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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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Diamantis P, Tavernelli I, Rothlisberger U. Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair. J Chem Theory Comput 2019; 15:2042-2052. [PMID: 30681847 DOI: 10.1021/acs.jctc.8b00645] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To assess the effect of an 8-oxoguanine (8OG) defect base on the vertical ionization energies (VIEs) and electron affinities (VEAs) of DNA, density functional theory calculations were carried out for native and defect DNA bases and nucleotides, as well as for larger fragments containing one or multiple pairs. Absolute values of VIE and VEA under implicit solvation did not converge as a function of model size even up to the largest systems taken into consideration (3 base pairs/2 nucleotide pairs). Nonetheless, a consistent trend was observed for the relative difference in the VIE of native and damaged DNA showing that the defect was lowering the VIE by -0.1 eV for the largest fragments. This strongly suggests that the presence of 8OG makes the DNA more easily oxidizable and is in line with experimental evidence that a defect region can act as a sink of oxidative damage. In contrast, relative differences in VEA were very small and varied inconsistently around 0.01 eV. This seems to indicate that insertion of 8OG has a negligible effect on the electron capturing properties of DNA. Similar conclusions can be drawn by the adiabatic IEs and EAs computed for some of the larger fragments. Analysis of the hole and excess electron distributions was consistent with the above trends. The findings presented here support the possibility that a mechanism based on hole transport through DNA may be efficiently employed by the cell for the detection of defect bases.
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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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Wasserman A, Nafziger J, Jiang K, Kim MC, Sim E, Burke K. The Importance of Being Inconsistent. Annu Rev Phys Chem 2017; 68:555-581. [PMID: 28463652 DOI: 10.1146/annurev-physchem-052516-044957] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Adam Wasserman
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907
| | - Jonathan Nafziger
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Kaili Jiang
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907
| | - Min-Cheol Kim
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Eunji Sim
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Kieron Burke
- Department of Chemistry, University of California, Irvine, California 92697
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Gu J, Wang J, Leszczynski J. Electron interaction with a DNA duplex: dCpdC:dGpdG. Phys Chem Chem Phys 2016; 18:13657-65. [PMID: 27139598 DOI: 10.1039/c6cp01408a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron attachment to double-stranded cytosine-rich DNA, dCpdC:dGpdG, has been studied by density functional theory. This system represents a minimal descriptive unit of a cytosine-rich double-stranded DNA helix. A significant electron affinity for the formation of a cytosine-centered radical anion is revealed to be about 2.2 eV. The excess electron may reside on the nucleobase at the 5' position (dC˙(-)pdC:dGpdG) or at the 3' position (dCpdC˙(-):dGpdG). The inter-strand proton transfer between the radical anion centered cytosine (N3) and the paired guanine (HN1) results in the formation of radical anion center separated complexes dC1H˙pdC:dG2-H(-)pdG and dCpdC2H˙:dGpdG1-H(-). These distonic radical anions are found to be approximately 1 to 4 kcal mol(-1) more stable than the normal radical anions. Intra-strand cytosine π→π transition energies are below the electron detachment energy. Inter-strand π→π transitions of the excess electron from C to G are predicted to be less than 2.79 eV. Electron transfer might also be possible through the inter-strand base-jumping mode. An analysis of absorption visible spectra reveals the absorption bands ranging from 500 nm to 700 nm for the cytosine-rich radical anions of the DNA duplex. Electron attachment to cytidine oligomers might add color to the DNA duplex.