Single Molecule Enzyme Dynamics and Spectroelectrochemistry in Gold-Based Zero-Mode Waveguides

Doctoral Dissertation


The localization of optical fields is a powerful method to reduce spectroscopic background signals and enable studies of single fluorescent molecules. Zero-mode waveguides (ZMWs) strongly confine optical fields to zeptoliter volumes and are coupled with fluorescence microscopy to study the dynamics of single enzyme molecules, due to their excellent optical confinement, precise positioning, and massive parallelism. The work presented exploits arrays of Au-based nanopores derivatized with single copies of the redox enzyme, monomeric sarcosine oxidase (MSOX). MSOX contains a covalently bound flavin adenine dinucleotide (FAD) cofactor which is highly fluorescent in the oxidized state and dark in the reduced state, thus producing a characteristic on-off fluorescence signal synchronous with transitions between oxidation states. Although Al is the common choice for metallic overlayer in ZMW construction, Au is used here to access its unique surface-binding chemistry. In particular, the signal-to-noise ratio is improved for Au-based ZMWs by selective Au passivation. For MSOX reactions involving both the nominal substrate (sarcosine) and an analogous substrate (proline), statistical analyses of single-molecule temporal trajectories reveal the static heterogeneity of single enzyme reaction rates. In addition, the single molecule data confirm the independence of reductive and oxidative reactions. These structures open the way for systematic studies of the effect of molecular crowding on enzyme dynamics.

The features of ZMWs are extended to single molecule electrocatalysis. In contrast to its behavior in flavoenzymes, where the transitions are coupled to chemical redox events, the research presented here studies single FAD molecules that are chemically immobilized to the Au region of a ZMW array through a pyrroloquinoline quinone (PQQ) linker. In this structure, the Au functions both to confine the optical field in the ZMW and as the working electrode in a potentiostatically controlled 3-elecrode system, thus allowing potential-dependent blinking to be studied in single FAD molecules. The subset of ZMW nanopores housing a single molecule are identified statistically, and these are subjected to detailed study. Using equilibrium potential, Eeq, values determined from macroscopic planar Au electrodes, single molecule blinking behavior is characterized at potentials E < Eeq, E ~ Eeq, and E > Eeq. The probability of observing a reduced (oxidized) state is observed to increase (decrease) as the potential is scanned cathodic of Eeq. This is understood to reflect the potential-dependent probability of electron transfer for single FAD molecules. Furthermore, the observed transition rate reaches a maximum near Eeq and decreases to either anodic or cathodic values, as expected, since the rate is dependent on having significant probabilities for both redox states, a condition that obtains only near Eeq.


Attribute NameValues
  • etd-07192013-014202

Author Jing Zhao
Advisor Paul Bohn
Contributor Paul Bohn, Committee Member
Contributor Gregory Hartland, Committee Member
Contributor William Phillip, Committee Member
Contributor David Leighton, Committee Member
Degree Level Doctoral Dissertation
Degree Discipline Chemical Engineering
Degree Name PhD
Defense Date
  • 2013-07-10

Submission Date 2013-07-19
  • United States of America

  • spectroelectrochemistry

  • fluorescence

  • enzyme dynamics

  • single molecules

  • zero-mode waveguide

  • University of Notre Dame

  • English

Record Visibility Public
Content License
  • All rights reserved

Departments and Units


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