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Xue P, Huang D, Pu J, Zhou Y. DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283. J Phys Chem B 2024; 128:6670-6683. [PMID: 38982772 DOI: 10.1021/acs.jpcb.4c01011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
DNA photolyase targets the primary ultraviolet (UV)-induced DNA lesion─cyclobutane pyrimidine dimer (CPD), attaches to it, and catalyzes its dissociation. The catalytic mechanism of DNA photolyase and the role of the conserved residue E283 remain subjects of debate. This study employs two-dimensional potential energy surface maps and minimum free energy paths calculated at the ωB97XD/6-31G/MM level to elucidate these mechanisms. Results suggest that the catalytic process follows a sequential, stepwise reaction in which the C5-C5 and C6-C6 bonds are cleaved in order, facilitated by a protonated E283. Activation free energies for these cleavages are calculated at 4.4 and 4.2 kcal·mol-1, respectively. Protonation of E283 reduces electrostatic repulsion with CPD and forms dual hydrogen bonds with it and provides better solvation, stabilizing the CPD radical anion, particularly during intermediate state. This stabilization renders the initial splitting step exergonic, slows reverse reactions of the C5-C5 bond cleavage and electron transfer, and ensures a high quantum yield. Furthermore, the protonation state of E283 significantly affects the type of bond cleavage. Other residues in the active site were also investigated for their roles in the mechanism.
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Affiliation(s)
- Pei Xue
- Guangxi Key Laboratory for Polysaccharide Materials and Modification, Guangxi Higher Education Institutes Key Laboratory for New Chemical and Biological Transformation Process Technology, School of Chemistry and Chemical Engineering, Guangxi Minzu University, 188 Daxue East Road, Nanning, Guangxi 530006, China
| | - Donglian Huang
- Guangxi Key Laboratory for Polysaccharide Materials and Modification, Guangxi Higher Education Institutes Key Laboratory for New Chemical and Biological Transformation Process Technology, School of Chemistry and Chemical Engineering, Guangxi Minzu University, 188 Daxue East Road, Nanning, Guangxi 530006, China
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, Indiana 46202, United States
| | - Yan Zhou
- Guangxi Key Laboratory for Polysaccharide Materials and Modification, Guangxi Higher Education Institutes Key Laboratory for New Chemical and Biological Transformation Process Technology, School of Chemistry and Chemical Engineering, Guangxi Minzu University, 188 Daxue East Road, Nanning, Guangxi 530006, China
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2
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Semmeq A, Monari A, Badawi M, Ouaskit S. Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations. Chemistry 2019; 25:15525-15534. [PMID: 31373410 DOI: 10.1002/chem.201902462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/31/2019] [Indexed: 11/08/2022]
Abstract
Thymine radiation-induced fragmentation is characterised by ring opening and the loss of HNCO/NCO. These pathways have been investigated using DFT calculations in the presence of zero, one and two water molecules. In addition to the already characterised stepwise fragmentation mechanism, we propose a novel concerted pathway reported here for the first time. We show that both the stepwise and concerted mechanisms are competitive with activation energies of 2.05 eV and 2.00 eV, respectively, in the gas phase. The effect of microhydration on these mechanisms are examined based on the most stable conformations found by an exploration of the potential energy surface performed by using DFT-based ab initio molecular dynamics. Microhydration is also accompanied by an increase in the activation energies, with respect to gas phase, amounting to 0.47 eV-an increase that is associated to a stabilising effect of water in agreement with recent experimental studies. However, we also point out that this effect is greatly dependent on the specific water arrangement around thymine and could be limited to only 0.13 eV for some configurations.
