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Ramírez-Gamboa D, Díaz-Zamorano AL, Meléndez-Sánchez ER, Reyes-Pardo H, Villaseñor-Zepeda KR, López-Arellanes ME, Sosa-Hernández JE, Coronado-Apodaca KG, Gámez-Méndez A, Afewerki S, Iqbal HMN, Parra-Saldivar R, Martínez-Ruiz M. Photolyase Production and Current Applications: A Review. Molecules 2022; 27:molecules27185998. [PMID: 36144740 PMCID: PMC9505440 DOI: 10.3390/molecules27185998] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The photolyase family consists of flavoproteins with enzyme activity able to repair ultraviolet light radiation damage by photoreactivation. DNA damage by the formation of a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct can lead to multiple affections such as cellular apoptosis and mutagenesis that can evolve into skin cancer. The development of integrated applications to prevent the negative effects of prolonged sunlight exposure, usually during outdoor activities, is imperative. This study presents the functions, characteristics, and types of photolyases, their therapeutic and cosmetic applications, and additionally explores some photolyase-producing microorganisms and drug delivery systems.
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Affiliation(s)
- Diana Ramírez-Gamboa
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | | | - Humberto Reyes-Pardo
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | | | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Karina G. Coronado-Apodaca
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Ana Gámez-Méndez
- Department of Basic Sciences, Universidad de Monterrey, Av. Ignacio Morones Prieto 4500 Pte, San Pedro Garza Garcia 66238, Mexico
| | - Samson Afewerki
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Roberto Parra-Saldivar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
- Correspondence: (R.P.-S.); (M.M.-R.)
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
- Correspondence: (R.P.-S.); (M.M.-R.)
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Ramírez N, Serey M, Illanes A, Piumetti M, Ottone C. Immobilization strategies of photolyases: Challenges and perspectives for DNA repairing application. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 215:112113. [PMID: 33383556 DOI: 10.1016/j.jphotobiol.2020.112113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/27/2020] [Accepted: 12/19/2020] [Indexed: 02/08/2023]
Abstract
Photolyases are enzymes that repair DNA damage caused by solar radiation. Due to their photorepair potential, photolyases added in topical creams and used in medical treatments has allowed to reverse skin damage and prevent the development of different diseases, including actinic keratosis, premature photoaging and cancer. For this reason, research has been oriented to the study of new photolyases performing in extreme environments, where high doses of UV radiation may be a key factor for these enzymes to have perfected their photorepair potential. Generally, the extracted enzymes are first encapsulated and then added to the topical creams to increase their stability. However, other well consolidated immobilization methods are interesting strategies to be studied that may improve the biocatalyst performance. This review aims to go through the different Antarctic organisms that have exhibited photoreactivation activity, explaining the main mechanisms of photolyase DNA photorepair. The challenges of immobilizing these enzymes on porous and nanostructured supports is also discussed. The comparison of the most reported immobilization methods with respect to the structure of photolyases show that both covalent and ionic immobilization methods produced an increase in their stability. Moreover, the use of nanosized materials as photolyase support would permit the incorporation of the biocatalyst into the target cell, which is a technological requirement that photolyase based biocatalysts must fulfill.
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Affiliation(s)
- Nicolás Ramírez
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Marcela Serey
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Andrés Illanes
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Marco Piumetti
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
| | - Carminna Ottone
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile.
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Cyclobutane pyrimidine dimers from UVB exposure induce a hypermetabolic state in keratinocytes via mitochondrial oxidative stress. Redox Biol 2020; 38:101808. [PMID: 33264701 PMCID: PMC7708942 DOI: 10.1016/j.redox.2020.101808] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022] Open
Abstract
Ultraviolet B radiation (UVB) is an environmental complete carcinogen, which induces and promotes keratinocyte carcinomas, the most common human malignancies. UVB induces the formation of cyclobutane pyrimidine dimers (CPDs). Repairing CPDs through nucleotide excision repair is slow and error-prone in placental mammals. In addition to the mutagenic and malignancy-inducing effects, UVB also elicits poorly understood complex metabolic changes in keratinocytes, possibly through CPDs. To determine the effects of CPDs, CPD-photolyase was overexpressed in keratinocytes using an N1-methyl pseudouridine-containing in vitro-transcribed mRNA. CPD-photolyase, which is normally not present in placental mammals, can efficiently and rapidly repair CPDs to block signaling pathways elicited by CPDs. Keratinocytes surviving UVB irradiation turn hypermetabolic. We show that CPD-evoked mitochondrial reactive oxygen species production, followed by the activation of several energy sensor enzymes, including sirtuins, AMPK, mTORC1, mTORC2, p53, and ATM, is responsible for the compensatory metabolic adaptations in keratinocytes surviving UVB irradiation. Compensatory metabolic changes consist of enhanced glycolytic flux, Szent-Györgyi-Krebs cycle, and terminal oxidation. Furthermore, mitochondrial fusion, mitochondrial biogenesis, and lipophagy characterize compensatory hypermetabolism in UVB-exposed keratinocytes. These properties not only support the survival of keratinocytes, but also contribute to UVB-induced differentiation of keratinocytes. Our results indicate that CPD-dependent signaling acutely maintains skin integrity by supporting cellular energy metabolism.
