1
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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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Vechtomova YL, Telegina TA, Buglak AA, Kritsky MS. UV Radiation in DNA Damage and Repair Involving DNA-Photolyases and Cryptochromes. Biomedicines 2021; 9:biomedicines9111564. [PMID: 34829793 PMCID: PMC8615538 DOI: 10.3390/biomedicines9111564] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/15/2021] [Accepted: 10/22/2021] [Indexed: 01/10/2023] Open
Abstract
Prolonged exposure to ultraviolet radiation on human skin can lead to mutations in DNA, photoaging, suppression of the immune system, and other damage up to skin cancer (melanoma, basal cell, and squamous cell carcinoma). We reviewed the state of knowledge of the damaging action of UVB and UVA on DNA, and also the mechanisms of DNA repair with the participation of the DNA-photolyase enzyme or of the nucleotide excision repair (NER) system. In the course of evolution, most mammals lost the possibility of DNA photoreparation due to the disappearance of DNA photolyase genes, but they retained closely related cryptochromes that regulate the transcription of the NER system enzymes. We analyze the published relationships between DNA photolyases/cryptochromes and carcinogenesis, as well as their possible role in the prevention and treatment of diseases caused by UV radiation.
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Affiliation(s)
- Yuliya L. Vechtomova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (T.A.T.); (M.S.K.)
- Correspondence:
| | - Taisiya A. Telegina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (T.A.T.); (M.S.K.)
| | - Andrey A. Buglak
- Faculty of Physics, Saint Petersburg State University, 199034 Saint Petersburg, Russia;
| | - Mikhail S. Kritsky
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (T.A.T.); (M.S.K.)
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3
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Sato R, Mori Y, Matsui R, Okimoto N, Yamamoto J, Taiji M. Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH. Biophys Physicobiol 2020; 17:113-124. [PMID: 33194514 PMCID: PMC7610064 DOI: 10.2142/biophysico.bsj-2020010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/28/2020] [Indexed: 12/01/2022] Open
Abstract
Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD.
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Affiliation(s)
- Ryuma Sato
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
| | - Yoshiharu Mori
- School of Pharmacy, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Risa Matsui
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Noriaki Okimoto
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Makoto Taiji
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
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4
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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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5
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Narayanan M, Singh VR, Kodali G, Moravcevic K, Morris KJ, Stanley RJ. An Ethenoadenine FAD Analog Accelerates UV Dimer Repair by DNA Photolyase. Photochem Photobiol 2018; 93:343-354. [PMID: 27935052 DOI: 10.1111/php.12684] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/21/2016] [Indexed: 11/28/2022]
Abstract
Reduced anionic flavin adenine dinucleotide (FADH- ) is the critical cofactor in DNA photolyase (PL) for the repair of cyclobutane pyrimidine dimers (CPD) in UV-damaged DNA. The initial step involves photoinduced electron transfer from *FADH- to the CPD. The adenine (Ade) moiety is nearly stacked with the flavin ring, an unusual conformation compared to other FAD-dependent proteins. The role of this proximity has not been unequivocally elucidated. Some studies suggest that Ade is a radical intermediate, but others conclude that Ade modulates the electron transfer rate constant (kET ) through superexchange. No study has succeeded in removing or modifying this Ade to test these hypotheses. Here, FAD analogs containing either an ethano- or etheno-bridged Ade between the AN1 and AN6 atoms (e-FAD and ε-FAD, respectively) were used to reconstitute apo-PL, giving e-PL and ε-PL respectively. The reconstitution yield of e-PL was very poor, suggesting that the hydrophobicity of the ethano group prevented its uptake, while ε-PL showed 50% reconstitution yield. The substrate binding constants for ε-PL and rPL were identical. ε-PL showed a 15% higher steady-state repair yield compared to FAD-reconstituted photolyase (rPL). The acceleration of repair in ε-PL is discussed in terms of an ε-Ade radical intermediate vs superexchange mechanism.
