1
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Wong JR, Shao F. Hole Transport in A-form DNA/RNA Hybrid Duplexes. Sci Rep 2017; 7:40293. [PMID: 28084308 PMCID: PMC5233965 DOI: 10.1038/srep40293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/01/2016] [Indexed: 01/28/2023] Open
Abstract
DNA/RNA hybrid duplexes are prevalent in many cellular functions and are an attractive target form for electrochemical biosensing and electric nanodevice. However the electronic conductivities of DNA/RNA hybrid duplex remain relatively unexplored and limited further technological applications. Here cyclopropyl-modified deoxyribose- and ribose-adenosines were developed to explore hole transport (HT) in both DNA duplex and DNA/RNA hybrids by probing the transient hole occupancies on adenine tracts. HT yields through both B-form and A-form double helixes displayed similar shallow distance dependence, although the HT yields of DNA/RNA hybrid duplexes were lower than those of DNA duplexes. The lack of oscillatory periods and direction dependence in HT through both helixes implied efficient hole propagation can be achieved via the hole delocalization and coherent HT over adenine tracts, regardless of the structural variations.
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Affiliation(s)
- Jiun Ru Wong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)
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2
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Arnold AR, Grodick MA, Barton JK. DNA Charge Transport: from Chemical Principles to the Cell. Cell Chem Biol 2016; 23:183-197. [PMID: 26933744 DOI: 10.1016/j.chembiol.2015.11.010] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/18/2015] [Accepted: 11/18/2015] [Indexed: 11/30/2022]
Abstract
The DNA double helix has captured the imagination of many, bringing it to the forefront of biological research. DNA has unique features that extend our interest into areas of chemistry, physics, material science, and engineering. Our laboratory has focused on studies of DNA charge transport (CT), wherein charges can efficiently travel long molecular distances through the DNA helix while maintaining an exquisite sensitivity to base pair π-stacking. Because DNA CT chemistry reports on the integrity of the DNA duplex, this property may be exploited to develop electrochemical devices to detect DNA lesions and DNA-binding proteins. Furthermore, studies now indicate that DNA CT may also be used in the cell by, for example, DNA repair proteins, as a cellular diagnostic, in order to scan the genome to localize efficiently to damage sites. In this review, we describe this evolution of DNA CT chemistry from the discovery of fundamental chemical principles to applications in diagnostic strategies and possible roles in biology.
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Affiliation(s)
- Anna R Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael A Grodick
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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3
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Abstract
Abstract
In the present work, the reaction operator for radical pairs of the main equation of spin chemistry has been modified on the basis of an exactly solvable model. The model contains both the reversible and irreversible transitions. For this model, expression for the reaction operator is more complex due to the expanded basis of spin states. The reaction operator of a phenomenological equation is a particular case of a more general approach and only in the limiting case of the completely irreversible recombination process, these operators coincide.
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Affiliation(s)
- Petr A. Purtov
- Institute of Chemical Kinetics and Combustion, SB RAS, Novosibirsk State University, Novosibirsk 630090, Institutskaya Str. 3, Russian Federation
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4
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Sengupta C, Basu S. A spectroscopic study to decipher the mode of interaction of some common acridine derivatives with CT DNA within nanosecond and femtosecond time domains. RSC Adv 2015. [DOI: 10.1039/c5ra13035b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Our spectroscopic investigation with acridine derivatives presents the electronic control of their substituents on intercalation, solvation and PET with DNA.
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Affiliation(s)
- Chaitrali Sengupta
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
| | - Samita Basu
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
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6
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Wong JR, Shao F. 8-Cyclopropyl-2′-Deoxyguanosine: A Hole Trap for DNA-Mediated Charge Transport. Chembiochem 2014; 15:1171-5. [DOI: 10.1002/cbic.201402018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 11/08/2022]
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7
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Campbell NP, Rokita SE. Electron transport in DNA initiated by diaminonaphthalene donors alternatively bound by non-covalent and covalent association. Org Biomol Chem 2014; 12:1143-8. [DOI: 10.1039/c3ob42433b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Non-covalent association can identify active donors for study of charge transfer in DNA but may not establish detailed correlations between donor structure and transfer efficiency.
