding of nanopore analysis, in future we will be able to detect and unravel important physical phenomena in the single molecule world.