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Affiliation(s)
| | - Vijay R Singh
- Postdoctoral Fellow at the Department of Nanoscience and Engineering, Indian Institute of Science, Bangalore, India
| | | | - Katarina Moravcevic
- Large Molecule Analytical Development, Janssen Research & Development, LLC, Horsham, PA
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6
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Faraji S, Dreuw A. Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory. Photochem Photobiol 2017; 93:37-50. [PMID: 27925218 DOI: 10.1111/php.12679] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/18/2016] [Indexed: 01/25/2023]
Abstract
Ultraviolet radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) Photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH- ) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, that is light absorption and resonance energy transfer, photoinduced electron transfer and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Heidelberg, Germany
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7
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Faraji S, Zhong D, Dreuw A. Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases. Angew Chem Int Ed Engl 2016; 55:5175-8. [PMID: 26996356 PMCID: PMC4921128 DOI: 10.1002/anie.201511950] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 01/27/2016] [Indexed: 11/09/2022]
Abstract
Quantum mechanics/molecular mechanics calculations are employed to assign previously recorded experimental spectroscopic signatures of the intermediates occurring during the photo-induced repair of (6-4) photolesions by photolyases to specific molecular structures. Based on this close comparison of experiment and theory it is demonstrated that the acting repair mechanism involves proton transfer from the protonated His365 to the N3' nitrogen of the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane-like transition state.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Dongping Zhong
- Departments of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics and Biochemistry, The Ohio State University, Columbus Ohio 43210, USA,
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany,
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8
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Faraji S, Zhong D, Dreuw A. Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-
4) Photolesions by Photolyases. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing; Ruprecht-Karls University Heidelberg; Im Neuenheimer Feld 205A 69120 Heidelberg Germany
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics and Biochemistry; The Ohio State University; Columbus OH 43210 USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing; Ruprecht-Karls University Heidelberg; Im Neuenheimer Feld 205A 69120 Heidelberg Germany
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9
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Abstract
Photolyase is a flavin photoenzyme that repairs two DNA base damage products induced by ultraviolet (UV) light: cyclobutane pyrimidine dimers and 6-4 photoproducts. With femtosecond spectroscopy and site-directed mutagenesis, investigators have recently made significant advances in our understanding of UV-damaged DNA repair, and the entire enzymatic dynamics can now be mapped out in real time. For dimer repair, six elementary steps have been characterized, including three electron transfer reactions and two bond-breaking processes, and their reaction times have been determined. A unique electron-tunneling pathway was identified, and the critical residues in modulating the repair function at the active site were determined. The dynamic synergy between the elementary reactions for maintaining high repair efficiency was elucidated, and the biological nature of the flavin active state was uncovered. For 6-4 photoproduct repair, a proton-coupled electron transfer repair mechanism has been revealed. The elucidation of electron transfer mechanisms and two repair photocycles is significant and provides a molecular basis for future practical applications, such as in rational drug design for curing skin cancer.
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Affiliation(s)
- Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210;
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10
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The molecular origin of high DNA-repair efficiency by photolyase. Nat Commun 2015; 6:7302. [PMID: 26065359 DOI: 10.1038/ncomms8302] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 04/24/2015] [Indexed: 11/08/2022] Open
Abstract
The primary dynamics in photomachinery such as charge separation in photosynthesis and bond isomerization in sensory photoreceptor are typically ultrafast to accelerate functional dynamics and avoid energy dissipation. The same is also true for the DNA repair enzyme, photolyase. However, it is not known how the photoinduced step is optimized in photolyase to attain maximum efficiency. Here, we analyse the primary reaction steps of repair of ultraviolet-damaged DNA by photolyase using femtosecond spectroscopy. With systematic mutations of the amino acids involved in binding of the flavin cofactor and the cyclobutane pyrimidine dimer substrate, we report our direct deconvolution of the catalytic dynamics with three electron-transfer and two bond-breaking elementary steps and thus the fine tuning of the biological repair function for optimal efficiency. We found that the maximum repair efficiency is not enhanced by the ultrafast photoinduced process but achieved by the synergistic optimization of all steps in the complex repair reaction.
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11
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Abstract
Photolyases, a class of flavoproteins, use blue light to repair two types of ultraviolet-induced DNA damage, a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct (6-4PP). In this perspective, we review the recent progress in the repair dynamics and mechanisms of both types of DNA restoration by photolyases. We first report the spectroscopic characterization of flavin in various redox states and the active-site solvation dynamics in photolyases. We then systematically summarize the detailed repair dynamics of damaged DNA by photolyases and a biomimetic system through resolving all elementary steps on ultrafast timescales, including multiple intermolecular electron- and proton-transfer reactions and bond-breaking and -making processes. We determined the unique electron tunneling pathways, identified the key functional residues and revealed the molecular origin of high repair efficiency, and thus elucidate the molecular mechanisms and repair photocycles at the most fundamental level. We finally conclude that the active sites of photolyases, unlike the aqueous solution for the biomimetic system, provide a unique electrostatic environment and local flexibility and thus a dedicated synergy for all elementary dynamics to maximize the repair efficiency. This repair photomachine is the first enzyme that the entire functional evolution is completely mapped out in real time.
