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Okuda T, Kawashima Y, Kasahara Y, Takagi T, Yamamoto J, Iwai S, Obika S. Inhibiting guanine oxidation and enhancing the excess-electron-transfer efficiency of a pyrene-modified oligonucleotide by introducing an electron-donating group on pyrene. Chem Commun (Camb) 2019; 55:14062-14065. [DOI: 10.1039/c9cc06498b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PipPyU and OMePyU enhance the reduction efficiency without oxidizing guanine in DNA-mediated electron transfer.
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Affiliation(s)
- Takumi Okuda
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
| | - Yusuke Kawashima
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
- National Institutes of Biomedical Innovation
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science
- Osaka University
- Osaka
- Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science
- Osaka University
- Osaka
- Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
- National Institutes of Biomedical Innovation
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2
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Barlev A, Sen D. DNA's Encounter with Ultraviolet Light: An Instinct for Self-Preservation? Acc Chem Res 2018; 51:526-533. [PMID: 29419284 DOI: 10.1021/acs.accounts.7b00582] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Photochemical modification is the major class of environmental damage suffered by DNA, the genetic material of all free-living organisms. Photolyases are enzymes that carry out direct photochemical repair (photoreactivation) of covalent pyrimidine dimers formed in DNA from exposure to ultraviolet light. The discovery of catalytic RNAs in the 1980s led to the "RNA world hypothesis", which posits that early in evolution RNA or a similar polymer served both genetic and catalytic functions. Intrigued by the RNA world hypothesis, we set out to test whether a catalytic RNA (or a surrogate, a catalytic DNA) with photolyase activity could be contemplated. In vitro selection from a random-sequence DNA pool yielded two DNA enzymes (DNAzymes): Sero1C, which requires serotonin as an obligate cofactor, and UV1C, which is cofactor-independent and optimally uses light of 300-310 nm wavelength to repair cyclobutane thymine dimers within a gapped DNA substrate. Both Sero1C and UV1C show multiple turnover kinetics, and UV1C repairs its substrate with a quantum yield of ∼0.05, on the same order as the quantum yields of certain classes of photolyase enzymes. Intensive study of UV1C has revealed that its catalytic core consists of a guanine quadruplex (G-quadruplex) positioned proximally to the bound substrate's thymine dimer. We hypothesize that electron transfer from photoexcited guanines within UV1C's G-quadruplex is responsible for substrate photoreactivation, analogous to electron transfer to pyrimidine dimers within a DNA substrate from photoexcited flavin cofactors located within natural photolyase enzymes. Though the analogy to evolution is necessarily limited, a comparison of the properties of UV1C and Sero1C, which arose out of the same in vitro selection experiment, reveals that although the two DNAzymes comparably accelerate the rate of thymine dimer repair, Sero1C has a substantially broader substrate repertoire, as it can repair many more kinds of pyrimidine dimers than UV1C. Therefore, the co-opting of an amino acid-like cofactor by a nucleic acid enzyme in this case contributes functional versatility rather than a greater rate enhancement. In recent work on UV1C, we have succeeded in shifting its action spectrum from the UVB into the blue region of the spectrum and determined that although it catalyzes both repair and de novo formation of thymine dimers, UV1C is primarily a catalyst for thymine dimer repair. Our work on photolyase DNAzymes has stimulated broader questions about whether analogous, purely nucleotide-based photoreactivation also occurs in double-helical DNA, the dominant form of DNA in living cells. Recently, a number of different groups have reported that this kind of repair is indeed operational in DNA duplexes, i.e., that there exist nucleotide sequences that actively protect, by way of photoreactivation (rather than by simply preventing their formation), pyrimidine dimers located proximal to them. Nucleotide-based photoreactivation thus appears to be a salient, if unanticipated, property of DNA and RNA. The phenomenon also offers pointers in the direction of how in primordial evolution-in an RNA world-early nucleic acids may have protected themselves from structural and functional damage wrought by ultraviolet light.
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Affiliation(s)
- Adam Barlev
- Department
of Chemistry and ‡Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department
of Chemistry and ‡Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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3
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Hensel S, Eckey K, Scharf P, Megger N, Karst U, Müller J. Excess Electron Transfer through DNA Duplexes Comprising a Metal‐Mediated Base Pair. Chemistry 2017; 23:10244-10248. [DOI: 10.1002/chem.201702241] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Susanne Hensel
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Kevin Eckey
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Philipp Scharf
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Nicole Megger
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Uwe Karst
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische Chemie Corrensstraße 30 48149 Münster Germany
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4
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Fujitsuka M, Majima T. Charge transfer dynamics in DNA revealed by time-resolved spectroscopy. Chem Sci 2017; 8:1752-1762. [PMID: 28451299 PMCID: PMC5396511 DOI: 10.1039/c6sc03428d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/08/2016] [Indexed: 01/18/2023] Open
Abstract
In the past few decades, charge transfer in DNA has attracted considerable attention from researchers in a wide variety of fields, including bioscience, physical chemistry, and nanotechnology. Charge transfer in DNA has been investigated using various techniques. Among them, time-resolved spectroscopic methods have yielded valuable information on charge transfer dynamics in DNA, providing an important basis for numerical practical applications such as development of new therapy applications and nanomaterials. In DNA, holes and excess electrons act as positive and negative charge carriers, respectively. Although hole transfer dynamics have been investigated in detail, the dynamics of excess electron transfer have only become clearer relatively recently. In the present paper, we summarize studies on the dynamics of hole and excess electron transfer conducted by several groups including our own.