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Affiliation(s)
- Abderrahmane Semmeq
- Laboratoire Physique et Chimie Théoriques UMR 7019, CNRS, Université de Lorraine, BP239, Boulevard des Aiguillettes, 54506, Vandoeuvre-lès-Nancy-Cedex, France.,Laboratoire de Physique de la Matière Condensée, Faculté des Sciences Ben M'sik, Université Hassan II de Casablanca, B.P 7955, Av Driss El Harti, Sidi Othmane, Casablanca, Maroc
| | - Antonio Monari
- Laboratoire Physique et Chimie Théoriques UMR 7019, CNRS, Université de Lorraine, BP239, Boulevard des Aiguillettes, 54506, Vandoeuvre-lès-Nancy-Cedex, France
| | - Michael Badawi
- Laboratoire Physique et Chimie Théoriques UMR 7019, CNRS, Université de Lorraine, BP239, Boulevard des Aiguillettes, 54506, Vandoeuvre-lès-Nancy-Cedex, France
| | - Said Ouaskit
- Laboratoire de Physique de la Matière Condensée, Faculté des Sciences Ben M'sik, Université Hassan II de Casablanca, B.P 7955, Av Driss El Harti, Sidi Othmane, Casablanca, Maroc
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3
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Huang D, Chen S, Pu J, Tan X, Zhou Y. Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically. J Phys Chem A 2019; 123:2025-2039. [PMID: 30776239 DOI: 10.1021/acs.jpca.8b12345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cyclobutane pyrimidine dimer (CPD) is a major photoproduct of deoxyribonucleic acid (DNA) that is damaged by ultraviolet light. This DNA lesion can be repaired by DNA photolyase with the aid of UV light and two cofactors. To understand the repair mechanism of CPD and whether protonation of CPD participates in the DNA repair process, the cycloreversion reactions of four CPD models and proton transfers between the adjacent residue Glu283 and CPD models were explored through the quantum mechanical method. Two-dimensional maps of potential energy surface in a vacuum and in implicit water solution were calculated at the ωB97XD/6-311++G(2df,2pd) level. One-dimensional potential energy profiles were computed for proton transfer reactions. Among the models that have been considered, both in a vacuum and in water solution, the results indicate that the most likely repair mechanism involves CPD•2- radical anion splitting in a stepwise manner. C5-C5' splits first, and C6-C6' splits later. The computed free energies of activation of the two splitting steps are 0.9 and 3.1 kcal/mol, respectively. The adjacent Glu283 may stabilize the CPD•2- radical anion through hydrogen bond and increase the quantum yield; however, protonating the CPD radical anion by Glu283 cannot accelerate the rate of ring opening.
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Affiliation(s)
- Donglian Huang
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China
| | - Shanfeng Chen
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology , Indiana University-Purdue University Indianapolis , 402 N. Blackford St. , Indianapolis , Indiana 46202 , United States
| | - Xuecai Tan
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China
| | - Yan Zhou
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , 188 Daxue East Road , Nanning , Guangxi 530006 , China
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4
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Chen D, Han X, Jin W, Zhang B. Metal nanoparticle catalyzed cyclobutane cleavage reaction. RSC Adv 2015. [DOI: 10.1039/c5ra21225a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pyridine substituted cyclobutane cleavage reaction can be catalyzed directly by metallic silver/gold nanoparticles.
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Affiliation(s)
- Dengtai Chen
- Department of Chemistry
- Harbin Institute of Technology
- Harbin
- China
| | - Xijiang Han
- Department of Chemistry
- Harbin Institute of Technology
- Harbin
- China
| | - Wen Jin
- Department of Chemistry
- Harbin Institute of Technology
- Harbin
- China
| | - Bin Zhang
- Department of Chemistry
- Harbin Institute of Technology
- Harbin
- China
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5
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Ando H, Fingerhut BP, Dorfman KE, Biggs JD, Mukamel S. Femtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: a computational study. J Am Chem Soc 2014; 136:14801-10. [PMID: 25238196 PMCID: PMC4210081 DOI: 10.1021/ja5063955] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C-C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C═O and C═C/C-C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3'→5')thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C₅-C₅' splitting and a main barrier for the C₆-C₆' splitting, and identify the appearance of two C₅═C₆ stretch vibrations due to the C₆-C₆' splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes.
