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Bull GD, Thompson KC. The oxidation of guanine by photoionized 2-aminopurine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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2
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Diamantis P, Tavernelli I, Rothlisberger U. Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:6690-6701. [PMID: 32926773 DOI: 10.1021/acs.jctc.0c00568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. The quantum region of the native fragment comprised 3 G-C base pairs, while one G was replaced by an 8oxoG in the defect fragment. The calculated values for the redox free energy are 6.55 ± 0.28 eV and 5.62 ± 0.30 eV for the native and the 8oxoG-containing fragment, respectively. The respective estimates for the reorganization free energy are 1.25 ± 0.18 eV and 1.00 ± 0.18 eV. Both reactions follow the Marcus theory for electron transfer. The large difference in redox potential between the two fragments shows that replacement of a G by an 8oxoG renders the DNA more easily oxidizable. This finding is in agreement with the suggestion that DNA fragments containing an 8oxoG defect can act as sinks of oxidative damage that protect the rest of the genome from assault. In addition, the difference in redox potential between the native and the defect DNA fragment indicates that a charge transfer-based mechanism for the recognition of DNA defects might be feasible, in line with recent suggestions based on experimental observations.
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Affiliation(s)
- Polydefkis Diamantis
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
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3
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Reprint of "Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces". J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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The Dynamics of Hole Transfer in DNA. Molecules 2019; 24:molecules24224044. [PMID: 31703470 PMCID: PMC6891780 DOI: 10.3390/molecules24224044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.
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6
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Landi A, Borrelli R, Capobianco A, Peluso A. Transient and Enduring Electronic Resonances Drive Coherent Long Distance Charge Transport in Molecular Wires. J Phys Chem Lett 2019; 10:1845-1851. [PMID: 30939015 DOI: 10.1021/acs.jpclett.9b00650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It is shown that the yields of oxidative damage observed in double-stranded DNA oligomers consisting of two guanines separated by adenine-thymine (A:T) n bridges of various lengths are reliably accounted for by a multistep mechanism, in which transient and nontransient electronic resonances induce charge transport and solvent relaxation stabilizes the hole transfer products. The proposed multistep mechanism leads to results in excellent agreement with the observed yield ratios for both the short and the long distance regime; the almost distance independence of yield ratios for longer bridges ( n ≥ 3) is the consequence of the significant energy decrease of the electronic levels of the bridge, which, as the bridge length increases, become quasi-degenerate with those of the acceptor and donor groups (enduring resonance). These results provide significant guidelines for the design of novel DNA sequences to be employed in organic electronics.
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Affiliation(s)
- Alessandro Landi
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Raffaele Borrelli
- Department of Agricultural, Forestry and Food Science , University of Torino , Via Leonardo da Vinci 44 , I-10095 Grugliasco , Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
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7
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Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Schwalb NK, Orr-Ewing AJ, Temps F. Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations. J Phys Chem B 2019; 123:2904-2914. [PMID: 30875228 DOI: 10.1021/acs.jpcb.9b02361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA structures and conformational dynamics. However, detailed understanding of the processes responsible for fluorescence quenching remains largely elusive on a fundamental level. Although attempts have been made to ascribe decreased excited-state lifetimes to intrastrand charge-transfer and stacking interactions, possible influences from dynamic interstrand H-bonding have been widely ignored. Here, we investigate the electronic relaxation of UV-excited 2AP·T in Watson-Crick (WC) and Hoogsteen (HS) conformations. Although the WC conformation features slowed-down, monomer-like electronic relaxation in τ ∼ 1.6 ns toward ground-state recovery and triplet formation, the dynamics associated with 2AP·T in the HS motif exhibit faster deactivation in τ ∼ 70 ps. As recent research has revealed abundant transient interstrand H-bonding in the Hoogsteen motif for duplex DNA, the established model for dynamic fluorescence quenching may need to be revised in the light of our results. The underlying supramolecular photophysical mechanisms are discussed in terms of a proposed excited-state double-proton transfer as an efficient deactivation channel for recovery of the HS species in the electronic ground state.