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Affiliation(s)
- Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN) , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan . ;
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN) , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan . ;
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Antusch L, Gaß N, Wagenknecht HA. Elucidation of the Dexter-Type Energy Transfer in DNA by Thymine-Thymine Dimer Formation Using Photosensitizers as Artificial Nucleosides. Angew Chem Int Ed Engl 2016; 56:1385-1389. [PMID: 28026075 DOI: 10.1002/anie.201610065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/28/2016] [Indexed: 01/26/2023]
Abstract
C-nucleosides of 4-methylbenzophenone, 4-methoxybenzophenone, and 2'-methoxyacetophenone were synthetically incorporated as internal photosensitizers into DNA double strands. This structurally new approach makes it possible to study the distance dependence of thymidine dimer formation because the site of photoinduced triplet energy transfer injection is clearly defined. The counterstrands to these modified strands lacked the phosphodiester bond between the two adjacent thymidines that are supposed to react with each other. Their dimerization could be evidenced by gel electrophoresis because the covalent connection by cyclobutane formation between the two thymidines changes the mobility. A shallow exponential distance dependence for the formation of thymidine dimers over up to 10 A-T base pairs was observed that agrees with a Dexter-type triplet-triplet energy transfer mechanism. Concomitantly, a significant amount of photoinduced DNA crosslinking was observed.
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Affiliation(s)
- Linda Antusch
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Nadine Gaß
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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Antusch L, Gaß N, Wagenknecht H. Aufklärung des Dexter‐Energietransfers in DNA an der Thymin‐Thymin‐Dimerbildung mithilfe von Photosensibilisatoren als artifizielle Nucleoside. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Linda Antusch
- Institut für Organische Chemie Karlsruher Institut für Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Nadine Gaß
- Institut für Organische Chemie Karlsruher Institut für Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Hans‐Achim Wagenknecht
- Institut für Organische Chemie Karlsruher Institut für Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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Lin SH, Fujitsuka M, Majima T. Excess-Electron Transfer in DNA by a Fluctuation-Assisted Hopping Mechanism. J Phys Chem B 2016; 120:660-6. [DOI: 10.1021/acs.jpcb.5b10857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shih-Hsun Lin
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific
and Industrial Research (SANKEN), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan
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8
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Lin SH, Fujitsuka M, Majima T. Dynamics of Excess-Electron Transfer through Alternating Adenine:Thymine Sequences in DNA. Chemistry 2015; 21:16190-4. [PMID: 26398266 DOI: 10.1002/chem.201503115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 12/16/2022]
Abstract
This paper presents the results of an investigation into the sequence-dependent excess-electron transfer (EET) dynamics in DNA, which plays an important role in DNA damage/repair. There are many published studies on EET in consecutive adenine:thymine (A:T) sequences (Tn), but those in alternating A:T sequences (ATn) remain limited. Here, two series of functionalized DNA oligomers, Tn and ATn, were synthesized with a strongly electron-donating photosensitizer, a trimer of ethylenedioxythiophene (3 E), and an electron acceptor, diphenylacetylene (DPA). Laser flash photolysis experiments showed that the EET rate constant of AT3 is two times lower than that of T3 due to the lack of π-stacking of Ts in AT3. Thus, it was indicated that excess-electron hopping is affected by the interaction between LUMOs of nucleotides.
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Affiliation(s)
- Shih-Hsun Lin
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047 (Japan), Fax: (+81) 6-6879-8499
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047 (Japan), Fax: (+81) 6-6879-8499.
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047 (Japan), Fax: (+81) 6-6879-8499.
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9
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Lin SH, Fujitsuka M, Majima T. How Does Guanine-Cytosine Base Pair Affect Excess-Electron Transfer in DNA? J Phys Chem B 2015; 119:7994-8000. [PMID: 26042867 DOI: 10.1021/acs.jpcb.5b03494] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Charge transfer and proton transfer in DNA have attracted wide attention due to their relevance in biological processes and so on. Especially, excess-electron transfer (EET) in DNA has strong relation to DNA repair. However, our understanding on EET in DNA still remains limited. Herein, by using a strongly electron-donating photosensitizer, trimer of 3,4-ethylenedioxythiophene (3E), and an electron acceptor, diphenylacetylene (DPA), two series of functionalized DNA oligomers were synthesized for investigation of EET dynamics in DNA. The transient absorption measurements during femtosecond laser flash photolysis showed that guanine:cytosine (G:C) base pair affects EET dynamics in DNA by two possible mechanisms: the excess-electron quenching by proton transfer with the complementary G after formation of C(•-) and the EET hindrance by inserting a G:C base pair as a potential barrier in consecutive thymines (T's). In the present paper, we provided useful information based on the direct kinetic measurements, which allowed us to discuss EET through oligonucleotides for the investigation of DNA damage/repair.