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Formation and Recognition of UV-Induced DNA Damage within Genome Complexity. Int J Mol Sci 2020; 21:ijms21186689. [PMID: 32932704 PMCID: PMC7555853 DOI: 10.3390/ijms21186689] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022] Open
Abstract
Ultraviolet (UV) light is a natural genotoxic agent leading to the formation of photolesions endangering the genomic integrity and thereby the survival of living organisms. To prevent the mutagenetic effect of UV, several specific DNA repair mechanisms are mobilized to accurately maintain genome integrity at photodamaged sites within the complexity of genome structures. However, a fundamental gap remains to be filled in the identification and characterization of factors at the nexus of UV-induced DNA damage, DNA repair, and epigenetics. This review brings together the impact of the epigenomic context on the susceptibility of genomic regions to form photodamage and focuses on the mechanisms of photolesions recognition through the different DNA repair pathways.
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Vallejos-Almirall A, Folch-Cano C, Rosas A, Vergara C. Development of liquid chromatography tandem mass spectrometry method to quantify cyclobutane pyrimidine dimer photolyase activity by detection of 15mer oligonucleotide as reaction product. J Chromatogr A 2019; 1611:460577. [PMID: 31591040 DOI: 10.1016/j.chroma.2019.460577] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/11/2019] [Accepted: 09/26/2019] [Indexed: 11/15/2022]
Abstract
Ultraviolet radiation from sunlight causes DNA damage in skin cells by formation of photoproducts, mainly cyclobutane pyrimidine dimers (CPD), which are reverted by exogenous CPD-photolyase, preventing photoaging and skin cancer. High performance liquid chromatography tandem mass spectrometry method for quantification of CPD-photolyase activity was developed to search new enzymes sources for dermatology or clinical studies. The method was based in the enzymatic conversion of a 15mer oligonucleotide, containing a center cyclobutane thymidine dimer, to the restored 15mer oligonucleotide. Three ion pair reagent were evaluated by response surface methodology to increase mass intensities. Additionally, chromatographic separation of oligonucleotides was performed. The selected mobile phase was 15 mM diisopropylethylamine/20 mM hexafluoroisopropanol in methanol. The method allowed total separation between the oligonucleotides studied (resolution of 2.3) by using the core shell technology, which reduce the diffusion time of the analyte into the column, increasing the efficiency and minimizing the analysis time at 7 min. The mass spectrometry detection allowed a high selectivity and sensitivity. This is the first time where MRM modality has been employed with this specific purpose. Oligonucleotides recovery from reaction mixture was ∼ 94% and the limit of quantification was 13.4 nM for 15mer. The method was evaluated with a recombinant CPD-photolyase from Synechococcus leopoliensis using purified and crude protein extract. CPD-photolyase could be measured in terms of activity for enzymatic kinetics studies, for evaluation of UV-R effects in (micro)organisms and to identify new enzymes.
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Affiliation(s)
- A Vallejos-Almirall
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - C Folch-Cano
- Departamento de Agroindustrias, Facultad de Ingeniería Agrícola, Universidad de Concepción, Chillán, Chile
| | - A Rosas
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile
| | - C Vergara
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile.
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Draft Genome Sequence of the UV-Resistant Antarctic Bacterium Sphingomonas sp. Strain UV9. Microbiol Resour Announc 2019; 8:MRA01651-18. [PMID: 30801068 PMCID: PMC6376427 DOI: 10.1128/mra.01651-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/23/2019] [Indexed: 12/02/2022] Open
Abstract
We report the draft genome sequence of the Antarctic UV-resistant bacterium Sphingomonas sp. strain UV9. The strain has a genome size of 4.25 Mb, a 65.62% GC content, and 3,879 protein-coding sequences. We report the draft genome sequence of the Antarctic UV-resistant bacterium Sphingomonas sp. strain UV9. The strain has a genome size of 4.25 Mb, a 65.62% GC content, and 3,879 protein-coding sequences. Among others, genes encoding the resolving of the DNA damage produced by the UV irradiation were identified.