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Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Katharina Röttger
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany.,School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Rebecca A Ingle
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Hugo J B Marroux
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Mats Bohnsack
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Nina K Schwalb
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Andrew J Orr-Ewing
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Friedrich Temps
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
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8
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Astakhova TY, Vinogradov GA, Kashin VA. Effect of External Factors on Physical and Chemical Transformations Polaron in an Electric Field as a Generator of Coherent Lattice Vibrations. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2019. [DOI: 10.1134/s1990793118050147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Sun H, Zheng L, Greenberg MM. Independent Generation of Reactive Intermediates Leads to an Alternative Mechanism for Strand Damage Induced by Hole Transfer in Poly(dA-T) Sequences. J Am Chem Soc 2018; 140:11308-11316. [PMID: 30169029 DOI: 10.1021/jacs.8b05484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Purine radical cations (dA•+ and dG•+) are the primary hole carriers of DNA hole migration due to their favorable oxidation potential. Much less is known about the reactivity of higher energy pyrimidine radical cations. The thymidine radical cation (T•+) was produced at a defined position in DNA from a photochemical precursor for the first time. T•+ initiates hole transfer to dGGG triplets in DNA. Hole localization in a dGGG sequence accounts for ∼26% of T•+ formed under aerobic conditions in 9. Reduction to yield thymidine is also quantified. 5-Formyl-2'-deoxyuridine is formed in low yield in DNA when T•+ is independently generated. This is inconsistent with mechanistic proposals concerning product formation from electron transfer in poly(dA-T) sequences, following hole injection by a photoexcited anthraquinone. Additional evidence that is inconsistent with the original mechanism was obtained using hole injection by a photoexcited anthraquinone in DNA. Instead of requiring the intermediacy of T•+, the strand damage patterns observed in those studies, in which thymidine is oxidized, are reproduced by independent generation of 2'-deoxyadenosin- N6-yl radical (dA•). Tandem lesion formation by dA• provides the basis for an alternative mechanism for thymidine oxidation ascribed to hole migration in poly(dA-T) sequences. Overall, these experiments indicate that the final products formed following DNA hole transfer in poly(dA-T) sequences do not result from deprotonation or hydration of T•+, but rather from deprotonation of the more stable dA•+, to form dA•, which produces tandem lesions in which 5'-flanking thymidines are oxidized.
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Affiliation(s)
- Huabing Sun
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Liwei Zheng
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
| | - Marc M Greenberg
- Department of Chemistry , Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
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10
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Michaeli K, Kantor-Uriel N, Naaman R, Waldeck DH. The electron's spin and molecular chirality - how are they related and how do they affect life processes? Chem Soc Rev 2018; 45:6478-6487. [PMID: 27734046 DOI: 10.1039/c6cs00369a] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The recently discovered chiral induced spin selectivity (CISS) effect gives rise to a spin selective electron transmission through biomolecules. Here we review the mechanism behind the CISS effect and its implication for processes in Biology. Specifically, three processes are discussed: long-range electron transfer, spin effects on the oxidation of water, and enantioselectivity in bio-recognition events. These phenomena imply that chirality and spin may play several important roles in biology, which have not been considered so far.
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Affiliation(s)
- Karen Michaeli
- Department of Condensed Matter Physics, Weizmann Institute, Rehovot 76100, Israel
| | - Nirit Kantor-Uriel
- Department of Chemical Physics, Weizmann Institute, Rehovot 76100, Israel.
| | - Ron Naaman
- Department of Chemical Physics, Weizmann Institute, Rehovot 76100, Israel.
| | - David H Waldeck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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11
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Tanaka M, Matsumoto T, Iida H. Attenuation of guanine oxidation via DNA-mediated electron transfer in a crowded environment using small cosolutes. Org Biomol Chem 2018; 16:6695-6702. [DOI: 10.1039/c8ob02003e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Guanine oxidation induced by photoirradiation on a pyrene-modified oligonucleotide was investigated under molecular crowding using small cosolutes such as glycerol.
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Affiliation(s)
- Makiko Tanaka
- Department of Engineering Science
- Graduate School of Informatics and Engineering
- The University of Electro-Communications
- Chofu
- Japan
| | - Takayuki Matsumoto
- Department of Engineering Science
- Graduate School of Informatics and Engineering
- The University of Electro-Communications
- Chofu
- Japan
| | - Hiroki Iida
- Department of Engineering Science
- Graduate School of Informatics and Engineering
- The University of Electro-Communications
- Chofu
- Japan
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12
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Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Orr-Ewing AJ, Temps F. Efficient intersystem crossing in 2-aminopurine riboside probed by femtosecond time-resolved transient vibrational absorption spectroscopy. Phys Chem Chem Phys 2018; 20:20033-20042. [DOI: 10.1039/c8cp02664e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The photophysical dynamics of 2-aminopurine, a fluorescent analogue of the canonical nucleobase adenine, has been studied by femtosecond transient vibrational absorption spectroscopy.
