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Synthesis and Use of Single-Walled Carbon Nanotube Transistors for Single-Molecule Studies of DNA Polymerase I

  • Author(s): Gul, Osman Tolga
  • Advisor(s): Collins, Philip G
  • et al.
Abstract

The first half of this dissertation is focused on the synthesis of high quality single-walled carbon nanotubes (SWCNTs). The project goal was to improve SWCNT yields by tuning different growth conditions. Improvements in catalyst activity were observed with an H2O2 surface treatment and by tuning the hydrogen reduction time of the catalysts. In addition, a water-assisted chemical vapor deposition (CVD) was developed that used dry feedstocks with a small, controlled quantity of molecular oxygen. In this process, reactions between oxygen and hydrogen in the reaction zone provided precise water concentrations at the point of synthesis and short time constants. This water vapor dramatically increased SWCNT yield, but the added oxygen also changed the resulting SWCNT diameter distribution. SWCNTs were synthesized with a mean diameter of 0.7 nm and a narrow diameter distribution from 0.5 to 1.0 nm. Improvement in yield reached the limit where each particle resulted in one SWCNT. This allowed the catalyst concentration to be reduced by 102 to 103, greatly reducing catalyst contamination.

In the second half of this dissertation, SWCNT field effect transistors (FETs) were used as single-molecule biosensors to investigate DNA polymerase I. DNA polymerases are critical enzymes for DNA replication, and because of their complex catalytic cycle they are excellent targets for investigation by single-molecule experimental techniques. The Klenow fragment (KF) of DNA polymerase I was studied by attaching single KF molecules to sensitive SWCNT FETs.

Using these devices, this work investigated two aspects of KF activity. First, the kinetics of native dNTPs were compared to analog dNTPs. Analogs like α-thio-dNTP, 2-thio-dTTP, 2-thio-dCTP, and 6-chloro-dGTP each proved that analogs had almost no effect on the duration of KF's closed conformation, the portion of the catalytic cycle during which a dNTP is incorporated. Instead, the entire effect of these analogs was to change the duration of the open conformation. The thiolated and chlorinated analogs appeared to interfere with KF's recognition and binding, two key steps that determine ensemble turnover rates. Second, KF devices were probed with small concentrations (<10 nM) of template to investigate KF's variability in processing single template molecules. Base pair counting demonstrated that the SWCNT FET could read template lengths with an accuracy <1 base and easily distinguish different template lengths.

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