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Sequence Dependence of Charge Transport through DNA Domains

Shao, Fangwei and Augustyn, Katherine and Barton, Jacqueline K. (2005) Sequence Dependence of Charge Transport through DNA Domains. Journal of the American Chemical Society, 127 (49). pp. 17445-17452. ISSN 0002-7863. https://resolver.caltech.edu/CaltechAUTHORS:20160229-085222275

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Abstract

Here we examine the photooxidation of two kinetically fast electron hole traps, N_4-cyclopropylcytosine (^(CP)C) and N_2-cyclopropylamine-guanosine (CPG), incorporated in DNA duplexes of various sequence using different photooxidants. DNA oxidation studies are carried out either with noncovalently bound [Ru(phen)(dppz)(bpy‘)]^(3+) (dppz = dipyridophenazine) and [Rh(phi)_2(bpy)]^(3+) (phi = phenanthrenequinone diimine) or with anthraquinone tethered to DNA. Because the cyclopropylamine-substituted bases decompose rapidly upon oxidation, their efficiency of decomposition provides a measure of relative hole localization. Consistent with a higher oxidation potential for ^(CP)C versus ^(CP)G in DNA, ^(CP)C decomposes with photooxidation by [Rh(phi)_2(bpy)]^(3+), while CPG undergoes ring-opening both with photoexcited [Rh(phi)_2(bpy)]^(3+) and with [Ru(phen)(dppz)(bpy‘)]^(3+). Anthraquinone-modified DNA assemblies of identical base composition but different base sequence are also probed. Single and double base substitutions within adenine tracts modulate ^(CP)C decomposition. In fact, the entire sequence within the DNA assembly is seen to govern ^(CP)C oxidation, not simply the bases intervening between ^(CP)C and the tethered photooxidant. These data are reconciled in the context of a mechanistic model of conformationally gated charge transport through delocalized DNA domains. Photooxidations of anthraquinone-modified DNA assemblies containing both ^(CP)C and ^(CP)G, but with varied distances separating the modified bases, point to a domain size of at least three bases. Our model for DNA charge transport is distinguished from polaron models. In our model, delocalized domains within the base pair stack form transiently based upon sequence-dependent DNA structure and dynamics. Given these results, DNA charge transport is indeed remarkably sensitive to DNA sequence and structure.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/ja0563399DOIArticle
ORCID:
AuthorORCID
Shao, Fangwei0000-0003-2007-3920
Barton, Jacqueline K.0000-0001-9883-1600
Additional Information:© 2005 American Chemical Society. Received September 14, 2005. Publication Date (Web): November 17, 2005. We are grateful to the NIH (GM49216) for their financial support of this work. We also thank D. Ceres for helpful discussions.
Funders:
Funding AgencyGrant Number
NIHGM49216
Issue or Number:49
Record Number:CaltechAUTHORS:20160229-085222275
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160229-085222275
Official Citation:Sequence Dependence of Charge Transport through DNA Domains Fangwei Shao, Katherine Augustyn, and Jacqueline K. Barton Journal of the American Chemical Society 2005 127 (49), 17445-17452 DOI: 10.1021/ja0563399
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:64838
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:29 Feb 2016 18:33
Last Modified:14 Feb 2020 17:46

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