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Affiliation(s)
- Neil P. Campbell
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park, USA
| | - Steven E. Rokita
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park, USA
- Department of Chemistry
- Johns Hopkins University
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8
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Osakada Y, Kawai K, Majima T. Kinetics of Charge Transfer through DNA across Guanine–Cytosine Repeats Intervened by Adenine–Thymine Base Pair(s). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yasuko Osakada
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
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9
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Wohlgamuth CH, McWilliams MA, Slinker JD. Temperature dependence of electrochemical DNA charge transport: influence of a mismatch. Anal Chem 2013; 85:1462-7. [PMID: 23252597 DOI: 10.1021/ac302508f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charge transfer through DNA is of interest as DNA is both the quintessential biomolecule of all living organisms and a self-organizing element in bioelectronic circuits and sensing applications. Here, we report the temperature-dependent properties of DNA charge transport in an electronically relevant arrangement of DNA monolayers on gold under biologically relevant conditions, and we track the effects of incorporating a CA single base pair mismatch. Charge transfer (CT) through double stranded, 17mer monolayers was monitored by following the yield of electrochemical reduction of a Nile blue redox probe conjugated to a modified thymine. Analysis with cyclic voltammetry and square wave voltammetry shows that DNA CT increases significantly with temperature, indicative of more DNA bridges becoming active for transport. The mismatch was found to attenuate DNA CT at lower temperatures, but the effect of the mismatch diminished as temperature was increased. Voltammograms were analyzed to extract the electron transfer rate k(0), the electron transfer coefficient α, and the redox-active surface coverage Γ*. Arrhenius behavior was observed, with activation energies of 100 meV for electron transfer through well-matched DNA. Single CA mismatches increased the activation energy by 60 meV. These results have clear implications for sensing applications and are evaluated with respect to the prominent models of DNA CT.
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Affiliation(s)
- Chris H Wohlgamuth
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
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10
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Fakhari F, Chen YYK, Rokita SE. Enhancing excess electron transport in DNA. Chem Commun (Camb) 2013; 49:7073-5. [DOI: 10.1039/c3cc43887b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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11
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Muren NB, Olmon ED, Barton JK. Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport. Phys Chem Chem Phys 2012; 14:13754-71. [PMID: 22850865 PMCID: PMC3478128 DOI: 10.1039/c2cp41602f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics.
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Affiliation(s)
- Natalie B. Muren
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Eric D. Olmon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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13
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Imaoka T, Inoue N, Yamamoto K. Electron-transfer through potential gradient based on a dendrimer architecture. Chem Commun (Camb) 2012; 48:7235-7. [DOI: 10.1039/c2cc31954c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Olmon ED, Sontz PA, Blanco-Rodríguez AM, Towrie M, Clark IP, Vlček A, Barton JK. Charge photoinjection in intercalated and covalently bound [Re(CO)3(dppz)(py)]+-DNA constructs monitored by time-resolved visible and infrared spectroscopy. J Am Chem Soc 2011; 133:13718-30. [PMID: 21827149 PMCID: PMC3227519 DOI: 10.1021/ja205568r] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The complex [Re(CO)(3)(dppz)(py'-OR)](+) (dppz = dipyrido[3,2-a:2',3'-c]phenazine; py'-OR = 4-functionalized pyridine) offers IR sensitivity and can oxidize DNA directly from the excited state, making it a promising probe for the study of DNA-mediated charge transport (CT). The behavior of several covalent and noncovalent Re-DNA constructs was monitored by time-resolved IR (TRIR) and UV/visible spectroscopies, as well as biochemical methods, confirming the long-range oxidation of DNA by the excited complex. Optical excitation of the complex leads to population of MLCT and at least two distinct intraligand states. Experimental observations that are consistent with charge injection from these excited states include similarity between long-time TRIR spectra and the reduced state spectrum observed by spectroelectrochemistry, the appearance of a guanine radical signal in TRIR spectra, and the eventual formation of permanent guanine oxidation products. The majority of reactivity occurs on the ultrafast time scale, although processes dependent on slower conformational motions of DNA, such as the accumulation of oxidative damage at guanine, are also observed. The ability to measure events on such disparate time scales, its superior selectivity in comparison to other spectroscopic techniques, and the ability to simultaneously monitor carbonyl ligand and DNA IR absorption bands make TRIR a valuable tool for the study of CT in DNA.