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Affiliation(s)
- Zheyun Liu
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
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12
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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13
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Guo X, Liu Z, Song Q, Wang L, Zhong D. Dynamics and mechanism of UV-damaged DNA repair in indole-thymine dimer adduct: molecular origin of low repair quantum efficiency. J Phys Chem B 2015; 119:3446-55. [PMID: 25635531 DOI: 10.1021/jp512413t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many biomimetic chemical systems for repair of UV-damaged DNA showed very low repair efficiency, and the molecular origin is still unknown. Here, we report our systematic characterization of the repair dynamics of a model compound of indole-thymine dimer adduct in three solvents with different polarity. By resolving all elementary steps including three electron-transfer processes and two bond-breaking and bond-formation dynamics with femtosecond resolution, we observed the slow electron injection in 580 ps in water, 4 ns in acetonitrile, and 1.38 ns in dioxane, the fast back electron transfer without repair in 120, 150, and 180 ps, and the slow bond splitting in 550 ps, 1.9 ns, and 4.5 ns, respectively. The dimer bond cleavage is clearly accelerated by the solvent polarity. By comparing with the biological repair machine photolyase with a slow back electron transfer (2.4 ns) and a fast bond cleavage (90 ps), the low repair efficiency in the biomimetic system is mainly determined by the fast back electron transfer and slow bond breakage. We also found that the model system exists in a dynamic heterogeneous C-clamped conformation, leading to a stretched dynamic behavior. In water, we even identified another stacked form with ultrafast cyclic electron transfer, significantly reducing the repair efficiency. Thus, the comparison of the repair efficiency in different solvents is complicated and should be cautious, and only the dynamics by resolving all elementary steps can finally determine the total repair efficiency. Finally, we use the Marcus electron-transfer theory to analyze all electron-transfer reactions and rationalize all observed electron-transfer dynamics.
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Affiliation(s)
- Xunmin Guo
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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14
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Barbatti M. Computational reference data for the photochemistry of cyclobutane pyrimidine dimers. Chemphyschem 2014; 15:3342-54. [PMID: 25044616 DOI: 10.1002/cphc.201402302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/19/2023]
Abstract
The cis-syn cyclobutane pyrimidine dimer is one of the major classes of carcinogenic UV-induced DNA photoproducts. In this work, diverse high-level quantum-chemical methods were used to determine the spectroscopic properties of neutral (singlet and triplet) and charged (cation and anion) species of thymine dimers. Maps of potential energy, charge distribution, electron affinity, and ionization potential of the thymidine dimers were computed along the two dimerization coordinates for neutral and charged species, as well as for the singlet excited state. This set of data aims at providing consistent results computed with the same methods as for photodamage and repair. Based on these results, several different photo-, heat-, and charge-induced mechanisms of dimerization and repair are characterized and discussed. Additionally, a new stable dimer with methylmethylidene-hexahydropyrimidine structure was found in the S0 state.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).
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15
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Faraji S, Dreuw A. Physicochemical Mechanism of Light-Driven DNA Repair by (6-4) Photolyases. Annu Rev Phys Chem 2014; 65:275-92. [DOI: 10.1146/annurev-physchem-040513-103626] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, 69120 Heidelberg, Germany; ,
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, 69120 Heidelberg, Germany; ,
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16
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Matsubara T, Araida N, Hayashi D, Yamada H. Computational Study on the Mechanism of the Electron-Transfer-Induced Repair of the (6–4) T–T Photoproduct of DNA by Photolyase: Possibility of a Radical Cation Pathway. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Nozomi Araida
- Department of Chemistry, Faculty of Science, Kanagawa University
| | - Daichi Hayashi
- Department of Chemistry, Faculty of Science, Kanagawa University
| | - Hatsumi Yamada
- Department of Chemistry, Faculty of Science, Kanagawa University
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17
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Yuan S, Shen Z, Zhang W, Dou Y, Lo GV. Thymine dimer splitting in the T<>T-G trinucleotide model system: a semiclassical dynamics and TD-DFT study. Int J Biol Macromol 2014; 66:267-72. [PMID: 24589472 DOI: 10.1016/j.ijbiomac.2014.02.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
Abstract
The mechanism leading to bond cleavage of a thymine-thymine cyclobutane dimer (T<>T) in a model system consisting of the dimer flanked by guanine trinucleotide was studied using semiclassical dynamics simulation. Pulsed laser excitation of the guanine molecule is found to cause electron transfer from the guanine molecule to the dimer, which then dissociates via sequential cleavage of the C5C5' and C6C6' bonds. Subsequently, electrons transfer back to the guanine molecule as the dimer splits into two monomers. The splitting of the cyclobutane dimer was found to be in the femtosecond time scale.
