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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.


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 $sim$ 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:26 Dec 2012 03:10

Thesis Files

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