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Lee W, Matsika S. Mechanistic Aspects of the Effect of Flanking Nucleotide Sequence on CPD Formation and CPD Self-Repair in DNA. J Phys Chem B 2023; 127:18-25. [PMID: 36574488 DOI: 10.1021/acs.jpcb.2c06680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A cyclobutane pyrimidine dimer (CPD) is a photolesion which is produced by a cycloaddition reaction between two stacked pyrimidine bases upon UV light absorption. Because of its harmful effect on important cellular processes involving DNA and especially its relevance to skin cancer, the mechanisms of how a CPD is formed or repaired have been studied extensively, and it has been demonstrated that flanking nucleotide sequences play a crucial role in CPD formation or self-repair. Understanding the mechanisms behind this sequence dependence of CPD formation or self-repair is of great importance because it can give us valuable information on which sequence will be vulnerable to this DNA photodamage. This Perspective focuses on the mechanisms of how flanking nucleotide sequences affect CPD formation or self-repair, especially highlighting the role of computational studies in this field.
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Affiliation(s)
- Wook Lee
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, Korea
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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2
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Bucher DB, Kufner CL, Schlueter A, Carell T, Zinth W. UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair. J Am Chem Soc 2015; 138:186-90. [PMID: 26651219 DOI: 10.1021/jacs.5b09753] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Absorption of UV-radiation in nucleotides initiates a number of photophysical and photochemical processes, which may finally cause DNA damage. One major decay channel of photoexcited DNA leads to reactive charge transfer states. This study shows that these states trigger self-repair of DNA photolesions. The experiments were performed by UV spectroscopy and HPLC on different single and double stranded oligonucleotides containing a cyclobutane pyrimidine dimer (CPD) lesion. In a first experiment we show that photoexcitation of adenine adjacent to a CPD has no influence on this lesion. However, excitation of a guanine (G) adenine (A) sequence leads to reformation of the intact thymine (T) bases. The involvement of two bases for the repair points to a long-living charge transfer state between G and A to be responsible for the repair. The negatively charged A radical anion donates an electron to the CPD, inducing ring splitting and repair. In contrast, a TA sequence, having an inverted charge distribution (T radical anion, A radical cation), is not able to repair the CPD lesion. The investigations show that the presence of an adjacent radical ion is not sufficient for repair. More likely it is the driving power represented by the oxidation potential of the radical ion, which controls the repair. Thus, repair capacities are strongly sequence-dependent, creating DNA regions with different tendencies of self-repair. This self-healing activity represents the simplest sequence-dependent DNA repair system.
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Affiliation(s)
- Dominik Benjamin Bucher
- BioMolecular Optics and Center for Integrated Protein Science, Ludwigs-Maximilians-Universität München , Oettingenstrasse 67, 80538 München, Germany.,Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München , Butenandtstrasse 5-13, 81377 München, Germany
| | - Corinna Lucia Kufner
- BioMolecular Optics and Center for Integrated Protein Science, Ludwigs-Maximilians-Universität München , Oettingenstrasse 67, 80538 München, Germany
| | - Alexander Schlueter
- BioMolecular Optics and Center for Integrated Protein Science, Ludwigs-Maximilians-Universität München , Oettingenstrasse 67, 80538 München, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München , Butenandtstrasse 5-13, 81377 München, Germany
| | - Wolfgang Zinth
- BioMolecular Optics and Center for Integrated Protein Science, Ludwigs-Maximilians-Universität München , Oettingenstrasse 67, 80538 München, Germany
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Sheng Z, Pan Y, Yan L, Hei X, Guo Z, Dai J, Song Q, Yu S. Steady-state and laser flash photolysis studies on the oxidative splitting of cyclobutane thymine dimer by triplet 9,10-anthraquinone-2-sulfonate. J Photochem Photobiol A Chem 2004. [DOI: 10.1016/s1010-6030(03)00279-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yamada M, Kato K, Nomizu M, Sakairi N, Ohkawa K, Yamamoto H, Nishi N. Preparation and characterization of DNA films induced by UV irradiation. Chemistry 2002; 8:1407-12. [PMID: 11921224 DOI: 10.1002/1521-3765(20020315)8:6<1407::aid-chem1407>3.0.co;2-l] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Large amounts of DNA-enriched materials, such as salmon milts and shellfish gonads, are discarded as industrial waste. We have been able to convert the discarded DNA to a useful material by preparing novel DNA films by UV irradiation. When DNA films were irradiated with UV light, the molecular weight of DNA was greatly increased. The reaction was inhibited by addition of the radical scavenger galvinoxyl suggesting that the DNA