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Precision Optical Measurements of DNA Structure and Synthesis


Ma, Ziyang (2008) Precision Optical Measurements of DNA Structure and Synthesis. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/VKNW-BS41.


The structure and synthesis of DNA is important. Traditionally,high-resolution structures are solved with X-ray crystallography, and kinetic measurements are taken with consumption of large amount of reagents. In this thesis, I developed new optical methods to probe the DNA structure and to measure kinetics of DNA synthesis.

I measured the helical rise of A-form DNA at the single molecule level using a near-field optical microscope that has sub-10 nm resolution. The microscope is a combination of an atomic force microscope (AFM) and a fluorescence microscope. Imaging at the single fluorophore level was allowed with the development of a novel phase filter that gives ~ 6 fold improvement in the signal-to-noise ratio. I was able to reliably and repeatedly image pairs of molecules separated by ~ 15 nm and demonstrate the first true Rayleigh resolution test for near-field images.

Various evidences, such as crystal structures and sequencing experiments, indicate that the primer-template DNA sequence may affect nucleotide incorporation. I developed a droplet-based microfluidic fast-mixing device that requires minimal sample consumption and measured kinetics of nucleotide incorporation with DNA sequence permutation. I showed that with careful and systematic kinetic measurements, one can obtain rich information of the process of DNA synthesis.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:DNA; DNA polymerase; droplet; fast mixing; kinetics; microfluidics; near-field optical microscopy
Degree Grantor:California Institute of Technology
Division:Physics, Mathematics and Astronomy
Major Option:Physics
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Quake, Stephen R.
Thesis Committee:
  • Quake, Stephen R. (chair)
  • Collier, C. Patrick
  • Politzer, Hugh David
  • Fraser, Scott E.
Defense Date:6 September 2007
Record Number:CaltechETD:etd-11212007-084606
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:4629
Deposited By: Imported from ETD-db
Deposited On:11 Dec 2007
Last Modified:03 Dec 2019 22:31

Thesis Files

PDF (thesis.pdf) - Final Version
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