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Affiliation(s)
- Shuai Yuan
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
| | - Zhi Shen
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
| | - Wenying Zhang
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
| | - Yusheng Dou
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China; Department of Physical Sciences, Nicholls State University, PO Box 2022, Thibodaux, LA 70310, USA.
| | - Glenn V Lo
- Department of Physical Sciences, Nicholls State University, PO Box 2022, Thibodaux, LA 70310, USA
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18
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Abstract
Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany,
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19
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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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Faraji S, Groenhof G, Dreuw A. Combined QM/MM investigation on the light-driven electron-induced repair of the (6-4) thymine dimer catalyzed by DNA photolyase. J Phys Chem B 2013; 117:10071-9. [PMID: 23915283 DOI: 10.1021/jp401662z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The (6-4) photolyases are blue-light-activated enzymes that selectively bind to DNA and initiate splitting of mutagenic thymine (6-4) thymine photoproducts (T(6-4)T-PP) via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-)) to the lesion triggering repair. In the present work, the repair mechanism after the initial electron transfer and the effect of the protein/DNA environment are investigated theoretically by means of hybrid quantum mechanical/molecular mechanical (QM/MM) simulations using X-ray structure of the enzyme-DNA complex. By comparison of three previously proposed repair mechanisms, we found that the lowest activation free energy is required for the pathway in which the key step governing the repair photocycle is electron transfer coupled with the proton transfer from the protonated histidine, His365, to the N3' nitrogen of the pyrimidone thymine. The transfer simultaneously occurs with concerted intramolecular OH transfer without formation of an oxetane or isolated water molecule intermediate. In contrast to previously suggested mechanisms, this newly identified pathway requires neither a subsequent two-photon process nor electronic excitation of the photolesion.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
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Vendrell-Criado V, Rodríguez-Muñiz GM, Cuquerella MC, Lhiaubet-Vallet V, Miranda MA. Photosensitization of DNA by 5-Methyl-2-Pyrimidone Deoxyribonucleoside: (6-4) Photoproduct as a Possible Trojan Horse. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302176] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Vendrell-Criado V, Rodríguez-Muñiz GM, Cuquerella MC, Lhiaubet-Vallet V, Miranda MA. Photosensitization of DNA by 5-methyl-2-pyrimidone deoxyribonucleoside: (6-4) photoproduct as a possible Trojan horse. Angew Chem Int Ed Engl 2013; 52:6476-9. [PMID: 23657994 DOI: 10.1002/anie.201302176] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Victoria Vendrell-Criado
- Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain
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Ebrahimi A, Habibi-Khorassani M, Shahraki A. The radical cationic repair pathway of cyclobutane pyrimidine dimer: the effect of sugar-phosphate backbone. Photochem Photobiol 2012; 89:74-82. [PMID: 22827513 DOI: 10.1111/j.1751-1097.2012.01206.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/13/2012] [Indexed: 12/01/2022]
Abstract
Radical cationic repair process of cis-syn thymine dimer has been investigated when (1) sugar-phosphate backbones were substituted by hydrogen atoms, (2) phosphate group was substituted by two hydrogen atoms each on a sugar ring and (3) sugar-phosphate backbone was taken into account. The effect of the interactions between N1 and N1' lone pairs and the C6-C6' antibonding orbital are the most important evidences for the cleavage of the C6-C6' bond in the first step of radical cationic repair mechanism in the absence of the sugar-phosphate backbone. The impact of the N1 and N1' lone pairs on the C6-C6' bond cleavage decreases and the energy barrier of the cleavage of that bond significantly increases in the presence of the deoxynucleoside sugars and the sugar-phosphate backbone.
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Affiliation(s)
- Ali Ebrahimi
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran.
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Liu Z, Guo X, Tan C, Li J, Kao YT, Wang L, Sancar A, Zhong D. Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase. J Am Chem Soc 2012; 134:8104-14. [PMID: 22533849 DOI: 10.1021/ja2105009] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photoinitiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a superexchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds, while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways, and the critical role of adenine ensure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron-transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding that the forward and futile back-electron transfer is in the normal region and that the final electron return of the catalytic cycle is in the inverted region.