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Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | - Katharina Röttger
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
- School of Chemistry
| | | | | | - Mats Bohnsack
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | | | - Friedrich Temps
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
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13
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Astakhova TY, Kashin VA, Likhachev VN, Vinogradov GA. Multipeaked polarons in a nonlinear lattice. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2017. [DOI: 10.1134/s1990793116060166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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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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15
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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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16
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Kilgour M, Segal D. Charge transport in molecular junctions: From tunneling to hopping with the probe technique. J Chem Phys 2016; 143:024111. [PMID: 26178094 DOI: 10.1063/1.4926395] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This "Landauer-Büttiker's probe technique" can properly replicate different transport mechanisms, phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) the electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer, but under large dephasing, the electrical conductance is suppressed. (iii) At high enough temperatures, kBT/ϵB > 1/25, with ϵB as the molecular-barrier height, the current is enhanced by a thermal activation (Arrhenius) factor. However, this enhancement takes place for both coherent and incoherent electrons and it does not readily indicate on the underlying mechanism. (iv) At finite-bias, dephasing effects may impede conduction in resonant situations. We further show that memory (non-Markovian) effects can be implemented within the Landauer-Büttiker's probe technique to model the interaction of electrons with a structured environment. Finally, we examine experimental results of electron transfer in conjugated molecular wires and show that our computational approach can reasonably reproduce reported values to provide mechanistic information.
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Affiliation(s)
- Michael Kilgour
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Dvira Segal
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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17
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Astakhova TY, Kashin VA, Vinogradov GA. An exact solution for polaron in the nonlinear lattice in the Su–Schrieffer–Heeger approximation. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2016. [DOI: 10.1134/s1990793116030167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Liu C, Beratan DN, Zhang P. Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise. J Phys Chem B 2016; 120:3624-33. [DOI: 10.1021/acs.jpcb.6b01018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chaoren Liu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Departments
of Biochemistry and Physics, Duke University, Durham, North Carolina 27708, United States
| | - Peng Zhang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
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19
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Guo C, Wang K, Zerah-Harush E, Hamill J, Wang B, Dubi Y, Xu B. Molecular rectifier composed of DNA with high rectification ratio enabled by intercalation. Nat Chem 2016; 8:484-90. [DOI: 10.1038/nchem.2480] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 02/22/2016] [Indexed: 12/22/2022]
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20
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Levine AD, Iv M, Peskin U. Length-independent transport rates in biomolecules by quantum mechanical unfurling. Chem Sci 2016; 7:1535-1542. [PMID: 28808530 PMCID: PMC5530864 DOI: 10.1039/c5sc03495g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/19/2015] [Indexed: 11/22/2022] Open
Abstract
Experiments on hole transfer in DNA between donor and acceptor moieties revealed transfer rates which are independent of the molecular bridge length (within experimental error). However, the physical origin of this intriguing observation is still unclear. The hopping model implies that the hole propagates in multiple steps along the bridge from one localized state to another, and therefore the longer the bridge, the slower the transfer. This can explain weak length-dependence but not a length-independent transfer rate. We show that the rigid molecular structure of a poly-A bridge supports single step transitions from a localized hole state to delocalized states, spread over the entire bridge. Since propagation to the bridge end is a single step process (termed quantum unfurling) the transfer rate becomes independent of the bridge length. This explanation is consistent with experimental results, and emphasizes the importance of structural order in charge transfer through bio-molecular systems.
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Affiliation(s)
- Ariel D Levine
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
| | - Michael Iv
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
| | - Uri Peskin
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Haifa 32000 , Israel .
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21
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Abstract
Ultraviolet (UV) radiation is a leading external hazard to the integrity of DNA. Exposure to UV radiation triggers a cascade of chemical reactions, and many molecular products (photolesions) have been isolated that are potentially dangerous for the cellular system. The early steps that take place after UV absorption by DNA have been studied by ultrafast spectroscopy. The review focuses on the evolution of excited electronic states, the formation of photolesions, and processes suppressing their formation. Emphasis is placed on lesions involving two thymine bases, such as the cyclobutane pyrimidine dimer, the (6-4) lesion, and its Dewar valence isomer.