polymerization with UV irradiation proceeded by a radical reaction. Although this UV-irradiated DNA film was water-insoluble and resistant to hydrolysis by nuclease, the structure of the DNA film in water was similar to non-irradiated DNA and maintained B-form structure. In addition, the UV-irradiated DNA film could effectively accumulate and condense harmful DNA-intercalating compounds, such as ethidium bromide and acridine orange, from diluted aqueous solutions. The binding constant and exclusion number of ethidium bromide for UV-irradiated DNA were determined to be 6.8 +/- 0.3 x 10(4) M(-1) and 1.6 +/- 0.2, respectively; these values are consisted with reported results for non-irradiated DNA. The UV-irradiated DNA films have potential uses as a biomaterial filter for the removal of harmful DNA intercalating compounds.
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Affiliation(s)
- Masanori Yamada
- Laboratory of Bio-Material, Chemistry Division of Bioscience, Graduate School of Environmental Earth Science, Hokkaido University, Kita-10, Nishi-5, Kita-ku, Sapporo 060-0810, Japan
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Vicic DA, Odom DT, Núñez ME, Gianolio DA, McLaughlin LW, Barton JK. Oxidative Repair of a Thymine Dimer in DNA from a Distance by a Covalently Linked Organic Intercalator. J Am Chem Soc 2000. [DOI: 10.1021/ja000280i] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David A. Vicic
- Contribution from the Division of Chemistry and Chemical Engineering, M/C 127-72, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Duncan T. Odom
- Contribution from the Division of Chemistry and Chemical Engineering, M/C 127-72, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Megan E. Núñez
- Contribution from the Division of Chemistry and Chemical Engineering, M/C 127-72, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Diego A. Gianolio
- Contribution from the Division of Chemistry and Chemical Engineering, M/C 127-72, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Larry W. McLaughlin
- Contribution from the Division of Chemistry and Chemical Engineering, M/C 127-72, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Jacqueline K. Barton
- Contribution from the Division of Chemistry and Chemical Engineering, M/C 127-72, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
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Dotse AK, Boone EK, Schuster GB. Remote cis−syn-Thymine [2 + 2] Dimers Are Not Repaired by Radical Cations Migrating in Duplex DNA. J Am Chem Soc 2000. [DOI: 10.1021/ja994028q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony K. Dotse
- Contribution from the School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Edna K. Boone
- Contribution from the School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Gary B. Schuster
- Contribution from the School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332
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Ito T, Shinohara H, Hatta H, Nishimoto SI, Fujita SI. Radiation-Induced and Photosensitized Splitting of C5−C5‘-Linked Dihydrothymine Dimers: Product and Laser Flash Photolysis Studies on the Oxidative Splitting Mechanism. J Phys Chem A 1999. [DOI: 10.1021/jp991877r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hideki Shinohara
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Hatta
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sei-ichi Nishimoto
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shin-ichi Fujita
- Research Institute of Advanced Technology, University of Osaka Prefecture,Osaka 599-8231, Japan
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A cyclic intermediate of the splitting reaction of cyclobutane-type pyrimidine dimer cation radicals. A computational finding as challenge for experimental techniques. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0166-1280(98)00629-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Huntley JJA, Nieman RA, Rose SD. Development and Investigation of a Novel Oxidative Pyrimidine Dimer Splitting Model. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb05298.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Aida M, Kaneko M, Dupuis M. Radiation-Induced DNA Damage and Repair: An Approach from AB Initio MO Method. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80081-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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12
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Holmlin RE, Dandliker PJ, Barton JK. Ladungsübertragung durch den DNA-Basenstapel. Angew Chem Int Ed Engl 1997. [DOI: 10.1002/ange.19971092404] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
The metallointercalator Rh(phi)2DMB3+ (phi, 9,10-phenanthrenequinone diimine; DMB, 4,4'-dimethyl-2,2'-bipyridine) catalyzed the repair of a thymine dimer incorporated site-specifically in a 16-base pair DNA duplex by means of visible light. This repair could be accomplished with rhodium noncovalently bound to the duplex and at long range (16 to 26 angstroms), with the rhodium intercalator tethered to either end of the duplex assembly. This long-range repair was mediated by the DNA helix. Repair efficiency did not decrease with increasing distance between intercalated rhodium and the thymine dimer, but it diminished with disruption of the intervening pi-stack.