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Affiliation(s)
- Zheyun Liu
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
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Condic-Jurkic K, Smith AS, Zipse H, Smith DM. The Protonation States of the Active-Site Histidines in (6-4) Photolyase. J Chem Theory Comput 2012; 8:1078-91. [PMID: 26593369 DOI: 10.1021/ct2005648] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The active sites of the (6-4) photolyases contain two conserved histidine residues, which, in the Drosophila melanogaster enzyme, correspond to His365 and His369. While there are nine combinations in which the three possible protonation states of the two histidines (with protons on Nδ (HID), Nε (HIE), or both Nδ and Nε (HIP)) can be paired, there is presently no consensus as to which of these states is present, let alone mechanistically relevant. EPR hyperfine couplings for selected protons of the FADH(•) radical have previously been used to address this issue. Our QM/MM calculations show, however, that the experimental couplings are equally well reproduced by each of the nine combinations. Since the EPR results seemingly cannot be used to unequivocally assign the protonation states, the pKa values of the two histidines were calculated using the popular PROPKA, H++, and APBS approaches, in various environments and for several lesions. These techniques consistently indicate that, at pH = 7, both His365 and His369 should be neutral, although His369 is found to be more prone to becoming protonated. In a comparative approach, a series of molecular dynamics simulations was performed with all nine combinations, employing various reference crystal structures and different oxidation states of the FAD cofactor. The overall result of this approach is in agreement with our pKa results. Consequently, although the introduction of the reduced cofactor results in an increased stability for selected protonated states, particularly the His365═HID and His369═HIP combination, the neutral combination His365═HID and His365═HIE stands out as the most relevant state for the activity of the enzyme.
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Affiliation(s)
- Karmen Condic-Jurkic
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.,Excellence Cluster, Engineering of Advanced Materials, University Erlangen-Nürnberg, Nägelsbachstrasse 49b, 91052 Erlangen, Germany
| | - Ana-Sunčana Smith
- Institute of Theoretical Physics, University Erlangen-Nürnberg, Staudtstrasse 9, 91058 Erlangen, Germany.,Excellence Cluster, Engineering of Advanced Materials, University Erlangen-Nürnberg, Nägelsbachstrasse 49b, 91052 Erlangen, Germany
| | - Hendrik Zipse
- Department of Chemistry, Ludwig-Maximilians Universität, Butenandtstrasse 13, 82131 München, Germany
| | - David M Smith
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.,Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
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26
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Pérez-Ruiz R, Sáez JA, Domingo LR, Jiménez MC, Miranda MA. Ring splitting of azetidin-2-ones via radical anions. Org Biomol Chem 2012; 10:7928-32. [DOI: 10.1039/c2ob26528a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Domratcheva T. Neutral Histidine and Photoinduced Electron Transfer in DNA Photolyases. J Am Chem Soc 2011; 133:18172-82. [DOI: 10.1021/ja203964d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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29
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Dynamics and mechanism of cyclobutane pyrimidine dimer repair by DNA photolyase. Proc Natl Acad Sci U S A 2011; 108:14831-6. [PMID: 21804035 DOI: 10.1073/pnas.1110927108] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photolyase uses blue light to restore the major ultraviolet (UV)-induced DNA damage, the cyclobutane pyrimidine dimer (CPD), to two normal bases by splitting the cyclobutane ring. Our earlier studies showed that the overall repair is completed in 700 ps through a cyclic electron-transfer radical mechanism. However, the two fundamental processes, electron-tunneling pathways and cyclobutane ring splitting, were not resolved. Here, we use ultrafast UV absorption spectroscopy to show that the CPD splits in two sequential steps within 90 ps and the electron tunnels between the cofactor and substrate through a remarkable route with an intervening adenine. Site-directed mutagenesis reveals that the active-site residues are critical to achieving high repair efficiency, a unique electrostatic environment to optimize the redox potentials and local flexibility, and thus balance all catalytic reactions to maximize enzyme activity. These key findings reveal the complete spatio-temporal molecular picture of CPD repair by photolyase and elucidate the underlying molecular mechanism of the enzyme's high repair efficiency.
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30
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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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31
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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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Hassanali AA, Zhong D, Singer SJ. An AIMD study of CPD repair mechanism in water: role of solvent in ring splitting. J Phys Chem B 2011; 115:3860-71. [PMID: 21417372 DOI: 10.1021/jp107723w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this paper, we continue to explore the repair mechanisms of the cyclobutane pyrimidine dimer. We find that a full description of both C5-C5' and C6-C6' bond splitting requires a multidimensional treatment involving a solvent coordinate in addition to changes in internal dimer coordinates. Nonequilibrium effects are likely to be important as well, although the initial conditions following forward electron transfer to the dimer, beyond the scope of this study, will ultimately determine the importance of these effects. Throughout the splitting of C5-C5' and C6-C6' bonds, a significant amount of excess charge is delocalized onto the solvent. We have verified that this is not an artifact of the electronic density functional theory (DFT) method used for this anionic system with Schrödinger equation-based quantum chemical cluster calculations. The amount and variability of charge delocalization changes with the course of the reaction. The splitting of the C6-C6' bond is accompanied by both an increase in electron density on the C6 and C6' carbon atoms and an increase in the water density near those atoms. These features are observed both in our equilibrium umbrella sampling simulations and nonequilibrium trajectories.