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Affiliation(s)
- Hideo Ando
- Department of Chemistry, 1102 Natural Sciences II, University of California , Irvine, California 92697-2025, United States
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6
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Lüdemann G, Woiczikowski PB, Kubař T, Elstner M, Steinbrecher TB. Charge transfer in E. coli DNA photolyase: understanding polarization and stabilization effects via QM/MM simulations. J Phys Chem B 2013; 117:10769-78. [PMID: 23964783 DOI: 10.1021/jp406319b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We study fast hole transfer events in E. coli DNA photolyase, a key step in the photoactivation process, using a multiscale computational method that combines nonadiabatic propagation schemes and linear-scaling quantum chemical methods with molecular mechanics force fields. This scheme allows us to follow the time-dependent evolution of the electron hole in an unbiased fashion; that is, no assumptions about hole wave function localization, time scale separation, or adiabaticity of the process have to be made beforehand. DNA photolyase facilitates an efficient long-range charge transport between its flavin adenine dinucleotide (FAD) cofactor and the protein surface via a chain of evolutionary conserved Trp residues on the sub-nanosecond time scale despite the existence of multiple potential trap states. By including a large number of aromatic residues along the charge transfer pathway into the quantum description, we are able to identify the main pathway among alternative possible routes. The simulations show that charge transfer, which is extremely fast in this protein, occurs on the same time scale as the protein response to the electrostatic changes; that is, time-scale separation as often presupposed in charge transfer studies seems to be inappropriate for this system. Therefore, coupled equations of motion, which propagate electrons and nuclei simultaneously, appear to be necessary. The applied computational model is shown to capture the essentials of the reaction kinetics and thermodynamics while allowing direct simulations of charge transfer events on their natural time scale.
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Affiliation(s)
- Gesa Lüdemann
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology , Kaiserstr. 12, 76131 Karlsruhe, Germany
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7
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Anusiewicz I, Świerszcz I, Skurski P, Simons J. Mechanism for Repair of Thymine Dimers by Photoexcitation of Proximal 8-Oxo-7,8-dihydroguanine. J Phys Chem A 2012; 117:1240-53. [DOI: 10.1021/jp305561u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iwona Anusiewicz
- Department of Chemistry and
Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah, United States
- Department of Chemistry, Univeristy of Gdańsk, 80-915 Gdańsk,
Poland
| | - Iwona Świerszcz
- Department of Chemistry, Univeristy of Gdańsk, 80-915 Gdańsk,
Poland
| | - Piotr Skurski
- Department of Chemistry and
Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah, United States
- Department of Chemistry, Univeristy of Gdańsk, 80-915 Gdańsk,
Poland
| | - Jack Simons
- Department of Chemistry and
Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah, United States
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8
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Nguyen KV, Burrows CJ. Photorepair of cyclobutane pyrimidine dimers by 8-oxopurine nucleosides. J PHYS ORG CHEM 2012. [DOI: 10.1002/poc.2919] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Khiem Van Nguyen
- Department of Chemistry; University of Utah; 315 S. 1400 East; Salt Lake City; UT; 84112-0850; USA
| | - Cynthia J. Burrows
- Department of Chemistry; University of Utah; 315 S. 1400 East; Salt Lake City; UT; 84112-0850; USA
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9
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Pan Z, Chen J, Schreier WJ, Kohler B, Lewis FD. Thymine dimer photoreversal in purine-containing trinucleotides. J Phys Chem B 2011; 116:698-704. [PMID: 22103806 DOI: 10.1021/jp210575g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cyclobutane-pyrimidine dimer yields in UV-irradiated DNA are controlled by the equilibrium between forward and reverse photoreactions. Past studies have shown that dimer yields are suppressed at sites adjacent to a purine base, but the underlying causes are unclear. In order to investigate whether this suppression is the result of repair by electron transfer from a neighboring nucleobase, the yields and dynamics of the reverse reaction were studied using trinucleotides containing a cis-syn dimer (T<>T) flanked on the 5' or the 3' side by adenine or guanine. The probability of forming an excited state on T<>T or on the purine base was varied by tuning the irradiation wavelength between 240 and 280 nm. Cleavage quantum yields decrease by an order of magnitude over this wavelength range and are less than 1% at 280 nm, a wavelength that excites the purine base with more than 95% probability. Conditional quantum yields of cleavage for the trinucleotides given excitation of T<>T are similar in magnitude to the quantum yield of cleavage of unmodified T<>T. These results indicate that within experimental uncertainty all photoreversal in these single-stranded substrates is the result of direct electronic excitation of T<>T. Photolyase-like repair of T<>T due to electron transfer from an adjacent purine is negligible in these substrates. Instead, the observed variation in photoreversal quantum yields for adenine- versus guanine-flanked cis-syn dimer could be due to uncertainties in absorption cross sections or to a modest quenching effect by the purine on the excited state of T<>T. Pump-probe measurements reveal that the excited-state lifetimes of A or G in the dimer-containing trinucleotides are unperturbed by the neighboring dimer, indicating that electron transfer from purine base to T<>T is not competitive with rapid excited-state deactivation. Pump-probe measurements on unmodified T<>T in aqueous solution indicate that cleavage is most likely complete on a picosecond or subpicosecond time scale.
