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Rodríguez-Muñiz GM, Gomez-Mendoza M, Miro P, García-Orduña P, Sastre G, Miranda MA, Marin ML. Topology and Excited State Multiplicity as Controlling Factors in the Carbazole-Photosensitized CPD Formation and Repair. J Org Chem 2022; 87:11433-11442. [PMID: 35980822 PMCID: PMC9447287 DOI: 10.1021/acs.joc.2c00942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Photosensitized thymine<>thymine (Thy<>Thy)
formation and
repair can be mediated by carbazole (Cbz). The former occurs from
the Cbz triplet excited state via energy transfer, while the latter
takes place from the singlet excited state via electron transfer.
Here, fundamental insight is provided into the role of the topology
and excited state multiplicity, as factors governing the balance between
both processes. This has been achieved upon designing and synthesizing
different isomers of trifunctional systems containing one Cbz and
two Thy units covalently linked to the rigid skeleton of the natural
deoxycholic acid. The results shown here prove that the Cbz photosensitized
dimerization is not counterbalanced by repair when the latter, instead
of operating through-space, has to proceed through-bond.
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Affiliation(s)
- Gemma M Rodríguez-Muñiz
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain
| | - Miguel Gomez-Mendoza
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain
| | - Paula Miro
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain
| | - Pilar García-Orduña
- Dpto. Química Inorgánica, ISQCH-Instituto de Síntesis Química y Catálisis Homogénea, Facultad de Ciencias, CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - German Sastre
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain
| | - Miguel A Miranda
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain
| | - M Luisa Marin
- Instituto de Tecnología Química, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain
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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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Wu QQ, Song QH. Photosensitized splitting of thymine dimer or oxetane unit by a covalently N-linked carbazole via electron transfer in different marcus regions. J Phys Chem B 2011; 114:9827-32. [PMID: 20614917 DOI: 10.1021/jp1035579] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although many similarities exist between the two classes of enzymes, cyclobutane photolyases and (6-4) photolyases have certain important differences. The most significant difference is in their repair quantum yields, cyclobutane photolyases with a uniformly high efficiency (0.7-0.98) and very low repair efficiency for (6-4) photolyases (0.05-0.1). To understand the significant difference, we prepared two classes of model compounds, covalently N-linked dimer- (1) or oxetane-carbazole (2) compounds with a dimethylene or trimethylene group as a linker. Under light irradiation, the dimer or oxetane unit of model compounds can be sensitized to split by the excited carbazole via an intramolecular electron transfer. The splitting reaction of dimer or oxetane unit in model compounds is strongly solvent dependent. In nonpolar solvents, such as cyclohexane or THF, no fluorescence quenching of the carbazole moiety of model compounds relative to a free carbazole, N-methylcarbazole, was observed and thus no splitting occurred. In polar solvents, two classes of model compounds reveal two reverse solvent effects on the splitting quantum yield. One is an inverse relation between the quantum yield and the polarity of the solvent for dimer-model systems, and another is a normal relation for oxetane-model systems. This phenomenon was also observed with another two classes of model compounds, covalently linked dimer- or oxetane-indole. Based on Marcus theory and thermodynamic data, it has been rationalized that the two reverse solvent effects derive from back electron transfer in the splitting process lying in the different Marcus regions. Back electron transfer lies in the Marcus inverted region for dimer-model systems and the normal region for oxetane-model systems. From repair solvent behavior of the two classes of model compounds, we gained some insights into the major difference in the repair efficiency for the two classes of photolyases.