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Affiliation(s)
- Ali A Hassanali
- Biophysics Program, Ohio State University, Columbus, Ohio 43210, USA.
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33
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Terazima M. Time-dependent intermolecular interaction during protein reactions. Phys Chem Chem Phys 2011; 13:16928-40. [DOI: 10.1039/c1cp21868a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Sadeghian K, Bocola M, Merz T, Schütz M. Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase. J Am Chem Soc 2010; 132:16285-95. [PMID: 20977236 DOI: 10.1021/ja108336t] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.
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Affiliation(s)
- Keyarash Sadeghian
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstraβe 31, D-93040 Regensburg, Germany
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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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Dou Y, Xiong S, Wu W, Yuan S, Tang H. Photoinduced dissociation of cyclobutane thymine dimer studied by semiclassical dynamics simulation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2010; 101:31-6. [PMID: 20656502 DOI: 10.1016/j.jphotobiol.2010.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 06/15/2010] [Accepted: 06/21/2010] [Indexed: 11/30/2022]
Abstract
Photoinduced dissociation of the thymine dimer is studied in a semiclassical dynamics simulation. The simulation follows excitation of an isolated thymine dimer by a 25 fs fwhm laser pulse, and finds that dissociation proceeds via an asynchronously concerted mechanism, in which the C(5)-C(5)' bond breaks soon after application of the laser pulse, followed by cleavage of the C(6)-C(6)' bond. The dissociation results in two thymine monomers, one in an electronically excited state and the other in the ground state. The former decays to the electronic ground state through an avoided crossing induced by deformation of the pyrimidine ring at the C(5)' and C(6)' sites.
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Affiliation(s)
- Yusheng Dou
- Institute of Computational Chemistry and Molecular Simulation, Chongqing University of Posts and Telecommunications, Chongqing 400065, PR China.
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Abstract
The short answer to the title question is that it acts as an electrostatic bouncer that shoves the charge flow from flavin toward the DNA lesion that photolyase repairs. This explanation is provided by an explicit time-dependent quantum mechanical approach, which is used to investigate the electron transfer process that triggers the repair mechanism. The transfer occurs from the flavin photolyase cofactor to the cyclobutane ring of DNA, previously formed by light-induced cycloaddition of adjacent pyrimidine bases. The electron wave function dynamics accurately accounts for the previously proposed mechanism of transfer via the terminal methyl group of the flavin moiety present in the catalytic electron-donor cofactor, FADH(-), which also contains adenine. This latter moiety, which has often been assumed to be present mainly for structural reasons, instantaneously modifies the interaction between acceptor and donor by a variation of the electrostatic interactions so that the presence of its local atomic charges is necessary to trigger the transfer. In principle, knowledge of the details of the electron transfer dynamics and of the important role of polarization effects can be exploited to improve the efficiency of the repair mechanism in artificial systems.
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Affiliation(s)
- Angela Acocella
- Dipartimento di Chimica G. Ciamician, Università di Bologna, V. F. Selmi 2, 40126, Bologna, Italy
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Krapf S, Koslowski T, Steinbrecher T. The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions. Phys Chem Chem Phys 2010; 12:9516-25. [DOI: 10.1039/c000876a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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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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40
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DNA photolyase of enterococci: possible explanation for its low sunlight inactivation rate. Biologia (Bratisl) 2009. [DOI: 10.2478/s11756-009-0168-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Aoki S, Tomiyama Y, Kageyama Y, Yamada Y, Shiro M, Kimura E. Photolysis of the sulfonamide bond of metal complexes of N-dansyl-1,4,7,10-tetraazacyclododecane in aqueous solution: a mechanistic study and application to the photorepair of cis,syn-cyclobutane thymine photodimer. Chem Asian J 2009; 4:561-73. [PMID: 19165842 DOI: 10.1002/asia.200800428] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sulfonamide constitutes a ubiquitous functional group that is frequently used in organic chemistry, analytical chemistry, and medicinal chemistry. We report herein on the photolysis of a dansylamide moiety of 1-dansyl-1,4,7,10-tetraazzacyclododecane (N-dansylcyclen, L(2)) in the presence of a zinc(II) ion in aqueous solution. By potentiometric pH titrations, the complexation constant for the 1:1 complex of L(2) and Zn(2+), log K(s)(ZnL(2)), in aqueous solution at 25 degrees C with I = 0.1 (NaNO(3)) was determined to be 6.5+/-0.1. The structure of the ZnL(2) complex was confirmed by single-crystal X-ray diffraction analysis. During fluorescence titrations of L(2) with Zn(2+) (irradiation at 308 or 350 nm) in aqueous solution at pH 7.4 (10 mM HEPES with I = 0.1 (NaNO(3))) and 25 degrees C, considerable enhancement in fluorescence emission of the Zn(2+) complex of L(2) (ZnL(2)) was observed, while metal-free L(2) exhibited only a negligible emission change upon UV irradiation. It was revealed that this emission enhancement arose from the photoinduced cleavage of a sulfonylamide moiety in ZnL(2), yielding the Zn(2+)-cyclen complex and 5-dimethylaminonaphthalene-1-sulfinic acid, which has a greater quantum yield (Phi) for fluorescence emission than that of L(2) and ZnL(2). For comparison, the photolysis of N-(1-naphthalenesulfonyl)cyclen (L(3)) and its Zn(2+) complex (ZnL(3)) under the same conditions (irradiation at 313 nm) gave the corresponding sulfonate (1-naphthylsulfonate). We also describe the results of a photoreversion reaction of cis,syn-cyclobutane thymine photodimer (T[c,s]T) utilizing the photolysis of ZnL(2) and ZnL(3).