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Affiliation(s)
- Shih-Hsun Lin
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan
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10
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Gorczak N, Fujii T, Mishra AK, Houtepen AJ, Grozema FC, Lewis FD. Mechanism and Dynamics of Electron Injection and Charge Recombination in DNA. Dependence on Neighboring Pyrimidines. J Phys Chem B 2015; 119:7673-80. [DOI: 10.1021/jp512113w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Natalie Gorczak
- Department of Chemical
Engineering, Delft University of Technology, 2628 BL Delft, The Netherlands
| | - Taiga Fujii
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ashutosh Kumar Mishra
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arjan J. Houtepen
- Department of Chemical
Engineering, Delft University of Technology, 2628 BL Delft, The Netherlands
| | - Ferdinand C. Grozema
- Department of Chemical
Engineering, Delft University of Technology, 2628 BL Delft, The Netherlands
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
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11
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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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12
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Yin X, Kong J, De Leon A, Li Y, Ma Z, Wierzbinski E, Achim C, Waldeck DH. Luminescence quenching by photoinduced charge transfer between metal complexes in peptide nucleic acids. J Phys Chem B 2014; 118:9037-45. [PMID: 24975518 DOI: 10.1021/jp5027042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new scaffold for studying photoinduced charge transfer has been constructed by connecting a [Ru(Bpy)3](2+) donor to a bis(8-hydroxyquinolinate)2 copper [CuQ2] acceptor through a peptide nucleic acid (PNA) bridge. The luminescence of the [Ru(Bpy)3](2+*) donor is quenched by electron transfer to the [CuQ2] acceptor. Photoluminescence studies of these donor-bridge-acceptor systems reveal a dependence of the charge transfer on the length and sequence of the PNA bridge and on the position of the donor and acceptor in the PNA. In cases where the [Ru(Bpy)3](2+) can access the π base stack at the terminus of the duplex, the luminescence decay is described well by a single exponential; but if the donor is sterically hindered from accessing the π base stack of the PNA duplex, a distribution of luminescence lifetimes for the donor [Ru(Bpy)3](2+*) is observed. Molecular dynamics simulations are used to explore the donor-PNA-acceptor structure and the resulting conformational distribution provides a possible explanation for the distribution of electron transfer rates.
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Affiliation(s)
- Xing Yin
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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Abstract
In the past few decades, charge transfer in DNA has attracted considerable
attention from researchers in a wide variety of fields ranging from bioscience
and physical chemistry to nanotechnology. Charge transfer in DNA has been
investigated using various techniques. Among them, time-resolved spectroscopic
methods have provided information on charge-transfer dynamics in DNA, an
important basis for therapy applications, nanomaterials, and so on. In charge
transfer in DNA, holes and excess electrons act as positive and negative charge
carriers, respectively. Hole-transfer (HT) dynamics have been investigated in
detail, while the dynamics of excess electron transfer (EET) have only become
clear rather recently. In the present paper, we summarize studies on the
dynamics of HT and EET by several groups including ourselves.
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Affiliation(s)
- Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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14
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Yu Y, Heidel B, Parapugna TL, Wenderhold-Reeb S, Song B, Schönherr H, Grininger M, Nöll G. Das Flavoprotein Dodecin als redoxaktive Sonde für Elektronentransfer durch DNA. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Yu Y, Heidel B, Parapugna TL, Wenderhold-Reeb S, Song B, Schönherr H, Grininger M, Nöll G. The flavoprotein dodecin as a redox probe for electron transfer through DNA. Angew Chem Int Ed Engl 2013; 52:4950-3. [PMID: 23532984 PMCID: PMC3743158 DOI: 10.1002/anie.201208987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Indexed: 11/18/2022]
Affiliation(s)
- Yaming Yu
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Björn Heidel
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Tamara Lourdes Parapugna
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Sabine Wenderhold-Reeb
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
| | - Bo Song
- Physikalische Chemie I, Universität Siegen, Fakultät IV, Department für Chemie und BiologieAdolf-Reichwein-Strasse 2, 57076 Siegen (Germany)
| | - Holger Schönherr
- Physikalische Chemie I, Universität Siegen, Fakultät IV, Department für Chemie und BiologieAdolf-Reichwein-Strasse 2, 57076 Siegen (Germany)
| | - Martin Grininger
- Institut für Organische Chemie und Chemische Biologie, Buchmann Institut für Molekulare Lebenswissenschaften, Cluster of Excellence “Macromolecular Complexes”, Goethe Universität FrankfurtMax-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany)
| | - Gilbert Nöll
- NRW Nachwuchsforschergruppe für Nanotechnologie, Organische Chemie, Universität SiegenFakultät IV, Department für Chemie und Biologie, Adolf-Reichwein-Strasse 2, 57076 Siegen (Germany) E-mail: Homepage: http://www.chemie-biologie.uni-siegen.de/oc/oc1/gruppe_noell/index.html
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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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17
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Choi J, Park J, Tanaka A, Park MJ, Jang YJ, Fujitsuka M, Kim SK, Majima T. Hole Trapping of G-Quartets in a G-Quadruplex. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201208149] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Choi J, Park J, Tanaka A, Park MJ, Jang YJ, Fujitsuka M, Kim SK, Majima T. Hole Trapping of G-Quartets in a G-Quadruplex. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/anie.201208149] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Fujitsuka M, Majima T. Hole and excess electron transfer dynamics in DNA. Phys Chem Chem Phys 2012; 14:11234-44. [PMID: 22806184 DOI: 10.1039/c2cp41576c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Charge transfer in DNA attracts substantial attention from researchers in a wide group of fields such as bioscience, nanotechnology and physical chemistry. It is well known that both positive and negative charges, which are holes and excess electrons, respectively, contribute to the charge transfer in DNA. In the case of hole transfer in DNA, detailed mechanisms and dynamical parameters have been estimated by means of time-resolved spectroscopic methods and product analysis. On the other hand, detailed dynamics of excess electron transfer have not been established yet, although several aspects have been revealed by the continuous efforts of various research groups. In the present Perspective, studies on the charge transfer dynamics in DNA are summarized.