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A highly efficient and cost-effective recombinant production of a bacterial photolyase from the Antarctic isolate Hymenobacter sp. UV11. Extremophiles 2018; 23:49-57. [DOI: 10.1007/s00792-018-1059-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/24/2018] [Indexed: 01/12/2023]
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Ransom M, Bryan DS, Hesselberth JR. High-Resolution Mapping of Modified DNA Nucleobases Using Excision Repair Enzymes. Methods Mol Biol 2018; 1672:63-76. [PMID: 29043617 DOI: 10.1007/978-1-4939-7306-4_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Modification of DNA nucleobases has a profound effect on genome function. We developed a method that maps the positions of the modified DNA nucleobases throughout genomic DNA. This method couples in vitro nucleobase excision with massively parallel DNA sequencing to determine the location of modified DNA nucleobases with single base precision. This protocol was used to map uracil incorporation and UV photodimers in DNA, and a modification of the protocol has been used to map sparse modification events in cells. The Excision-seq protocol is broadly applicable to a variety of base modifications for which an excision enzyme is available.
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Affiliation(s)
- Monica Ransom
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - D Suzi Bryan
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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Bryan DS, Ransom M, Adane B, York K, Hesselberth JR. High resolution mapping of modified DNA nucleobases using excision repair enzymes. Genome Res 2014; 24:1534-42. [PMID: 25015380 PMCID: PMC4158761 DOI: 10.1101/gr.174052.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/08/2014] [Indexed: 12/20/2022]
Abstract
The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the locations of modified nucleobases in genomic DNA. We applied the Excision-seq method to map uracil in E. coli and budding yeast and discovered significant variation in uracil content, wherein uracil is excluded from the earliest and latest replicating regions of the genome, possibly driven by changes in nucleotide pool composition. We also used Excision-seq to identify sites of pyrimidine dimer formation induced by UV light exposure, where the method could distinguish between sites of cyclobutane and 6-4 photoproduct formation. These UV mapping data enabled analysis of local sequence bias around pyrimidine dimers and suggested a preference for an adenosine downstream from 6-4 photoproducts. The Excision-seq method is broadly applicable for high precision, genome-wide mapping of modified nucleobases with cognate repair enzymes.
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Affiliation(s)
- D Suzi Bryan
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Monica Ransom
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Biniam Adane
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Kerri York
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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Teranishi M, Nakamura K, Furukawa H, Hidema J. Identification of a phosphorylation site in cyclobutane pyrimidine dimer photolyase of rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 63:24-29. [PMID: 23220084 DOI: 10.1016/j.plaphy.2012.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/12/2012] [Indexed: 05/29/2023]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyase monomerises ultraviolet (UV) radiation-induced CPDs present in DNA, using energy from UVA and visible light. In plants, CPD photolyase activity is a crucial factor for determining UVB sensitivity. We previously demonstrated that native rice CPD photolyase is phosphorylated. To determine the phosphorylation site(s), the phosphorylation status of CPD photolyase was analyzed in rice varieties that have amino acid alterations at the potential phosphorylation sites. In wild-rice species, CPD photolyase was phosphorylated. In Poaceae species, CPD photolyase was phosphorylated in wheat but not in maize. Mutant CPD photolyase proteins, in which these putative phosphorylated residues were replaced with alanine residues, were synthesized using an insect cell-free translation system. A slow-migrating band disappeared when the serine residue at position 7 was mutated. A phospho-specific antibody was generated to determine whether this residue is phosphorylated in CPD photolyase. Only the slow-migrating band of native rice CPD photolyase was detected using this antibody, indicating that the serine residue at position 7 is a phosphorylation site in native rice CPD photolyase.