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Affiliation(s)
- Zhengzheng Pan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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10
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Woiczikowski PB, Steinbrecher T, Kubař T, Elstner M. Nonadiabatic QM/MM Simulations of Fast Charge Transfer in Escherichia coli DNA Photolyase. J Phys Chem B 2011; 115:9846-63. [DOI: 10.1021/jp204696t] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Benjamin Woiczikowski
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
| | - Thomas Steinbrecher
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
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11
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Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV. Proc Natl Acad Sci U S A 2011; 108:9402-7. [PMID: 21606324 DOI: 10.1073/pnas.1101026108] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CPD photolyase uses light to repair cyclobutane pyrimidine dimers (CPDs) formed between adjacent pyrimidines in UV-irradiated DNA. The enzyme harbors an FAD cofactor in fully reduced state (FADH(-)). The CPD repair mechanism involves electron transfer from photoexcited FADH(-) to the CPD, splitting of its intradimer bonds, and electron return to restore catalytically active FADH(-). The two electron transfer processes occur on time scales of 10(-10) and 10(-9) s, respectively. Until now, CPD splitting itself has only been poorly characterized by experiments. Using a previously unreported transient absorption setup, we succeeded in monitoring cyclobutane thymine dimer repair in the main UV absorption band of intact thymine at 266 nm. Flavin transitions that overlay DNA-based absorption changes at 266 nm were monitored independently in the visible and subtracted to obtain the true repair kinetics. Restoration of intact thymine showed a short lag and a biexponential rise with time constants of 0.2 and 1.5 ns. We assign these two time constants to splitting of the intradimer bonds (creating one intact thymine and one thymine anion radical T(∘-)) and electron return from T(∘-) to the FAD cofactor with recovery of the second thymine, respectively. Previous model studies and computer simulations yielded various CPD splitting times between < 1 ps and < 100 ns. Our experimental results should serve as a benchmark for future efforts to model enzymatic photorepair. The technique and methods developed here may be applied to monitor other photoreactions involving DNA.
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12
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Cho DW, Lee CW, Park JG, Oh SW, Sung NK, Park HJ, Kim KM, Mariano PS, Yoon UC. Exploration of photochemical reactions of N-trimethylsilylmethyl-substituted uracil, pyridone, and pyrrolidone derivatives. Photochem Photobiol Sci 2011; 10:1169-80. [PMID: 21472163 DOI: 10.1039/c0pp00372g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemical reactions of N-trimethylsilylmethyl-substituted uracil, pyridone and pyrrolidone derivatives were carried out to determine if silicone containing substituents have an impact on excited state reaction profiles. The results show that ultraviolet irradiation of N-trimethylsilylmethyl substituted uracils in the presence of substituted alkenes leads to efficient formation of both dimeric and cross [2+2]-cycloaddition products. Qualitatively similar observations were made in a study of the photochemistry of N-trimethylsilylmethyl-2-pyridone. The combined results demonstrate that [2+2]-photocycloaddition is a more efficient excited state reaction pathway for the uracil and pyridone substrates as compared to other processes, such as ylide-forming trimethylsilyl group C-to-O migration. Finally, photoreactions of N-trimethylsilylmethyl-2-pyrrolidone in solutions containing dipolarophiles, such as methyl acrylate, lead to the formation of the desilylation product, N-methyl-2-pyrrolidone by way of a simple, non-ylide generating, protodesilylation process. In addition, observations were made which show that orbital symmetry allowed photocycloreversion reactions of dimeric uracil derivatives, involving cyclobutane ring splitting, to take place. These processes, which lead to the formation of monomeric uracils, appear to be stimulated by the presence of electron donor groups on the cyclobutane ring, a likely result of a new SET promoted cyclobutane ring cleavage pathway. In the cases of N-trimethylsilylmethyl-substituted cyclobutane derivatives that possess phthalimide groups, highly efficient excited state cleavage of the cyclobutane moiety occurs to produce uracil derivatives and corresponding vinyl phthalimide.