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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Gu J, Wang J, Leszczynski J. Electron interaction with phosphate cytidine oligomer dCpdC: base-centered radical anions and their electronic spectra. J Phys Chem B 2014; 118:915-20. [PMID: 24397482 DOI: 10.1021/jp409247d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational chemistry approach was applied to explore the nature of electron attachment to cytosine-rich DNA single strands. An oligomer dinucleoside phosphate deoxycytidylyl-3',5'-deoxycytidine (dCpdC) was selected as a model system for investigations by density functional theory. Electron distribution patterns for the radical anions of dCpdC in aqueous solution were explored. The excess electron may reside on the nucleobase at the 5' position (dC(•-)pdC) or at the 3' position (dCpdC(•-)). From comparison with electron attachment to the cytosine related DNA fragments, the electron affinity for the formation of the cytosine-centered radical anion in DNA is estimated to be around 2.2 eV. Electron attachment to cytosine sites in DNA single strands might cause perturbations of local structural characteristics. Visible absorption spectroscopy may be applied to validate computational results and determine experimentally the existence of the base-centered radical anion. The time-dependent DFT study shows the absorption around 550-600 nm for the cytosine-centered radical anions of DNA oligomers. This indicates that if such species are detected experimentally they would be characterized by a distinctive color.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 China
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Storoniak P, Rak J, Ko YJ, Wang H, Bowen KH. Photoelectron spectroscopic and density functional theoretical studies of the 2′-deoxycytidine homodimer radical anion. J Chem Phys 2013; 139:075101. [DOI: 10.1063/1.4817779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Alizadeh E, Sanche L. Precursors of solvated electrons in radiobiological physics and chemistry. Chem Rev 2012; 112:5578-602. [PMID: 22724633 DOI: 10.1021/cr300063r] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elahe Alizadeh
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
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Gu J, Leszczynski J, Schaefer HF. Interactions of electrons with bare and hydrated biomolecules: from nucleic acid bases to DNA segments. Chem Rev 2012; 112:5603-40. [PMID: 22694487 DOI: 10.1021/cr3000219] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, CAS, PR China.
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Gu J, Liang G, Xie Y, Schaefer HF. Electron attachment to solvated dGpdG: effects of stacking on base-centered and phosphate-centered valence-bound radical anions. Chemistry 2012; 18:5232-8. [PMID: 22431283 DOI: 10.1002/chem.201103850] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 01/30/2012] [Indexed: 11/06/2022]
Abstract
To explore the nature of electron attachment to guanine-centered DNA single strands in the presence of a polarizable medium, a theoretical investigation of the DNA oligomer dinucleoside phosphate deoxyguanylyl-3',5'-deoxyguanosine (dGpdG) was performed by using density functional theory. Four different electron-distribution patterns for the radical anions of dGpdG in aqueous solution have been located as local minima on the potential energy surface. The excess electron is found to reside on the proton of the phosphate group (dGp(H-)dG), or on the phosphate group (dGp(.-)dG), or on the nucleobase at the 5' position (dG(.-)pdG), or on the nucleobase at the 3' position (dGpdG(.-)), respectively. These four radical anions are all expected to be electronically viable species under the influence of the polarizable medium. The predicted energetics of the radical anions follows the order dGp(.-)dG>dG(.-)pdG>dGpdG(.-)>dGp(H-)dG. The base-base stacking pattern in DNA single strands seems unaffected by electron attachment. On the contrary, intrastrand H-bonding is greatly influenced by electron attachment, especially in the formation of base-centered radical anions. The intrastrand H-bonding patterns revealed in this study also suggest that intrastrand proton transfer might be possible between successive guanines due to electron attachment to DNA single strands.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, P. R. China.
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Gu J, Wang J, Leszczynski J. Electron Attachment to the Cytosine-Centered DNA Single Strands: Does Base Stacking Matter? J Phys Chem B 2012; 116:1458-66. [DOI: 10.1021/jp211386x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China
| | - Jing Wang
- Interdisciplinary Nanotoxicity
Center, Department of Chemistry, Jackson State University, Jackson,
Mississippi 39217, United States
| | - Jerzy Leszczynski
- Interdisciplinary Nanotoxicity
Center, Department of Chemistry, Jackson State University, Jackson,
Mississippi 39217, United States
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Kim MC, Sim E, Burke K. Communication: Avoiding unbound anions in density functional calculations. J Chem Phys 2011; 134:171103. [DOI: 10.1063/1.3590364] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Min-Cheol Kim
- Department of Chemistry and Institute of Nano-Bio Molecular Assemblies, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
| | - Eunji Sim
- Department of Chemistry and Institute of Nano-Bio Molecular Assemblies, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
| | - Kieron Burke
- Department of Chemistry, University of California, Irvine, California, 92697, USA
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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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