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Affiliation(s)
- Shin Aoki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan.
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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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Yamamoto J, Tanaka Y, Iwai S. Spectroscopic analysis of the pyrimidine(6-4)pyrimidone photoproduct: insights into the (6-4) photolyase reaction. Org Biomol Chem 2008; 7:161-6. [PMID: 19081959 DOI: 10.1039/b815458a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We synthesized a dinucleoside monophosphate of the (15)N-labeled (6-4) photoproduct, which is one of the major UV-induced lesions in DNA, to investigate the (6-4) photolyase repair mechanism, and characterized its protonation state by measuring (15)N NMR spectra as a function of pH. We expected that chemical-shift changes of the pyrimidone (15)N3, due to protonation, would be observed at pH 3, as observed for the (15)N-labeled 5-methylpyrimidin-2-one nucleoside. Interestingly, however, the changes were observed only in alkaline solutions. In UV absorption spectroscopy and HPLC analyses under acidic conditions, a change in the maximum absorption wavelength, due to the protonation-induced hydrolysis, was observed at and below pH 1, but not at pH 2, whereas the protonation of 5-methylpyrimidin-2-one occurred at pH values between 2 and 3. These results indicated that the pK(a) value for this N3 is remarkably lower than that of a normal pyrimidone ring, and strongly suggest that an intramolecular hydrogen bond is formed between the N3 of the 3' base and the 5-OH of the 5' base under physiological conditions. The results of this study have implications not only for the recognition and reaction mechanisms of (6-4) photolyase, but also for the chemical nature of the (6-4) photoproduct.
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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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Andreu I, Delgado J, Espinós A, Pérez-Ruiz R, Jiménez MC, Miranda MA. Cycloreversion of Azetidines via Oxidative Electron Transfer. Steady-State and Time-Resolved Studies. Org Lett 2008; 10:5207-10. [DOI: 10.1021/ol802181u] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Inmaculada Andreu
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universidad Politécnica de Valencia, Camino de Vera s/n, E-46022 Valencia, Spain
| | - Julio Delgado
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universidad Politécnica de Valencia, Camino de Vera s/n, E-46022 Valencia, Spain
| | - Amparo Espinós
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universidad Politécnica de Valencia, Camino de Vera s/n, E-46022 Valencia, Spain
| | - Raul Pérez-Ruiz
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universidad Politécnica de Valencia, Camino de Vera s/n, E-46022 Valencia, Spain
| | - M. Consuelo Jiménez
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universidad Politécnica de Valencia, Camino de Vera s/n, E-46022 Valencia, Spain
| | - Miguel A. Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universidad Politécnica de Valencia, Camino de Vera s/n, E-46022 Valencia, Spain
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Tachikawa H, Kawabata H. A direct ab initio molecular dynamics (MD) study on the repair reactions of stacked thymine dimer. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Zheng X, Garcia J, Stuchebrukhov AA. Theoretical study of excitation energy transfer in DNA photolyase. J Phys Chem B 2008; 112:8724-9. [PMID: 18588340 PMCID: PMC2699452 DOI: 10.1021/jp800053a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photolyase (PL) is a DNA repair enzyme which splits UV light-induced thymine dimers on DNA by an electron transfer reaction occurring between the photoactivated FADH(-) cofactor and the DNA dimer in the DNA/PL complex. The crystal structure of the DNA/photolyase complex from Anacystis nidulans has been solved. Here, using the experimental crystal structure, we re-examine the details of the repair electron transfer reaction and address the question of energy transfer from the antenna HDF to the redox active FADH(-) cofactor. The photoactivation of FADH(-) immediately preceding the electron transfer is a key step in the repair mechanism that is largely left unexamined theoretically. An important butterfly thermal motion of flavin is identified in ab initio calculations; we propose its role in the back electron transfer from DNA to photolyase. Molecular dynamics simulation of the whole protein/DNA complex is carried out to obtain relevant cofactor conformations for ZINDO/S spectroscopic absorption and fluorescence calculations. We find that significant thermal broadening of the spectral lines, due to protein dynamics, as well as the alignment of the donor HDF and the acceptor FADH(-) transition dipole moments both contribute to the efficiency of energy transfer. The geometric factor of Förster's dipolar coupling is calculated to be 1.82, a large increase from the experimentally estimated 0.67. Using Förster's mechanism, we find that the energy transfer occurs with remarkable efficiency, comparable with the experimentally determined value of 98%.