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Affiliation(s)
- Mika Teranishi
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
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Cannistraro VJ, Taylor JS. Acceleration of 5-methylcytosine deamination in cyclobutane dimers by G and its implications for UV-induced C-to-T mutation hotspots. J Mol Biol 2009; 392:1145-57. [PMID: 19631218 DOI: 10.1016/j.jmb.2009.07.048] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 07/15/2009] [Accepted: 07/16/2009] [Indexed: 10/20/2022]
Abstract
Sunlight-induced C-->T mutation hotspots occur most frequently at methylated CpG sites in tumor suppressor genes and are thought to arise from translesion synthesis past deaminated cyclobutane pyrimidine dimers (CPDs). While it is known that methylation enhances CPD formation in sunlight, little is known about the effect of methylation and sequence context on the deamination of 5-methylcytosine ((m)C) and its contribution to mutagenesis at these hotspots. Using an enzymatic method, we have determined the yields and deamination rates of C and (m)C in CPDs and find that the frequency of UVB-induced CPDs correlates with the oxidation potential of the flanking bases. We also found that the deamination of T(m)C and (m)CT CPDs is about 25-fold faster when flanked by G's than by A's, C's or T's in duplex DNA and appears to involve catalysis by the O6 group of guanine. In contrast, the first deamination of either C or (m)C in AC(m)CG with a flanking G was much slower (t(1/2) >250 h) and rate limiting, while the second deamination was much faster. The observation that C(m)CG dimers deaminate very slowly but at the same time correlate with C-->T mutation hotspots suggests that their repair must be slow enough to allow sufficient time for deamination. There are, however, a greater number of single C-->T mutations than CC-->TT mutations at C(m)CG sites even though the second deamination is very fast, which could reflect faster repair of doubly deaminated dimers.
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Jiang Y, Rabbi M, Kim M, Ke C, Lee W, Clark RL, Mieczkowski PA, Marszalek PE. UVA generates pyrimidine dimers in DNA directly. Biophys J 2009; 96:1151-8. [PMID: 19186150 DOI: 10.1016/j.bpj.2008.10.030] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 10/31/2008] [Indexed: 10/21/2022] Open
Abstract
There is increasing evidence that UVA radiation, which makes up approximately 95% of the solar UV light reaching the Earth's surface and is also commonly used for cosmetic purposes, is genotoxic. However, in contrast to UVC and UVB, the mechanisms by which UVA produces various DNA lesions are still unclear. In addition, the relative amounts of various types of UVA lesions and their mutagenic significance are also a subject of debate. Here, we exploit atomic force microscopy (AFM) imaging of individual DNA molecules, alone and in complexes with a suite of DNA repair enzymes and antibodies, to directly quantify UVA damage and reexamine its basic mechanisms at a single-molecule level. By combining the activity of endonuclease IV and T4 endonuclease V on highly purified and UVA-irradiated pUC18 plasmids, we show by direct AFM imaging that UVA produces a significant amount of abasic sites and cyclobutane pyrimidine dimers (CPDs). However, we find that only approximately 60% of the T4 endonuclease V-sensitive sites, which are commonly counted as CPDs, are true CPDs; the other 40% are abasic sites. Most importantly, our results obtained by AFM imaging of highly purified native and synthetic DNA using T4 endonuclease V, photolyase, and anti-CPD antibodies strongly suggest that CPDs are produced by UVA directly. Thus, our observations contradict the predominant view that as-yet-unidentified photosensitizers are required to transfer the energy of UVA to DNA to produce CPDs. Our results may help to resolve the long-standing controversy about the origin of UVA-produced CPDs in DNA.
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Affiliation(s)
- Yong Jiang
- Center for Biologically Inspired Materials and Material Systems, Duke University, Durham, North Carolina, USA
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Reardon JT, Sancar A. Purification and characterization of Escherichia coli and human nucleotide excision repair enzyme systems. Methods Enzymol 2006; 408:189-213. [PMID: 16793370 DOI: 10.1016/s0076-6879(06)08012-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Nucleotide excision repair is a multicomponent, multistep enzymatic system that removes a wide spectrum of DNA damage by dual incisions in the damaged strand on both sides of the lesion. The basic steps are damage recognition, dual incisions, resynthesis to replace the excised DNA, and ligation. Each step has been studied in vitro using cell extracts or highly purified repair factors and radiolabeled DNA of known sequence with DNA damage at a defined site. This chapter describes procedures for preparation of DNA substrates designed for analysis of damage recognition, either the 5' or the 3' incision event, excision (resulting from concerted dual incisions), and repair synthesis. Excision in Escherichia coli is accomplished by the three-subunit Uvr(A)BC excision nuclease and in humans by six repair factors: XPA, RPA, XPChR23B, TFIIH, XPFERCC1, and XPG. This chapter outlines methods for expression and purification of these essential repair factors and provides protocols for performing each of the in vitro repair assays with either the E. coli or the human excision nuclease.
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Affiliation(s)
- Joyce T Reardon
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, USA
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