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Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases. Molecules 2022; 27:molecules27217408. [DOI: 10.3390/molecules27217408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical–computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.
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Wagenknecht HA. Remote Photodamaging of DNA by Photoinduced Energy Transport. Chembiochem 2021; 23:e202100265. [PMID: 34569126 PMCID: PMC9292490 DOI: 10.1002/cbic.202100265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/14/2021] [Indexed: 12/11/2022]
Abstract
Local DNA photodamaging by light is well-studied and leads to a number of structurally identified direct damage, in particular cyclobutane pyrimidine dimers, and indirect oxidatively generated damage, such as 8-oxo-7,8-hydroxyguanine. Similar damages have now been found at remote sites, at least more than 105 Å (30 base pairs) away from the site of photoexcitation. In contrast to the established mechanisms of local DNA photodamaging, the processes of remote photodamage are only partially understood. Known pathways include those to remote oxidatively generated DNA photodamages, which were elucidated by studying electron hole transport through the DNA about 20 years ago. Recent studies with DNA photosensitizers and mechanistic proposals on photoinduced DNA-mediated energy transport are summarized in this minireview. These new mechanisms to a new type of remote DNA photodamaging provide an important extension to our general understanding to light-induced DNA damage and their mutations.
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Affiliation(s)
- Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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Kuhlmann A, Bihr L, Wagenknecht H. How Far Does Energy Migrate in DNA and Cause Damage? Evidence for Long-Range Photodamage to DNA. Angew Chem Int Ed Engl 2020; 59:17378-17382. [PMID: 32869949 PMCID: PMC7540310 DOI: 10.1002/anie.202009216] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Indexed: 12/23/2022]
Abstract
A new DNA architecture addresses the question, how far energy migrates in DNA and forms cyclobutane pyrimidine dimers (CPDs) as photodamages causing skin cancer. The 3-methoxyxanthone nucleoside allows site-selective photoenergy injection into DNA. The designated CPD site lacks the phosphodiester bond and can be placed in defined distances. The CPD formation links two oligonucleotides together and allows probing by gel electrophoresis. We obtained a sigmoidal distance dependence with R0 of 25±3 Å. Below R0 , short-range energy migration occurs with high CPD yields and shallow distance dependence, characteristic for a coherent process. 5-methyl-C as epigenetic modification on the 3'-side facilitates CPD formation. Above R0 , long-range incoherent energy migration occurs over 30 A-T pairs (105.4 Å). The evidence of long-range CPD formation is fundamental for our understanding of DNA photodamaging. Open access funding enabled and organized by Projekt DEAL.
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Affiliation(s)
- Arthur Kuhlmann
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Larissa Bihr
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
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Kuhlmann A, Bihr L, Wagenknecht H. Wie weit wandert Energie in der DNA und verursacht Schäden? Nachweis des langreichweitigen Photoschadens in DNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arthur Kuhlmann
- Institut für Organische Chemie Karlsruher Institut für Technologie (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Larissa Bihr
- Institut für Organische Chemie Karlsruher Institut für Technologie (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Hans‐Achim Wagenknecht
- Institut für Organische Chemie Karlsruher Institut für Technologie (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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Wu J, Meng Z, Lu Y, Shao F. Efficient Long-Range Hole Transport Through G-Quadruplexes. Chemistry 2017; 23:13980-13985. [PMID: 28703459 DOI: 10.1002/chem.201702478] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Indexed: 01/09/2023]
Abstract
DNA offers a means of long-range charge transport for biology and electric nanodevices. Here, a series of tetra-stranded G-quadruplexes were assembled within a dendritic DNA architecture to explore oxidative charge transport (hole transport) through the G-quadruplex. Efficient charge transport was achieved over 28 Å upon UV irradiation. Over a longer G-quadruplex bridge, hole transport was escalated to a higher efficiency, which resulted in a higher yield than that of the optimal duplex DNA for charge transport, that is, the adenine tract. Efficient long-range hole transport suggests tetra-stranded G-quadruplexes, instead of an oxidation hotspot, hold better potential as an electron conduit than duplex DNA.
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Affiliation(s)
- Jingyuan Wu
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Zhenyu Meng
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Yunpeng Lu
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Fangwei Shao
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
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Lin SH, Fujitsuka M, Majima T. Sequence-Dependent Photocurrent Generation through Long-Distance Excess-Electron Transfer in DNA. Angew Chem Int Ed Engl 2016; 55:8715-7. [PMID: 27243800 DOI: 10.1002/anie.201602850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 12/15/2022]
Abstract
Given its well-ordered continuous π stacking of nucleobases, DNA has been considered as a biomaterial for charge transfer in biosensors. For cathodic photocurrent generation resulting from hole transfer in DNA, sensitivity to DNA structure and base-pair stacking has been confirmed. However, such information has not been provided for anodic photocurrent generation resulting from excess-electron transfer in DNA. In the present study, we measured the anodic photocurrent of a DNA-modified Au electrode. Our results demonstrate long-distance excess-electron transfer in DNA, which is dominated by a hopping mechanism, and the photocurrent generation is sequence dependent.