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O'Neil LL, Wiest O. Structures and energetics of base flipping of the thymine dimer depend on DNA sequence. J Phys Chem B 2008; 112:4113-22. [PMID: 18335922 DOI: 10.1021/jp7102935] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cis,syn-cyclobutane pyrimidine dimer (CPD) is a photoinduced DNA lesion leading to a significant distortion of the DNA structure. Its repair by DNA photolyase requires a flip of the damaged base into an extrahelical position. This base flip is expected to be sequence-dependent, but the structures and energetics as a function of the bases 3' and 5' to the CPD lesion are unknown. Eight-nanosecond MD simulations of four different hexadecamer duplexes with the CPD were performed for the flipped-in and flipped-out structures. Analysis of these results indicates clear sequence-dependent differences. Significant disruptions of the base pairs to the 3' side of the CPD are observed for the flipped-out structures with adjacent A-T pairs, whereas those with G-C pairs adjacent show no such distortions. The conformational spaces occupied by these two duplexes are significantly different. The structural differences correlate well with the free energy differences for base flipping calculated using the previously established 2D potential of mean force (PMF) method. The energy differences for base flipping in duplexes containing A, T, G, and C pairs adjacent to the CPD were found to be 6.25-6.5, 5.25-5.5, 7.25-7.5, and 6.5-6.75 kcal/mol, respectively. These energy differences of up to 2 kcal/mol should be large enough to be detected experimentally using sensitive probes.
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Affiliation(s)
- Lauren L O'Neil
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, USA
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Johnson AT, Wiest O. Structure and dynamics of poly(T) single-strand DNA: implications toward CPD formation. J Phys Chem B 2007; 111:14398-404. [PMID: 18052367 DOI: 10.1021/jp076371k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formation of cyclobutane pyrimidine dimers between adjacent thymines by UV radiation is thought to be the first event in a cascade leading to skin cancer. Recent studies showed that thymine dimers are fully formed within 1 ps of UV irradiation, suggesting that the conformation at the moment of excitation is the determining factor in whether a given base pair dimerizes. MD simulations on the 50 ns time scale are used to study the populations of reactive conformers that exist at any given time in T18 single-strand DNA. Trajectory analysis shows that only a small percentage of the conformations fulfill distance and dihedral requirements for thymine dimerization, in line with the experimentally observed quantum yield of 3%. Plots of the pairwise interactions in the structures predict hot spots of DNA damage where dimerization in the ssT18 is predicted to be most favored. The importance of hairpin formation by intra-strand base pairing for distinguishing reactive and unreactive base pairs is discussed in detail. The data presented thus explain the structural origin of the results from the ultrafast studies of thymine dimer formation.
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Affiliation(s)
- Andrew T Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, USA
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Blancafort L, Voityuk AA. MS-CASPT2 calculation of excess electron transfer in stacked DNA nucleobases. J Phys Chem A 2007; 111:4714-9. [PMID: 17487989 DOI: 10.1021/jp067886z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Calculations using the complete active space self-consistent field (CASSCF) and complete active space second-order perturbation (CASPT2) methods, and the multistate formulation of CASPT2 (MS-CASPT2), are performed for the ground and excited states of radical anions consisting of two pi-stacked nucleobases. The electronic couplings for excess electron transfer (EET) in the pi-stacks are estimated by using the generalized Mulliken-Hush approach. We compare results obtained within the different methods with data derived using Koopmans' theorem approximation at the Hartree-Fock level. The results suggest that although the one-electron scheme cannot be applied to calculate electron affinities of nucleobases, it provides reasonable estimates for EET energies. The electronic couplings calculated with KTA lie between the CASPT2 and the MS-CASPT2 based values in almost all cases.
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Affiliation(s)
- Lluís Blancafort
- Institut de Química Computational, Departament de Química, Universitat de Girona, 17071 Girona, Spain.
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Pirogova E, Vojisavljevic V, Fang Q, Cosic I. Computational analysis of DNA photolyases using digital signal processing methods. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020601052997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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