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Affiliation(s)
- Dae Won Cho
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 609-735, Korea
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Hassanali AA, Zhong D, Singer SJ. An AIMD study of the CPD repair mechanism in water: reaction free energy surface and mechanistic implications. J Phys Chem B 2011; 115:3848-59. [PMID: 21417374 DOI: 10.1021/jp107722z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In a series of two papers, we report the detailed mechanism of cyclobutane pyrimidine dimer repair in aqueous solvent using ab initio molecular dynamics simulations (AIMD). Umbrella sampling is used to determine the free energy surface for dimer splitting. The two-dimensional free energy surface for splitting of the C5-C5' and C6-C6' bonds on the anion surface is reported. The splitting of the C5-C5' and C6-C6' bonds occurs on a picosecond time scale. The transition state along the splitting coordinate in the anion state coincides with a maximum in the free energy along the same coordinate on the neutral surface. The implication is that back electron transfer occurring before the anion reaches the transition state leads to reformation of the cyclobutane dimer, while back electron transfer after transit through the transition state, leads to successful repair. On the basis of our calculations for CPD splitting in water, we propose a framework for understanding how various factors, such as solvent polarity, can control repair efficiency. This framework explains why back electron transfer leads predominantly to unsuccessful repair in some situations, and successful repair in others. A key observation is that the same free energy surfaces that control dimer splitting also govern how the back electron transfer rate changes during the splitting process. Configurational changes of the dimer along the splitting coordinate are also documented.
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Affiliation(s)
- Ali A Hassanali
- Biophysics Program, Ohio State University, Columbus, Ohio 43210, USA.
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14
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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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15
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Brettel K, Byrdin M. Reaction mechanisms of DNA photolyase. Curr Opin Struct Biol 2010; 20:693-701. [PMID: 20705454 DOI: 10.1016/j.sbi.2010.07.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/08/2010] [Indexed: 10/19/2022]
Abstract
DNA photolyase uses visible light and a fully reduced flavin cofactor FADH(-) to repair major UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). Electron transfer from photoexcited FADH(-) to CPD, splitting of the two intradimer bonds, and back electron transfer to the transiently formed flavin radical FADH° occur in overall 1ns. Whereas the kinetics of FADH° was resolved, the DNA-based intermediates escaped unambiguous detection yet. Another light reaction, named photoactivation, reduces catalytically inactive FADH° to FADH(-) without implication of DNA. It involves electron hopping along a chain of three tryptophan residues in 30ps, as elucidated in detail by transient absorption spectroscopy. The same triple tryptophan chain is found in cryptochrome blue-light photoreceptors and may be involved in their primary photoreaction.
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Affiliation(s)
- Klaus Brettel
- CEA, IBITECS, Laboratoire de Photocatalyse et Biohydrogène, 91191 Gif-sur-Yvette, France.
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16
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Edtbauer A, Russell K, Feketeová L, Taubitz J, Mitterdorfer C, Denifl S, O'Hair RAJ, Märk TD, Scheier P, Wille U. Formation of pyrimidine dimer radical anions in the gas phase. Chem Commun (Camb) 2009:7291-3. [PMID: 20024205 DOI: 10.1039/b920282j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crossed-beam experiments revealed that attachment of a free electron to the cyclobutane pyrimidine dimers c,s-DMT<>DMT and c,a-DMT<>DMT leads to the formation of dimer radical anions with the lifetime of at least 80 micros, thus showing that the latter are much more stable than previously believed.
