Engineering optical traps for new environments and applications in the measurement of biological adhesives and motors

Abstract

Optical traps have played a central role in the exploration of biological systems through the examination of molecular motors, biopolymers, and many other interactions at the nano and micro length scales. This thesis seeks to extend the applications of optical trapping instrumentation and the knowledge of biological systems by building new tools, expanding traditional measurements and developing new assays. First, an economical design of a high-end optical trap is presented as a teaching implement for an undergraduate lab. In addition to equipment specifications and construction directions, three experimental modules highlighting concepts in biology and physics are put forward including single molecule measurement of protein motor torque and the mechanical properties of DNA. A second optical trap design is developed to promote the integration of optical forces and semiconductor materials. This project provides a non-invasive method for control, construction, and measurement that leverages existing semiconductor fabrication techniques while retaining the nanometer position resolution and piconewton force sensitivity of an optical trap encouraging applications in MEMS, microfluidics, and single molecule studies. To better understand the properties of components of biological assembly, assays for single molecule measurement of adhesion force and kinetic off rate are established and carried out for short 12 amino acid sequences previously selected to adhere to glass surfaces and sapphire substrates. Finally, the mechanism of motility for the biological motor kinesin is investigated in depth using the optical trap in two assays. One researches motility in a heterodimeric kinesin with one motor head unable to hydrolyze ATP. The second establishes the force generation mechanism of kinesin through selective mutation of the N-terminal coverstrand segment of the enzyme.