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Affiliation(s)
- Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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20
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Takagi S, Takada T, Matsuo N, Yokoyama S, Nakamura M, Yamana K. Gating electrical transport through DNA molecules that bridge between silicon nanogaps. NANOSCALE 2012; 4:1975-1977. [PMID: 22334054 DOI: 10.1039/c2nr12106a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA electronic devices were prepared on silicon-based three-terminal electrodes. Both ends of DNA molecules (400 bp long, mixed sequences) were bridged via chemical bonds between the source-drain nanogap (120 nm) electrodes. S-Shaped I-V curves were obtained and the electric current can be modulated by the gate voltage. The DNA molecules act as semiconducting p-type nanowires in the three-terminal device.
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Affiliation(s)
- Shogo Takagi
- Department of Materials Science and Chemistry, University of Hyogo, 2167 Shosha, Himeji 671-2201, Japan
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Fujitsuka M, Majima T. Photoinduced Electron Transfer Processes in Biological and Artificial Supramolecules. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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22
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Park MJ, Fujitsuka M, Kawai K, Majima T. Excess-Electron Injection and Transfer in Terthiophene-Modified DNA: Terthiophene as a Photosensitizing Electron Donor for Thymine, Cytosine, and Adenine. Chemistry 2012; 18:2056-62. [DOI: 10.1002/chem.201103663] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Indexed: 01/14/2023]
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Park MJ, Fujitsuka M, Nishitera H, Kawai K, Majima T. Excess electron transfer dynamics in DNA hairpins conjugated with N,N-dimethylaminopyrene as a photosensitizing electron donor. Chem Commun (Camb) 2012; 48:11008-10. [DOI: 10.1039/c2cc36054c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Electron transfer through RNA: chemical probing of dual distance dependence. Bioorg Med Chem 2011; 19:6881-4. [PMID: 22014752 DOI: 10.1016/j.bmc.2011.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 09/14/2011] [Accepted: 09/14/2011] [Indexed: 11/23/2022]
Abstract
Electron transfer (ET) through RNA duplexes possessing 2'-O-pyrenylmethy uridine (Upy) and 5-bromouracil (BrU) as an electron donor and accepter set was investigated. Reductive decomposition of the BrU resulted from the ET over long distances (up to ten AU base pairs) was detected in the RNA conjugates. The RNA mediated ET from the pyrene to BrU showed dual distance dependence. This is well consistent with the previous observation for ET from Upy to nitrobenzene in RNA. In contrast, little or no reductive decomposition of the BrU was observed in the DNA conjugates when the Upy and BrU were separated by more than four AT base pairs.
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26
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Park MJ, Fujitsuka M, Kawai K, Majima T. Direct measurement of the dynamics of excess electron transfer through consecutive thymine sequence in DNA. J Am Chem Soc 2011; 133:15320-3. [PMID: 21888400 DOI: 10.1021/ja2068017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Charge transfer in DNA is an essential process in biological systems because of its close relation to DNA damage and repair. DNA is also an important material used in nanotechnology for wiring and constructing various nanomaterials. Although hole transfer in DNA has been investigated by various researchers and the dynamic properties of this process have been well established, the dynamics of a negative charge, that is, excess electron, in DNA have not been revealed until now. In the present paper, we directly measured the rate of excess electron transfer (EET) through a consecutive thymine (T) sequence in nicked-dumbbell DNAs conjugated with a tetrathiophene derivative (4T) as an electron donor and diphenylacetylene (DPA) as an electron acceptor at both ends. The selective excitation of 4T by a femtosecond laser pulse caused the excess electron injection into DNA, and led to EET in DNA by a consecutive T-hopping mechanism, which eventually formed the DPA radical anion (DPA(•-)). The rate constant for the process of EET through consecutive T was determined to be (4.4 ± 0.3) × 10(10) s(-1) from an analysis of the kinetic traces of the ΔO.D. during the laser flash photolysis. It should be emphasized that the EET rate constant for T-hopping is faster than the rate constants for oxidative hole transfers in DNA (10(4) to 10(10) s(-1) for A- and G-hopping).