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Affiliation(s)
- Achim Edtbauer
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens-Universität, Technikerstr. 25, 6020 Innsbruck, Austria
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17
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A Reevaluation of the Ambident Reactivity of the Guanine Moiety Towards Hydroxyl Radicals. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805372] [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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18
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Chatgilialoglu C, D'Angelantonio M, Guerra M, Kaloudis P, Mulazzani Q. A Reevaluation of the Ambident Reactivity of the Guanine Moiety Towards Hydroxyl Radicals. Angew Chem Int Ed Engl 2009; 48:2214-7. [DOI: 10.1002/anie.200805372] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Masson F, Laino T, Rothlisberger U, Hutter J. A QM/MM Investigation of Thymine Dimer Radical Anion Splitting Catalyzed by DNA Photolyase. Chemphyschem 2009; 10:400-10. [DOI: 10.1002/cphc.200800624] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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D’Angelantonio M, Russo M, Kaloudis P, Mulazzani QG, Wardman P, Guerra M, Chatgilialoglu C. Reaction of Hydrated Electrons with Guanine Derivatives: Tautomerism of Intermediate Species. J Phys Chem B 2009; 113:2170-6. [DOI: 10.1021/jp809386c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mila D’Angelantonio
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy, and University of Oxford, Gray Cancer Institute, Mount Vernon Hospital, Northwood, Middlesex, HA6 2JR, U.K
| | - Marialuisa Russo
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy, and University of Oxford, Gray Cancer Institute, Mount Vernon Hospital, Northwood, Middlesex, HA6 2JR, U.K
| | - Panagiotis Kaloudis
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy, and University of Oxford, Gray Cancer Institute, Mount Vernon Hospital, Northwood, Middlesex, HA6 2JR, U.K
| | - Quinto G. Mulazzani
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy, and University of Oxford, Gray Cancer Institute, Mount Vernon Hospital, Northwood, Middlesex, HA6 2JR, U.K
| | - Peter Wardman
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy, and University of Oxford, Gray Cancer Institute, Mount Vernon Hospital, Northwood, Middlesex, HA6 2JR, U.K
| | - Maurizio Guerra
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy, and University of Oxford, Gray Cancer Institute, Mount Vernon Hospital, Northwood, Middlesex, HA6 2JR, U.K
| | - Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy, and University of Oxford, Gray Cancer Institute, Mount Vernon Hospital, Northwood, Middlesex, HA6 2JR, U.K
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Boussicault F, Robert M. Electron Transfer in DNA and in DNA-Related Biological Processes. Electrochemical Insights. Chem Rev 2008; 108:2622-45. [DOI: 10.1021/cr0680787] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Masson F, Laino T, Tavernelli I, Rothlisberger U, Hutter J. Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA. J Am Chem Soc 2008; 130:3443-50. [PMID: 18284237 DOI: 10.1021/ja076081h] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formation of the thymine dimer is one of the most important types of photochemical damage in DNA, responsible for several biological pathologies. Though specifically designed proteins (photolyases) can efficiently repair this type of damage in living cells, an autocatalytic activity of the DNA itself was recently discovered, allowing for a self-repair mechanism. In this paper, we provide the first molecular dynamics study of the splitting of thymine dimer radical anions, using a quantum mechanical/molecular mechanics (QM/MM) approach based on density functional theory (DFT) to describe the quantum region. A set of seven statistically representative molecular dynamics trajectories is analyzed. Our calculations predict an asynchronously concerted process in which C5-C5' bond breaking is barrierless while C6-C6' bond breaking is characterized by a small free energy barrier. An upper bound of 2.5 kcal/mol for this barrier is estimated. Moreover, the molecular dynamics study and the low free energy barrier involved in C6-C6' bond breaking characterize the full process as being an ultrafast reaction.
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Affiliation(s)
- Fanny Masson
- Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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