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Affiliation(s)
- Wolfgang J Schreier
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, 80538 München, Germany;
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22
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Astakhova TY, Kashin VA, Likhachev VN, Vinogradov GA. Exact solution for polarons on the anharmonic lattice and charge transfer in biopolymers. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414110028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Kratochvílová I, Golan M, Vala M, Špérová M, Weiter M, Páv O, Šebera J, Rosenberg I, Sychrovský V, Tanaka Y, Bickelhaupt FM. Theoretical and Experimental Study of Charge Transfer through DNA: Impact of Mercury Mediated T-Hg-T Base Pair. J Phys Chem B 2014; 118:5374-81. [DOI: 10.1021/jp501986a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Irena Kratochvílová
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Faculty of Nuclear Physics
and Physical Engineering, Czech Technical University in Prague, Zikova 1, 160 00 Prague 6, Czech Republic
| | - Martin Golan
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Institute of Physics,
Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Martin Vala
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Miroslava Špérová
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Martin Weiter
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Jakub Šebera
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Yoshiyuki Tanaka
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale
Modeling (ACMM), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Institute for Molecules and
Materials (IMM), Radboud University Nijmegen, Comeniuslaan 4, 6525 HP Nijmegen, The Netherlands
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24
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Lee DG, Kim IS, Park JW, Seo YJ. Multiplex fluorophore systems on DNA with new diverse fluorescence properties and ability to sense the hybridization dynamics. Chem Commun (Camb) 2014; 50:7273-6. [DOI: 10.1039/c4cc01378f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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25
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Astakhova TY, Likhachev VN, Vinogradov GA. Polaron on a one-dimensional lattice: II. A moving polaron. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2013. [DOI: 10.1134/s199079311305028x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Kratochvílová I, Vala M, Weiter M, Špérová M, Schneider B, Páv O, Šebera J, Rosenberg I, Sychrovský V. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: Complex theoretical and experimental studies. Biophys Chem 2013; 180-181:127-34. [DOI: 10.1016/j.bpc.2013.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/19/2013] [Accepted: 07/20/2013] [Indexed: 12/31/2022]
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27
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Hirsh DJ, McCracken J, Biczo R, Gesuelli KA. Saturation-Recovery EPR with Nitroxyl Radical–Dy(III) Spin Pairs: Distances and Orientations. J Phys Chem B 2013; 117:11960-77. [DOI: 10.1021/jp406159m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donald J. Hirsh
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Joselle McCracken
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Ryan Biczo
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Kelly-Ann Gesuelli
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
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28
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Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins. Proc Natl Acad Sci U S A 2013; 110:14867-71. [PMID: 23980166 DOI: 10.1073/pnas.1309139110] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels.
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29
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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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30
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Reichardt C, Wen C, Vogt RA, Crespo-Hernández CE. Role of intersystem crossing in the fluorescence quenching of 2-aminopurine 2′-deoxyriboside in solution. Photochem Photobiol Sci 2013; 12:1341-50. [DOI: 10.1039/c3pp25437b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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31
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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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32
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Adeyemi OO, Malinovskii VL, Biner SM, Calzaferri G, Häner R. Photon harvesting by excimer-forming multichromophores. Chem Commun (Camb) 2012; 48:9589-91. [DOI: 10.1039/c2cc34183b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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Zhang J, Valeev EF. Hybrid one-electron/many-electron methods for ionized states of molecular clusters. Phys Chem Chem Phys 2012; 14:7863-71. [DOI: 10.1039/c2cp40222j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Xie Z, Markus TZ, Cohen SR, Vager Z, Gutierrez R, Naaman R. Spin specific electron conduction through DNA oligomers. NANO LETTERS 2011; 11:4652-5. [PMID: 21961931 DOI: 10.1021/nl2021637] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Spin-based properties, applications, and devices are commonly related to magnetic effects and to magnetic materials. Most of the development in spintronics is currently based on inorganic materials. Despite the fact that the magnetoresistance effect has been observed in organic materials, until now spin selectivity of organic based spintronics devices originated from an inorganic ferromagnetic electrode and was not determined by the organic molecules themselves. Here we show that conduction through double-stranded DNA oligomers is spin selective, demonstrating a true organic spin filter. The selectivity exceeds that of any known system at room temperature. The spin dependent resistivity indicates that the effect cannot result solely from the atomic spin-orbit coupling and must relate to a special property resulting from the chirality symmetry. The results may reflect on the importance of spin in determining electron transfer rates through biological systems.
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Affiliation(s)
- Zuoti Xie
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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35
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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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36
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Motiei L, Kaminker R, Sassi M, van der Boom ME. Molecule and Electron Transfer through Coordination-Based Molecular Assemblies. J Am Chem Soc 2011; 133:14264-6. [DOI: 10.1021/ja206179a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leila Motiei
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Revital Kaminker
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mauro Sassi
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Milko E. van der Boom
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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37
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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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