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Affiliation(s)
- Man Jae Park
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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Takashima H, Kitano M, Hirai C, Murakami H, Tsukahara K. Photophysical and DNA-binding properties of cytochrome c modified with a platinum(II) complex. J Phys Chem B 2011; 114:13889-96. [PMID: 20936831 DOI: 10.1021/jp106121n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c (cyt c) derivatives modified with a platinum(II) complex at the lysine residue, cyt c(III)-[Pt(bpy)(dapap)](1) {bpy = 2,2'-bipyridine, and dapap = 3-(2,3-diaminopropionylamino)propionic acid}, have been prepared. The modified residues are Lys8, Lys13, Lys55, Lys60, Lys73, and Lys88. In the case of the cyt c(III)-[Pt(bpy)(dapap)](1) dyad, the photoexcited singlet state of (1)([Pt(bpy)(dapap)](1))* was quenched by the heme Fe(III) moiety through the intramolecular photoinduced energy-transfer reaction via a through-space mechanism. Next, in the presence of calf thymus (CT)-DNA, the DNA-responsive fluorescence properties of cyt c(III)-[Pt(bpy)(dapap)](1) isomers were investigated. The order of the obtained binding constants between the cyt c(III)-[Pt(bpy)(dapap)](1) isomer and CT-DNA in an aqueous solution suggested that the electrostatic interaction is one of the important factors to stabilize the cyt c-DNA complex. Finally, we discussed the rotational motion of the [Pt(bpy)(dapap)](2+) moiety at the surface of cyt c by fluorescence anisotropy measurement. The increase in the anisotropy parameter, r, for each cyt c isomer clearly revealed that the noncovalent recognition of the [Pt(bpy)(dapap)](2+) moiety by CT-DNA is an essential event in the formation of the cyt c-DNA complex and generation of DNA-sensitive fluorescence signals.
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Affiliation(s)
- Hiroshi Takashima
- Department of Chemistry, Faculty of Science, Nara Women's University, Nara, 630-8506 Japan.
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28
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Wenninger M, Fazio D, Megerle U, Trindler C, Schiesser S, Riedle E, Carell T. Flavin-Induced DNA Photooxidation and Charge Movement Probed by Ultrafast Transient Absorption Spectroscopy. Chembiochem 2011; 12:703-6. [DOI: 10.1002/cbic.201000730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Indexed: 02/03/2023]
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Kumar A, Sevilla MD. Proton-coupled electron transfer in DNA on formation of radiation-produced ion radicals. Chem Rev 2010; 110:7002-23. [PMID: 20443634 PMCID: PMC2947616 DOI: 10.1021/cr100023g] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309
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Fazio D, Trindler C, Heil K, Chatgilialoglu C, Carell T. Investigation of excess-electron transfer in DNA double-duplex systems allows estimation of absolute excess-electron transfer and CPD cleavage rates. Chemistry 2010; 17:206-12. [PMID: 21207617 DOI: 10.1002/chem.201001978] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Indexed: 11/09/2022]
Abstract
To investigate the parameters and rates that determine excess-electron transfer processes in DNA duplexes, we developed a DNA double-duplex system containing a reduced and deprotonated flavin donor at the junction of two duplexes with either the same or different electron acceptors in the individual duplex substructures. This model system allows us to bring the two electron acceptors in the duplex substructures into direct competition for injected electrons and this enables us to decipher how the kind of acceptor influences the transfer data. Measurements with the electron acceptors 8-bromo-dA (BrdA), 8-bromo-dG (BrdG), 5-bromo-dU (BrdU), and a cyclobutane pyrimidine dimer, which is a UV-induced DNA lesion, allowed us to obtain directly the maximum overall reaction rates of these acceptors and especially of the T=T dimer with the injected electrons in the duplex. In line with previous observations, we detected that the overall dimer cleavage rate is about one order of magnitude slower than the debromination of BrdU. Furthermore, we present a more detailed explanation of why sequence dependence cannot be observed when a T=T dimer is used as the acceptor and we estimate the absolute excess-electron hopping rates.
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Affiliation(s)
- Danila Fazio
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-University Munich, Butenandtstrasse 5-13, Haus F, 81377 Munich, Germany
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Heil K, Pearson D, Carell T. Chemical investigation of light induced DNA bipyrimidine damage and repair. Chem Soc Rev 2010; 40:4271-8. [PMID: 21076781 DOI: 10.1039/c000407n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In all organisms, genetic information is stored in DNA and RNA. Both of these macromolecules are damaged by many exogenous and endogenous events, with UV irradiation being one of the major sources of damage. The major photolesions formed are the cyclobutane pyrimidine dimers (CPD), pyrimidine-pyrimidone-(6-4)-photoproducts, Dewar valence isomers and, for dehydrated spore DNA, 5-(α-thyminyl)-5,6-dihydrothymine (SP). In order to be able to investigate how nature's repair and tolerance mechanisms protect the integrity of genetic information, oligonucleotides containing sequence and site-specific UV lesions are essential. This tutorial review provides an overview of synthetic procedures by which these oligonucleotides can be generated, either through phosphoramidite chemistry or direct irradiation of DNA. Moreover, a brief summary on their usage in analysing repair and tolerance processes as well as their biological effects is provided.