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Affiliation(s)
- Eric D Olmon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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15
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Abstract
In all organisms, oxidation threatens the integrity of the genome. DNA-mediated charge transport (CT) may play an important role in the generation and repair of this oxidative damage. In studies involving long-range CT from intercalating Ru and Rh complexes to 5'-GG-3' sites, we have examined the efficiency of CT as a function of distance, temperature, and the electronic coupling of metal oxidants bound to the base stack. Most striking is the shallow distance dependence and the sensitivity of DNA CT to how the metal complexes are stacked in the helix. Experiments with cyclopropylamine-modified bases have revealed that charge occupation occurs at all sites along the bridge. Using Ir complexes, we have seen that the process of DNA-mediated reduction is very similar to that of DNA-mediated oxidation. Studies involving metalloproteins have, furthermore, shown that their redox activity is DNA-dependent and can be DNA-mediated. Long range DNA-mediated CT can facilitate the oxidation of DNA-bound base excision repair proteins to initiate a redox-active search for DNA lesions. DNA CT can also activate the transcription factor SoxR, triggering a cellular response to oxidative stress. Indeed, these studies show that within the cell, redox-active proteins may utilize the same chemistry as that of synthetic metal complexes in vitro, and these proteins may harness DNA-mediated CT to reduce damage to the genome and regulate cellular processes.
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Affiliation(s)
- Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Eric D. Olmon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Pamela A. Sontz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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16
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Ito T, Uchida T, Tanabe K, Yamada H, Nishimoto SI. Photoinduced electron injection into DNA by N-cyclopropyl-1-aminonaphthalene. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2011.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Genereux JC, Wuerth SM, Barton JK. Single-step charge transport through DNA over long distances. J Am Chem Soc 2011; 133:3863-8. [PMID: 21348520 DOI: 10.1021/ja107033v] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum yields for charge transport across adenine tracts of increasing length have been measured by monitoring hole transport in synthetic oligonucleotides between photoexcited 2-aminopurine, a fluorescent analogue of adenine, and N(2)-cyclopropyl guanine. Using fluorescence quenching, a measure of hole injection, and hole trapping by the cyclopropyl guanine derivative, we separate the individual contributions of single- and multistep channels to DNA charge transport and find that with 7 or 8 intervening adenines the charge transport is a coherent, single-step process. Moreover, a transition occurs from multistep to single-step charge transport with increasing donor/acceptor separation, opposite to that generally observed in molecular wires. These results establish that coherent transport through DNA occurs preferentially across 10 base pairs, favored by delocalization over a full turn of the helix.
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Affiliation(s)
- Joseph C Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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18
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Slinker JD, Muren NB, Renfrew SE, Barton JK. DNA charge transport over 34 nm. Nat Chem 2011; 3:228-33. [PMID: 21336329 DOI: 10.1038/nchem.982] [Citation(s) in RCA: 270] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 12/17/2010] [Indexed: 12/12/2022]
Abstract
Molecular wires show promise in nanoscale electronics, but the synthesis of uniform, long conductive molecules is a significant challenge. Deoxyribonucleic acid (DNA) of precise length, by contrast, is synthesized easily, but its conductivity over the distances required for nanoscale devices has not been explored. Here we demonstrate DNA charge transport (CT) over 34 nm in 100-mer monolayers on gold. Multiplexed gold electrodes modified with 100-mer DNA yield sizable electrochemical signals from a distal, covalent Nile Blue redox probe. Significant signal attenuation upon incorporation of a single base-pair mismatch demonstrates that CT is DNA-mediated. Efficient cleavage of these 100-mers by a restriction enzyme indicates that the DNA adopts a native conformation accessible to protein binding. Similar electron-transfer rates measured through 100-mer and 17-mer monolayers are consistent with rate-limiting electron tunnelling through the saturated carbon linker. This DNA-mediated CT distance of 34 nm surpasses that of most reports of molecular wires.
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Affiliation(s)
- Jason D Slinker
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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19
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Conron SMM, Thazhathveetil AK, Wasielewski MR, Burin AL, Lewis FD. Direct Measurement of the Dynamics of Hole Hopping in Extended DNA G-Tracts. An Unbiased Random Walk. J Am Chem Soc 2010; 132:14388-90. [DOI: 10.1021/ja106991f] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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20
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Kratochvílová I, Todorciuc T, Král K, Nemec H, Buncek M, Sebera J, Zális S, Vokácová Z, Sychrovský V, Bednárová L, Mojzes P, Schneider B. Charge transport in DNA oligonucleotides with various base-pairing patterns. J Phys Chem B 2010; 114:5196-205. [PMID: 20353252 DOI: 10.1021/jp100264v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability.
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Affiliation(s)
- Irena Kratochvílová
- Institute of Physics AS CR, v.v.i., Na Slovance 2, CZ-182 21 Prague 8, Czech Republic.
