A whispering gallery mode based biosensor platform for single enzyme analysis

Abstract

Enzymes catalyze most of the biochemical reactions in our cells. The functionality of enzymes depends on their dynamics starting from small bond vibrations in the fs timescale to large domain motions in the microsecond-millisecond timescale. Understanding the precise and rapid positioning of atoms within a catalytic site by an enzyme’s molecular movements is crucial for understanding biomolecular processes and for realizing synthetic biomolecular machines in the longer term. Hence, sensors capable of studying enzymes over a wide range of amplitudes and timescale and ideally one enzyme at a time are required. Many capable single-molecule techniques have been established in the past three decades, each with its pros and cons. This thesis presents the development of one such single-molecule sensor. The sensor is based on plasmonically enhanced whispering gallery mode resonators and is capable of studying enzyme kinetics and large-scale dynamics over the timescale of ns-seconds. Unlike fluorescence techniques which require labeling of the enzymes with dyes, the technique presented in this work detects single enzymes immobilized on the surface of plasmonic gold nanoparticles. A fast, low-noise, lock-in method is utilized to extract sensor signals in the microsecond timescale. Using a model enzyme, the ability of the sensor to detect conformational fluctuations of single enzymes is shown. Further, the thermodynamics of the enzyme is studied and the relevant thermodynamic parameters are extracted from the single-molecule data. Additionally, we extract the heat capacity changes associated with the enzyme using the single-molecule data. The sensor system presented in this thesis in the future could enable a fast, real-time, rapid throughput, lab-on-chip sensor system for studying single enzymes for both research and clinical use.