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Affiliation(s)
- Korbinian Heil
- Center for Integrative Protein Science CiPSM at the Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
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Yamamoto J, Nishiguchi K, Manabe K, Masutani C, Hanaoka F, Iwai S. Photosensitized [2 + 2] cycloaddition of N-acetylated cytosine affords stereoselective formation of cyclobutane pyrimidine dimer. Nucleic Acids Res 2010; 39:1165-75. [PMID: 20880992 PMCID: PMC3035463 DOI: 10.1093/nar/gkq855] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Photocycloaddition between two adjacent bases in DNA produces a cyclobutane pyrimidine dimer (CPD), which is one of the major UV-induced DNA lesions, with either the cis-syn or trans-syn structure. In this study, we investigated the photosensitized intramolecular cycloaddition of partially-protected thymidylyl-(3'→5')-N(4)-acetyl-2'-deoxy-5-methylcytidine, to clarify the effect of the base modification on the cycloaddition reaction. The reaction resulted in the stereoselective formation of the trans-syn CPD, followed by hydrolysis of the acetylamino group. The same result was obtained for the photocycloaddition of thymidylyl-(3'→5')-N(4)-acetyl-2'-deoxycytidine, whereas both the cis-syn and trans-syn CPDs were formed from thymidylyl-(3'→5')-thymidine. Kinetic analyses revealed that the activation energy of the acid-catalyzed hydrolysis is comparable to that reported for the thymine-cytosine CPD. These findings provided a new strategy for the synthesis of oligonucleotides containing the trans-syn CPD. Using the synthesized oligonucleotide, translesion synthesis by human DNA polymerase η was analyzed.
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Affiliation(s)
- Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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Tainaka K, Fujitsuka M, Takada T, Kawai K, Majima T. Sequence Dependence of Excess Electron Transfer in DNA. J Phys Chem B 2010; 114:14657-63. [DOI: 10.1021/jp1024685] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuki Tainaka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tadao Takada
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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Daublain P, Thazhathveetil AK, Shafirovich V, Wang Q, Trifonov A, Fiebig T, Lewis FD. Dynamics and Efficiency of Electron Injection and Transport in DNA Using Pyrenecarboxamide as an Electron Donor and 5-Bromouracil as an Electron Acceptor. J Phys Chem B 2010; 114:14265-72. [DOI: 10.1021/jp9107393] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Pierre Daublain
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Arun K. Thazhathveetil
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Vladimir Shafirovich
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Qiang Wang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Anton Trifonov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Torsten Fiebig
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, and Department of Chemistry, New York University, New York, New York 10003
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35
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Fluorescent analysis of excess electron transfer through DNA. Bioorg Med Chem Lett 2010; 20:994-6. [DOI: 10.1016/j.bmcl.2009.12.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 12/10/2009] [Accepted: 12/11/2009] [Indexed: 11/23/2022]
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36
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Maie K, Miyagi K, Takada T, Nakamura M, Yamana K. RNA-mediated electron transfer: double exponential distance dependence. J Am Chem Soc 2010; 131:13188-9. [PMID: 19754178 DOI: 10.1021/ja902647j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the long-range excess electron transfer through RNA duplexes consisting of a pyrene electron donor and a nitrobenzene electron acceptor that shows double exponential distance dependence.
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Affiliation(s)
- Kenji Maie
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji 671-2201, Japan
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37
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Butchosa C, Simon S, Voityuk AA. Electron transfer from aromatic amino acids to guanine and adenine radical cations in π stacked and T-shaped complexes. Org Biomol Chem 2010; 8:1870-5. [DOI: 10.1039/b927134a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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38
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Espagne A, Byrdin M, Eker APM, Brettel K. Very fast product release and catalytic turnover of DNA photolyase. Chembiochem 2009; 10:1777-80. [PMID: 19565597 DOI: 10.1002/cbic.200900328] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Agathe Espagne
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, CNRS, URA 2096, 91191 Gif sur Yvette, France
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39
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Daublain P, Thazhathveetil AK, Wang Q, Trifonov A, Fiebig T, Lewis FD. Dynamics of Photochemical Electron Injection and Efficiency of Electron Transport in DNA. J Am Chem Soc 2009. [DOI: 10.1021/ja905140n] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pierre Daublain
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Arun K. Thazhathveetil
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Qiang Wang
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Anton Trifonov
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Torsten Fiebig
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Frederick D. Lewis
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
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Yamagami R, Kobayashi K, Tagawa S. Formation of spectral intermediate G-C and A-T anion complex in duplex DNA studied by pulse radiolysis. J Am Chem Soc 2008; 130:14772-7. [PMID: 18841971 DOI: 10.1021/ja805127e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of electron adducts of 2'-deoxynucleotides and oligonucelotides (ODNs) were measured spectroscopically by nanosecond pulse radiolysis. The radical anions of the nucleotides were produced within 10 ns by the reaction of hydrated electrons (e(aq)(-)) and were protonated to form the corresponding neutral radicals. At pH 7.0, the radical anion of deoxythymidine (dT(*-)) was protonated to form the neutral radical dT(H)(*) in the time range of microseconds. The rate constant for the protonation was determined as 1.8 x 10(10) M(-1) s(-1). In contrast, the neutral radical of dC(H)(*) was formed immediately after the pulse, suggesting that the protonation occurs within 10 ns. The transient spectra of excess electrons of the double-stranded ODNs 5'-TAATTTAATAT-3' (AT) and 5'-CGGCCCGGCGC-3' (GC) differed from those of pyrimidine radicals (C and T) and their composite. In contrast, the spectra of the electron adducts of the single-stranded ODNs GC and AT exhibited characteristics of C and T, respectively. These results suggest that, in duplex ODNs, the spectral intermediates of G-C and A-T anions complex were formed. On the microsecond time scale, the subsequent changes in absorbance of the ODN AT had a first-order rate constant of 4 x 10(4) s(-1), reflecting the protonation of T.
