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Exploring DNA-Mediated Charge Transport with Fast Radical Traps


Genereux, Joseph Charles (2010) Exploring DNA-Mediated Charge Transport with Fast Radical Traps. Dissertation (Ph.D.), California Institute of Technology.


The π-stack of DNA is competent for mediating charge transport (CT), both by single-step and multi-step mechanisms. The yield of long-range single-step CT from photoexcited 2-aminopurine to guanine across adenine tracts has a shallow, periodic distance dependence, with increasing amplitude and decreasing slope with temperature. To measure total CT yield, herein we employ the fast radical traps N2-cyclopropylguanine (CPG), and N6-cyclopropyladenine (CPA), which are similar to the unmodified bases, but undergo rapid decomposition upon oxidation. We find that decomposition of CPG by a photoexcited rhodium intercalator across an adenine tract has similar periodic distance dependence to quenching of 2-aminopurine by guanine, and the same temperature dependence as well. In contrast, decomposition of CPG by photoexcited 2-aminopurine is monotonic with respect to adenine tract length, and also competes with back electron transfer (BET). Eliminating BET by separating 2-aminopurine from the adenine tract with three high-potential inosines restores the non-monotonic distance dependence. We also determined decomposition of CPA along adenine tracts by photoexcited rhodium, and found the CT yield to be distance-independent, demonstrating that the periodicity associated with guanine oxidation is with respect to adenine tract length, not donor-acceptor separation. This length-dependent periodicity, and the associated temperature dependence, support a model of conformational gating in the formation of CT-active domains along the DNA.

DNA-mediated electrochemistry is facile in self-assembled monolayers on electrodes, and redox-active dyes are reduced through the DNA π-stack at potentials far lower than those of the individual bases. Since cytosine is the most readily reduced base, we incorporated CPC into DNA monolayers to assay for bridge occupation, and CPC decomposition was not observed.

To explore the relative contributions of single-step and multi-step mechanisms to CT yield across adenine tracts, we compared quantum yields previously collected from 2-aminopurine fluorescence quenching experiments to those of CPG decomposition. For seven or eight intervening adenines, single-step CT accounts for the entire CT yield, while for four to six adenines, multi-step CT is the dominant mechanism. We interrupted multi-step CT by substituting CPA for an adenine on the bridge, and found the total CT yield across five or six intervening adenines is lowered to the single-step CT yield. Blocking single-step CT by replacing the terminal guanine with redox-inactive inosine does not affect CPA decomposition on the bridge. These results imply that single-step and multi-step CT processes are not in direct competition for these assemblies, consistent with the model of conformationally gated CT-active states.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:photooxidation; self-assembled monolayers; adenine tracts; charge transport mechanism; DNA-mediated charge transport
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Mixed availability, specified at file level
Research Advisor(s):
  • Barton, Jacqueline K.
Thesis Committee:
  • Marcus, Rudolph A. (chair)
  • Zewail, Ahmed H.
  • Gray, Harry B.
  • Barton, Jacqueline K.
Defense Date:16 November 2009
Funding AgencyGrant Number
Record Number:CaltechTHESIS:01062010-125002622
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:5500
Deposited By: Joseph Genereux
Deposited On:19 Mar 2010 16:43
Last Modified:15 Mar 2017 22:56

Thesis Files

[img] PDF (Complete Thesis) - Final Version
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PDF (Title Page -- Acknowledgements -- Abstract -- TOC) - Final Version
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PDF (Chapter 1: Mechanisms for DNA Charge Transport) - Final Version
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[img] PDF (Chapter 2 :Interpreting Periodicity in DNA-mediated Charge Transport across Adenine Tracts) - Final Version
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[img] PDF (Chapter 3: Comparison of Incoherent and Coherent Yields of DNA-mediated Charge Transport) - Final Version
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[img] PDF (Chapter 4: Modeling Redox Signaling between DNA Repair Proteins for Efficient Lesion Detection) - Final Version
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[img] PDF (Chapter 5: Assaying Bridge Occupation in DNA mediated Electrochemistry) - Final Version
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