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Affiliation(s)
- P J Dandliker
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Pouwels PJ, Hartman RF, Rose SD, Kaptein R. Photo-CIDNP study of pyrimidine dimer splitting. I: Reactions involving pyrimidine radical cation intermediates. Photochem Photobiol 1995; 61:563-74. [PMID: 7568403 DOI: 10.1111/j.1751-1097.1995.tb09871.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The light-induced splitting of pyrimidine dimers was studied using the electron acceptor anthraquinone-2-sulfonate (AQS) as a photosensitizer. To this end, photochemically induced dynamic nuclear polarization (photo-CIDNP) experiments were performed on a series of pyrimidine monomers and dimers. The CIDNP spectra demonstrate the existence of both the dimer radical cation, which is formed by electron transfer from the dimer to the photoexcited sensitizer AQS*, and its dissociation product, the monomer radical cation. In spectra of 1,1'-trimethylene bridged cis, syn pyrimidine dimers, polarization is observed that originates from a spin-sorting process in the dimer radical pair. This points to a relatively long lifetime of the dimer radical cation involved, which is presumably due to stabilization by the trimethylene bridge. Polarization originating from a dimer radical pair is detected in the spectrum of trans,anti (1,3-dimethyluracil) dimer as well. The spectra of the bridged pyrimidines also demonstrate the reversibility of the dissociation of dimer radical cation into monomer radical cation, which is concluded from the observation of polarization in the dimer as a result of spin sorting in the monomer radical pair.
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Affiliation(s)
- P J Pouwels
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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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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Heelis PF, Kim ST, Okamura T, Sancar A. The photo repair of pyrimidine dimers by DNA photolyase and model systems. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1993; 17:219-28. [PMID: 8492239 DOI: 10.1016/1011-1344(93)80019-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Pyrimidine dimers are eliminated from DNA by a number of different mechanisms known as DNA repair. Photoreactivation, the reversal of the harmful effects of short wavelength radiation by subsequent exposure to longer wavelengths, is one such mechanism. In photoreactivation, the enzyme DNA photolyase utilises light in order to catalyse the cleavage of the cyclobutane ring of the pyrimidine dimer. The results of recent studies of E. coli DNA photolyase and model systems using techniques such as steady state and flash photolysis, time resolved fluorescence and photo CIDNP are surveyed. A mechanism is proposed for the in vitro reaction of E. coli DNA photolyase which involves photoreduction of the FAD radical cofactor followed by electron donation to the dimer from the excited singlet state of reduced FAD.
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Affiliation(s)
- P F Heelis
- North East Wales Institute, Deeside, Clwyd, UK
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Heelis PF, Hartman RF, Rose SD. Detection of radical ion intermediates in flavin-photosensitized pyrimidine dimer splitting. Photochem Photobiol 1993; 57:442-6. [PMID: 8475177 DOI: 10.1111/j.1751-1097.1993.tb02316.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Photosensitized splitting of cis-syn- and trans-syn-1,3-dimethyluracil dimers by 2',3',4',5'-tetraacetylriboflavin in acetonitrile containing a trace of perchloric acid was studied by laser flash photolysis. Protonation of the flavin prior to excitation resulted in excited singlet and triplet states that abstracted an electron from the dimers and yielded the protonated flavin radical (FlH2.+), which was detected by absorption spectroscopy. Electron abstraction by the excited singlet state predominated over abstraction by the triplet state. Approximately one-third to one-half of the excited states quenched by the trans-syn dimer yielded FlH2.+, the balance presumably undergoing back electron transfer within the geminate radical ion pair generated by the initial electron transfer. A covalently linked dimer-flavin exhibited very inefficient flavin radical ion formation, consistent with the known low efficiency of dimer splitting in this system. These results constitute the first identification of a flavin radical ion intermediate in photosensitized pyrimidine dimer splitting.