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Affiliation(s)
- Ryuhei Yamagami
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan
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Takashima H, Fujimoto E, Hirai C, Tsukahara K. Synthesis and Spectroscopic Properties of Reconstituted ZincMyoglobin Appending a DNA-Binding Platinum(II) Complex. Chem Biodivers 2008; 5:2101-2112. [DOI: 10.1002/cbdv.200890191] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Ko S, Jang J. Label-free target DNA recognition using oligonucleotide-functionalized polypyrrole nanotubes. Ultramicroscopy 2008; 108:1328-33. [PMID: 18554802 DOI: 10.1016/j.ultramic.2008.04.045] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Conjugated polymers for oligonucleotide immobilization offer extraordinary potential as transducers for detecting DNA duplex formation, because the electrical, optical, and electrochemical properties are strongly affected by relatively small perturbations. Moreover, carboxylated conducting polymer supports are an attractive alternative due to their versatile immobilization with DNA, protein, and enzyme using various pendant groups: -SH, -NH(2), and -COOH. Therefore, we report the fabrication of carboxylic acid-functionalized polypyrrole nanotubes (CPPy NTs) using oxidant-impregnated template synthesis. The diverse number of carboxylates on the surface of CPPy NTs was applied to binding sites for amino-terminal oligonucleotides. Conductance of single DNA strands (ssDNA) and hybridized DNA helix were readily measured by means of depositing DNA-functionalized nanotubes on gold leads, and indicated high sensitivity (DeltaR/R(0)=1.7) even at low concentration (1 nmol) of target DNA. In addition, target DNA concentration was distinguished up to a narrow difference of 2 nmol. The successful DNA immobilization on polymer nanotubes was confirmed and visualized by the photoluminescence of fluorescein isothiocyanate (FITC)-tagged target DNA using confocal laser scanning microscopy.
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Affiliation(s)
- Sungrok Ko
- Hyperstructured Organic Materials Research Center and School of Chemical and Biological Engineering, Seoul National University, San 56-1 Shinlimdong, Gwanakgu, Seoul 151-742, Republic of Korea
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43
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Grigorenko NA, Leumann CJ. Electron transfer through a stable phenanthrenyl pair in DNA. Chem Commun (Camb) 2008:5417-9. [DOI: 10.1039/b810751c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ito T, Kondo A, Terada S, Nishimoto SI. Flavin-sensitized photoreduction of thymidine glycol. Bioorg Med Chem Lett 2007; 17:6129-33. [PMID: 17897825 DOI: 10.1016/j.bmcl.2007.09.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/07/2007] [Accepted: 09/10/2007] [Indexed: 11/23/2022]
Abstract
Photochemical reactivity of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) toward thymidine glycol (dTg) has been investigated. Fluorescence intensity of FAD was enhanced as increasing the concentration of dTg, suggesting that adenosine moiety of FAD interacts with dTg. However, photoreduction of dTg using reduced form of FAD gave repaired thymidine in almost the same yield as when reduced FMN was used alternatively, and thus such interaction seems to have no effect on the reduction. Oligodeoxynucleotides containing dTg were also photochemically repaired by reduced form of flavins in different yields depending on the sequence, which could be related to electron affinity of the nucleobases in DNA.