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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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Sequence-Dependent Photocurrent Generation through Long-Distance Excess-Electron Transfer in DNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Ehrenschwender T, Liang Y, Unterreiner AN, Wagenknecht HA, Wolf TJA. Fluorescence quenching over short range in a donor-DNA-acceptor system. Chemphyschem 2013; 14:1197-204. [PMID: 23532955 DOI: 10.1002/cphc.201200924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/15/2013] [Indexed: 11/07/2022]
Abstract
A new donor-DNA-acceptor system has been synthesized containing Nile red-modified 2'-deoxyuridine as charge donor and 6-N,N-dimethylaminopyrene-modified 2'-deoxyuridine as acceptor to investigate the charge transfer in DNA duplexes using fluorescence spectroscopy and time-resolved femtosecond pump-probe techniques. Fluorescence quenching experiments revealed that the quenching efficiency of Nile red depends on two components: 1) the presence of a charge acceptor and 2) the number of intervening CG and AT base pairs between donor and acceptor. Surprisingly, the quenching efficiency of two base pairs (73% for CG and the same for AT) is higher than that for one base pair (68% for CG and 37% for AT), while at a separation of three base pairs less than 10% quenching is observed. A comparison with the results of time-resolved measurements revealed a correlation between quenching efficiency and the first ultrafast time constant suggesting that quenching proceeds via a charge transfer from the donor to the acceptor. All transients are satisfactorily described with two decays: a rapid charge transfer with 600 fs (∼10(12) s(-1)) that depends strongly and in a non-linear fashion on the distance between donor and acceptor, and a slower time constant of a few picoseconds (∼10(11) s(-1)) with weak distance dependence. A third time constant on a nanosecond time scale represents the fluorescence lifetime of the donor molecule. According to these results and time-dependent density functional theory (TDDFT) calculations a combination of single-step superexchange and multistep hopping mechanisms can be proposed for this short-range charge transfer. Furthermore, significantly less quenching efficiency and slower charge transfer rates at very short distances indicate that the direct interaction between donor and acceptor leads to a local structural distortion of DNA duplexes which may provide some uncertainty in identifying the charge transfer rates in short-range systems.
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Affiliation(s)
- Thomas Ehrenschwender
- Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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Renaud N, Berlin YA, Lewis FD, Ratner MA. Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins. J Am Chem Soc 2013; 135:3953-63. [PMID: 23402652 DOI: 10.1021/ja3113998] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-βR), with β = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.
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Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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Wenge U, Wengel J, Wagenknecht HA. Photoinduced reductive electron transfer in LNA:DNA hybrids: a compromise between conformation and base stacking. Angew Chem Int Ed Engl 2012; 51:10026-9. [PMID: 22945791 DOI: 10.1002/anie.201204901] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Ulrike Wenge
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, Karlsruhe, Germany
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Wenge U, Wengel J, Wagenknecht HA. Photoinduzierter reduktiver Elektronentransfer in LNA:DNA-Hybriden: Kompromiss aus Konformation und Basenstapelung. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204901] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Szyperska A, Rak J, Leszczynski J, Li X, Ko YJ, Wang H, Bowen KH. Low-Energy-Barrier Proton Transfer Induced by Electron Attachment to the Guanine⋅⋅⋅Cytosine Base Pair. Chemphyschem 2010; 11:880-8. [DOI: 10.1002/cphc.200900810] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lewis F, Daublain P, Cohen B, Vura-Weis J, Wasielewski M. The Influence of Guanine on DNA Hole Transport Efficiency. Angew Chem Int Ed Engl 2008; 47:3798-800. [DOI: 10.1002/anie.200705903] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Lewis F, Daublain P, Cohen B, Vura-Weis J, Wasielewski M. The Influence of Guanine on DNA Hole Transport Efficiency. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kawai K, Osakada Y, Fujitsuka M, Majima T. Mechanism of Charge Separation in DNA by Hole Transfer through Consecutive Adenines. Chemistry 2008; 14:3721-6. [DOI: 10.1002/chem.200701835] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Affiliation(s)
- Benjamin Elias
- Chimie Organique et Médicinale, Université catholique de Louvain (Belgium)
| | - Joseph C. Genereux
- 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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Augustyn K, Genereux J, Barton J. Distance-Independent DNA Charge Transport across an Adenine Tract. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701522] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Augustyn KE, Genereux JC, Barton JK. Distance-Independent DNA Charge Transport across an Adenine Tract. Angew Chem Int Ed Engl 2007; 46:5731-3. [PMID: 17607671 DOI: 10.1002/anie.200701522] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katherine E Augustyn
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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