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Affiliation(s)
- P F Heelis
- Faculty of Science, Health and Medical Studies, North East Wales Institute, Deeside, Clwyd, UK
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Hartman RF, Rose SD, Pouwels PJ, Kaptein R. Flavin-sensitized photochemically induced dynamic nuclear polarization detection of pyrimidine dimer radicals. Photochem Photobiol 1992; 56:305-10. [PMID: 1438565 DOI: 10.1111/j.1751-1097.1992.tb02164.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A photochemically induced dynamic nuclear polarization (photo-CIDNP) study of carboxymethyllumiflavin-sensitized splitting of pyrimidine dimers has been carried out. In aqueous solution at high pH, an emission signal (delta 3.9 ppm) was observed from the dimer C(6)- and C(6')-protons of an N(1), N(1')-trimethylene-bridged thymine dimer (1). The dimer photo-CIDNP signal was seen only above pD 11.6 and was most intense at pD 12.9. Also observed were weak enhanced absorption signals from the product of splitting, trimethylenebis(thymine) (delta 1.7 and 7.2 ppm). In contrast, cis, syn-thymine dimer (3) gave no photo-CIDNP signals from the dimer. An enhanced absorption at 1.8 ppm, however, due to the product of splitting (thymine) was observed. It was found that dimer 1 and, to a lesser extent, dimer 3 quenched flavin fluorescence. An N(3),N(3')-dimethylated derivative of 1, however, failed to quench flavin fluorescence. Comparison of the pD profile of the dimer photo-CIDNP signal to the pKa values for thymidine dimer suggested that principally the dideprotonated dimer undergoes electron abstraction by the excited flavin.
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Affiliation(s)
- R F Hartman
- Department of Chemistry and Biochemistry, Arizona State University, Tempe 85287-1604
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Kim ST, Sancar A. Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase. Biochemistry 1991; 30:8623-30. [PMID: 1716150 DOI: 10.1021/bi00099a019] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Photolyases reverse the effects of UV light on cells by converting cyclobutane dipyrimidine photoproducts (pyrimidine dimers, Pyr mean value of Pyr) into pyrimidine monomers in a light-dependent reaction. Previous work has suggested that, based on substrate preference, there are two classes of photolyase: DNA photolyase as exemplified by the Escherichia coli enzyme, and RNA photolyases found in plants such as Nicotiana tabacum and Phaseolus vulgaris. In experiments aimed at identifying substrate determinants, including the pentose ring, for binding and catalysis by E. coli DNA photolyase we tested several Pyr mean value of Pyr. We found that the enzyme has relative affinities for photodimers of T mean value of T greater than or equal to U mean value of T greater than U mean value of U much greater than C mean value of C and that the E-FADH2 form of the enzyme repairs these dimers at 366 nm with absolute quantum yields of 0.9 (T mean value of T), 0.8 (U mean value of T), 0.6 (U mean value of U), and 0.05 (C mean value of C). The enzyme also repairs an isolated thymine dimer and the synthetic substrate, 1,1'-trimethylene-bis (thymine) cyclobutane dimer. Unexpectedly, we found that this enzyme, previously thought to be specific for DNA, repairs uracil cyclobutane dimers in poly(rU). The affinity of photolyase for a uracil dimer in RNA is about 10(4)-fold lower than that for a U mean value of U in DNA; however, once bound, the enzyme repairs the photodimer with the same quantum yield whether the dimer is in ribonucleoside or deoxyribonucleoside form.
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Affiliation(s)
- S T Kim
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill 27599
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