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Affiliation(s)
- Qing-Qing Wu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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4
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Tang WJ, Guo QX, Song QH. Origin of solvent dependence of photosensitized splitting of a cyclobutane pyrimidine dimer by a covalently linked chromophore. J Phys Chem B 2009; 113:7205-10. [PMID: 19405487 DOI: 10.1021/jp805965e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In model studies involving the mechanisms of DNA photolyases, two reverse solvent effects on the quantum yield of photosensitized splitting of a cyclobutane pyrimidine dimer (CPD) by a covalently linked chromophore have been reported. One is an increase in the splitting efficiency in lower polarity solvents for model compounds with a short linker between the dimer and the chromophore. Another is more efficient splitting in higher polarity solvents for model compounds with a flexible and long linker. To unravel mechanisms of two opposite solvent effects, five covalently linked indole-dimer compounds with different-length linkers were prepared. Two solvent effects as described above were observed through measuring quantum yields of dimer splitting of these model compounds in four solvents. According to Marcus theory, back electron transfer in the splitting reaction was analyzed quantitatively in light of relative data of a model compound in four solvents. It was demonstrated that the dependence of the quantum yield on solvent polarity for the flexible long-linker system would derive from the change in the distance between a dimer unit (acceptor) and an indole moiety (electron donor) in different solvents. With increasing solvent polarity, a U-shaped conformation of the model compound would become a preferred conformation because of the hydrophobic interaction between indole and dimer moiety, and their distances would become closer. On the basis of Marcus theory, calculated results reveal that the rate of back electron transfer would be slowed down with increasing solvent polarity and the distance reduced, giving a more efficient splitting. Meanwhile, some new insights into mechanisms of DNA photoreactivation mediated by photolyases were gained.
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Affiliation(s)
- Wen-Jian Tang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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Thorne RE, Chinnapen DJF, Sekhon GS, Sen D. A deoxyribozyme, Sero1C, uses light and serotonin to repair diverse pyrimidine dimers in DNA. J Mol Biol 2009; 388:21-9. [PMID: 19281822 DOI: 10.1016/j.jmb.2009.02.064] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Revised: 02/10/2009] [Accepted: 02/28/2009] [Indexed: 11/19/2022]
Abstract
An in vitro selection search for DNAs capable of catalyzing photochemistry yielded two distinctive deoxyribozymes (DNAzymes) with photolyase activity: UV1C, which repaired thymine dimers within DNA using a UV light of >300 nm wavelength and no extraneous cofactor, and Sero1C, which required the tryptophan metabolite serotonin as cofactor in addition to the UV light. Catalysis by Sero1C conformed to Michaelis-Menten kinetics, and analysis of the action spectrum of Sero1C confirmed that serotonin did indeed serve as a catalytic cofactor rather than as a structural cofactor. Sero1C and UV1C showed strikingly distinct wavelength optima for their respective photoreactivation catalyses. Although the rate enhancements characteristic of the two DNAzymes were similar, the cofactor-requiring Sero1C repaired a substantially broader range of substrates compared to UV1C, including thymine, uracil, and a range of chimeric deoxypyrimidine and ribopyrimidine dimers. Similarities and differences in the properties of these two photolyase DNAzymes suggest, first, that the harnessing of less damaging UV light for the repair of photolesions may have been a primordial catalytic activity of nucleic acids, and, second, the broader substrate range of Sero1C may highlight an evolutionary advantage to coopting amino-acid-like cofactors by functionality-poor nucleic acid enzymes.
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Affiliation(s)
- Rebecca E Thorne
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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Song QH, Tang WJ, Ji XB, Wang HB, Guo QX. Do photolyases need to provide considerable activation energy for the splitting of cyclobutane pyrimidine dimer radical anions? Chemistry 2007; 13:7762-70. [PMID: 17568458 DOI: 10.1002/chem.200700251] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
cis-syn Cyclobutane pyrimidine dimers, major UV-induced DNA lesions, are efficiently repaired by DNA photolyases. The key step of the repair reaction is a light-driven electron transfer from the FADH(-) cofactor to the dimer; the resulting radical anion splits spontaneously. Whether the splitting reaction requires considerable activation energy is still under dispute. Recent reports show that the splitting reaction of a dimer radical anion has a significant activation barrier (0.45 eV), and so photolyases have to provide considerable energy. However, these results contradict observations that cis-syn dimer radical anions split into monomers at -196 degrees C, and that the full process of DNA photoreactivation was fast (1.5-2 ns). To investigate the activation energies of dimer radical anions, three model compounds 1-3 were prepared. These include a covalently linked cyclobutane thymine dimer and a tryptophan residue (1) or a flavin unit (3), and the covalently linked uracil dimer and tryptophan (2). Their properties of photosensitised splitting of the dimer units by tryptophan or flavin unit were investigated over a large temperature range, -196 to 70 degrees C. The activation energies were obtained from the temperature dependency of splitting reactions for 1 and 2, 1.9 kJ mol(-1) and 0.9 kJ mol(-1) for the thymine and uracil dimer radical anions, respectively. These values are much lower than that obtained for E. coli photolyase (0.45 eV), and are surmountable at -196 degrees C. The activation energies provide support for previous observations that repair efficiencies for uracil dimers are higher than thymine dimers, both in enzymatic and model systems. The mechanisms of highly efficient enzymatic DNA repair are discussed.