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21
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Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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Genereux JC, Boal AK, Barton JK. DNA-mediated charge transport in redox sensing and signaling. J Am Chem Soc 2010; 132:891-905. [PMID: 20047321 PMCID: PMC2902267 DOI: 10.1021/ja907669c] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The transport of charge through the DNA base-pair stack offers a route to carry out redox chemistry at a distance. Here we describe characteristics of this chemistry that have been elucidated and how this chemistry may be utilized within the cell. The shallow distance dependence associated with these redox reactions permits DNA-mediated signaling over long molecular distances in the genome and facilitates the activation of redox-sensitive transcription factors globally in response to oxidative stress. The long-range funneling of oxidative damage to sites of low oxidation potential in the genome also may provide a means of protection within the cell. Furthermore, the sensitivity of DNA charge transport to perturbations in base-pair stacking, as may arise with base lesions and mismatches, may be used as a route to scan the genome for damage as a first step in DNA repair. Thus, the ability of double-helical DNA in mediating redox chemistry at a distance provides a natural mechanism for redox sensing and signaling in the genome.
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Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125,
| | - Amie K. Boal
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125,
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125,
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23
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Cao Y, Rabinowitz DJ, Dixon DW, Netzel TL. Synthesis, Electrochemistry, and Hydrolysis of Anthraquinone Derivatives. SYNTHETIC COMMUN 2009. [DOI: 10.1080/00397910902898585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Vázquez-Mayagoitia Á, Huertas O, Brancolini G, Migliore A, Sumpter BG, Orozco M, Luque FJ, Di Felice R, Fuentes-Cabrera M. Ab initio Study of the Structural, Tautomeric, Pairing, and Electronic Properties of Seleno-Derivatives of Thymine. J Phys Chem B 2009; 113:14465-72. [DOI: 10.1021/jp9057077] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Álvaro Vázquez-Mayagoitia
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
| | - Oscar Huertas
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
| | - Giorgia Brancolini
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
| | - Agostino Migliore
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
| | - Bobby G. Sumpter
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
| | - Modesto Orozco
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
| | - F. Javier Luque
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
| | - Rosa Di Felice
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
| | - Miguel Fuentes-Cabrera
- Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona, 08028, Spain, National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41125 Modena, Italy, Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street,
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25
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Poulin KW, Smirnov AV, Hawkins ME, Balis FM, Knutson JR. Conformational heterogeneity and quasi-static self-quenching in DNA containing a fluorescent guanine analogue, 3MI or 6MI. Biochemistry 2009; 48:8861-8. [PMID: 19610668 PMCID: PMC3412956 DOI: 10.1021/bi9003414] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two different microenvironments in the DNA sequence 5'-act aGa gat ccc tca gac cct ttt agt cag tGt gga-3' (in both single- and double-stranded forms) are explored using two similar fluorescent nucleoside analogues, 3MI and 6MI. Each probe was evaluated in two environments, one strand with the probe flanked by thymines (PTRT) and the other by adenines (PTRA) with positions indicated by G's in the sequence. Both time-resolved anisotropies and lifetimes of the probes depend upon local interactions, and these are altered by duplex formation. Integrals of lifetime curves compared with quantum yields reveal that each probe displays a "dark" component (below detection limits, with a lifetime of <70 ps). For 6MI in PTRA, this QSSQ "quasi-static self-quenching" or "dark" component represents approximately half the molecules, whether in single- or double-stranded form. In PTRT, 6MI displays an unusual increase in the quantum yield upon formation of the double strand (from 0.107 to 0.189) apparently the result of escape from QSSQ which simultaneously declines from 66 to 33%. This is also accompanied by doubling of steady-state anisotropy. Only 6MI in the PTRT duplex displays a rotational correlation time of >7 ns. In other words, the DS 6MI PTRA environment fails to constrain local motion and QSSQ remains the same as in the single strand; in contrast, the flanking T duplex environment restricts local motion and halves QSSQ. We collected both steady-state and time-resolved fluorescence quenching titrations of 3MI and 6MI in solution with the mononucleotides AMP, CMP, GMP, and TMP. The dynamic quenching rank of the free probes (quenching constant, kq: T > A > G > C) is totally different from that of incorporated probes. We hypothesize the production of weak 3MI.C or 6MI.C complexes that are somehow rendered less subject to dynamic quenching by collision with subsequent C molecules.
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Affiliation(s)
- Kristi Wojtuszewski Poulin
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Aleksandr V. Smirnov
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Mary E. Hawkins
- Pharmacology and Experimental Therapeutics Section, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Frank M. Balis
- Pharmacology and Experimental Therapeutics Section, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Jay R. Knutson
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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