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Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
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45
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Ito T, Kondo A, Terada S, Nishimoto SI. Photoinduced reductive repair of thymine glycol: implications for excess electron transfer through DNA containing modified bases. J Am Chem Soc 2007; 128:10934-42. [PMID: 16910690 DOI: 10.1021/ja061304+] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced reduction of thymine glycol in oligodeoxynucleotides was investigated using either a reduced form of flavin adenine dinucleotide (FADH(-)) as an intermolecular electron donor or covalently linked phenothiazine (PTZ) as an intramolecular electron donor. Intermolecular electron donation from photoexcited flavin (FADH(-)) to free thymidine glycol generated thymidine in high yield, along with a small amount of 6-hydroxy-5,6-dihydrothymidine. In the case of photoreduction of 4-mer long single-stranded oligodeoxynucleotides containing thymine glycol by *FADH(-), the restoration yield of thymine was varied depending on the sequence of oligodeoxynucleotides. Time-resolved spectroscopic study on the photoreduction by laser-excited N,N-dimethylaniline (DMA) suggested elimination of a hydroxyl ion from the radical anion of thymidine glycol with a rate constant of approximately 10(4) s(-1) generates 6-hydroxy-5,6-dihydrothymidine (6-HOT(*)) as a key intermediate, followed by further reduction of 6-HOT(*) to thymidine or 6-hydroxy-5,6-dihydrothymdine (6-HOT). On the other hand, an excess electron injected into double-stranded DNA containing thymine glycol was not trapped at the lesion but was further transported along the duplex. Considering redox properties of the nucleobases and PTZ, competitive excess electron trapping at pyrimidine bases (thymine, T and cytosine, C) which leads to protonation of the radical anion (T(-)(*), C(-)(*)) or rapid back electron transfer to the radical cation of PTZ (PTZ(+)(*)), is presumably faster than elimination of the hydroxyl ion from the radical anion of thymine glycol in DNA.
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Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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Xu L, Jin J, Lal M, Daublain P, Newcomb M. Compatible Injection and Detection Systems for Studying the Kinetics of Excess Electron Transfer. Org Lett 2007; 9:1837-40. [PMID: 17373807 DOI: 10.1021/ol070593j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] A design for fast kinetic studies of electron transfer in radical anions is reported. alpha-Hydroxy radicals formed by 355 nm laser flash photolysis of alpha-phenacyl alcohols are deprotonated under basic conditions to give ketyl radical anions that serve as electron injectors in inter- and intramolecular electron-transfer reactions. The 2,2-diphenylcyclopropyl group serves as a reporter. When an electron is injected and transferred such that spin character is adjacent to the reporter, cyclopropyl ring opening gives a readily detected diphenylalkyl radical.
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Affiliation(s)
- Libin Xu
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA
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Mizuki K, Nojima T, Juskowiak B, Takenaka S. Tetrakis-acridinyl peptide: distance dependence of photoinduced electron transfer in deoxyribonucleic acid assemblies. Anal Chim Acta 2006; 578:88-92. [PMID: 17723698 DOI: 10.1016/j.aca.2006.05.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Revised: 05/11/2006] [Accepted: 05/13/2006] [Indexed: 11/28/2022]
Abstract
The distance dependence of photoinduced electron transfer in deoxyribonucleic acid (DNA) duplex was investigated using the "TAP cassette" systems of the general formula (AT)6A(n)XA(9-n) (X denote guanine (G) or cytosine (C)). The tetrakis-9-acridinyl peptide (TAP) binds tightly with (AT)6 duplex region showing strong fluorescence that was not quenched by the A(n)XA(9-n) single-stranded region. Quenching was observed after duplex formation with the complementary T(9-n)XT(n) strand (G-C pairing), showing clear dependence on the distance between the TAP and a guanine. An extremely low beta value of 0.22 was obtained in our electron transfer (ET) system that suggests exceptional good mediation of ET process. Experiments with G-mismatches showed negligible quenching for systems with guanine separated by more than one AT base pair that indicated rather inefficient ET process for duplexes containing disrupted pi-electronic system.
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Affiliation(s)
- Keiji Mizuki
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Fukuoka 812-8581, Japan
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48
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Breeger S, von Meltzer M, Hennecke U, Carell T. Investigation of the Pathways of Excess Electron Transfer in DNA with Flavin-Donor and Oxetane-Acceptor Modified DNA Hairpins. Chemistry 2006; 12:6469-77. [PMID: 16832796 DOI: 10.1002/chem.200600074] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Oxetane is a potential intermediate that is enzymatically formed during the repair of (6-4) DNA lesions by special repair enzymes (6-4 DNA photolyases). These enzymes use a reduced and deprotonated flavin to cleave the oxetane by single electron donation. Herein we report synthesis of DNA hairpin model compounds containing a flavin as the hairpin head and two different oxetanes in the stem structure of the hairpin. The data show that the electron moves through the duplex even over distances of 17 A. Attempts to trap the moving electron with N2O showed no reduction of the cleavage efficiency showing that the electron moves through the duplex and not through solution. The electron transfer is sequence dependent. The efficiency is reduced by a factor of 2 in GC rich DNA hairpins.
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Affiliation(s)
- Sascha Breeger
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-University Munich, Butenandtstrasse 5-13, Haus F, 81377 Munich, Germany
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Manetto A, Breeger S, Chatgilialoglu C, Carell T. Komplexe Sequenzabhängigkeit beim Transport von Überschusselektronen durch DNA mit verschieden starken Acceptoren. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502551] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wagenknecht HA. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Nat Prod Rep 2006; 23:973-1006. [PMID: 17119642 DOI: 10.1039/b504754b] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.
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Affiliation(s)
- Hans-Achim Wagenknecht
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany.
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