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Affiliation(s)
- Qin-Hua Song
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, Anhui, P. R. China.
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Carell T, Epple R, Gramlich V. Synthesis and structure of (carboxymethyl)-functionalized cyclobuta-fused uracil dimers. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19970800718] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Nakamura T, Takagi K, Sawaki Y. The One-Electron Transfer Induced Photocycloreversion of Stilbazolium Cyclodimers. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1998. [DOI: 10.1246/bcsj.71.419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Affiliation(s)
- T Douki
- CEA/Département de Recherche Fondamentale sur la Matière Condensée-SESAM/LAN, Grenoble, France
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Kim ST, Sancar A. Photochemistry, photophysics, and mechanism of pyrimidine dimer repair by DNA photolyase. Photochem Photobiol 1993; 57:895-904. [PMID: 8337263 DOI: 10.1111/j.1751-1097.1993.tb09232.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
DNA photolyases photorepair pyrimidine dimers (Pyr < > Pyr) in DNA as well as RNA and thus reverse the harmful effects of UV-A (320-400 nm) and UV-B (280-320 nm) radiations. Photolyases from various organisms have been found to contain two noncovalently bound cofactors; one is a fully reduced flavin adenine dinucleotide (FADH-) and the other, commonly known as second chromophore, is either methenyltetrahydrofolate (MTHF) or 8-hydroxydeazaflavin (8-HDF). The second chromophore in photolyase is a light-harvesting molecule that absorbs mostly in the near-UV and visible wavelengths (300-500 nm) with its high extinction coefficient. The second chromophore then transfers its excitation energy to the FADH-. Subsequently, the photoexcited FADH- transfers an electron to the Pyr < > Pyr generating a dimer radical anion (Pyr < > Pyr.-) and a neutral flavin radical (FADH.). The Pyr < > Pyr.- is very unstable and undergoes spontaneous splitting followed by a back electron transfer to the FADH.. In addition to the main catalytic cofactor FADH-, a Trp (Trp277 in Escherichia coli) in apophotolyase, independent of other chromophores, also functions as a sensitizer to repair Pyr < > Pyr by direct electron transfer.
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Affiliation(s)
- S T Kim
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599-7260
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Kim ST, Rose SD. Pyrimidine dimer splitting in covalently linked dimer-arylamine systems. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1992; 12:179-91. [PMID: 1619516 DOI: 10.1016/1011-1344(92)85007-h] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cyclobutadipyrimidines (pyrimidine dimers) undergo photosplitting which is sensitized by electron donors. We prepared a series of compounds in which a dimer is directly linked to an arylamine, which acts as sensitizer for dimer splitting. Two diastereomers of the dimer-arylamine exhibited very different splitting efficiencies. Also studied were N-methyl, ring methoxy, as well as deuterated derivatives of the sensitizer. These dimer-arylamines had an absorption band with lambda max approximately 300 nm. In each case intramolecular photosensitization of dimer splitting was highly dependent on the solvent, ranging in one instance from phi spl = 0.02 in water to a high value of 0.31 in the least polar solvent mixture examined (1,4-dioxane: isopentane, 1:99). A mechanism is proposed which involves photoinduced electron transfer from arylamine to dimer and splitting of the dimer radical anion. The dependence of splitting on the solvent was rationalized on the basis of retardation of back electron transfer due to Marcus inverted behavior of the charge-separated species. Photolyases might achieve their high efficiency of dimer splitting in part by employing a hydrophobic active site to slow back electron transfer in a similar manner.
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Affiliation(s)
- S T Kim
- Department of Chemistry and Biochemistry, Arizona State University, Tempe 85287-1604
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