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Nature Protocols Mar 2023The comet assay is a versatile method to detect nuclear DNA damage in individual eukaryotic cells, from yeast to human. The types of damage detected encompass DNA strand... (Review)
Review
The comet assay is a versatile method to detect nuclear DNA damage in individual eukaryotic cells, from yeast to human. The types of damage detected encompass DNA strand breaks and alkali-labile sites (e.g., apurinic/apyrimidinic sites), alkylated and oxidized nucleobases, DNA-DNA crosslinks, UV-induced cyclobutane pyrimidine dimers and some chemically induced DNA adducts. Depending on the specimen type, there are important modifications to the comet assay protocol to avoid the formation of additional DNA damage during the processing of samples and to ensure sufficient sensitivity to detect differences in damage levels between sample groups. Various applications of the comet assay have been validated by research groups in academia, industry and regulatory agencies, and its strengths are highlighted by the adoption of the comet assay as an in vivo test for genotoxicity in animal organs by the Organisation for Economic Co-operation and Development. The present document includes a series of consensus protocols that describe the application of the comet assay to a wide variety of cell types, species and types of DNA damage, thereby demonstrating its versatility.
Topics: Animals; Humans; Comet Assay; DNA Damage; Pyrimidine Dimers; Eukaryotic Cells; DNA
PubMed: 36707722
DOI: 10.1038/s41596-022-00754-y -
IUCrData Mar 2020In the title compound, CHClNOS, the dihedral angle between the pyrrolo-[1,2-]pyrimidine ring system (r.m.s. deviation = 0.008 Å) and the benzene ring is 80.2 (9)°....
In the title compound, CHClNOS, the dihedral angle between the pyrrolo-[1,2-]pyrimidine ring system (r.m.s. deviation = 0.008 Å) and the benzene ring is 80.2 (9)°. In the crystal, inversion dimers linked by pairs of C-H⋯O inter-actions generate (16) loops. Several aromatic π-π stacking inter-actions between the pyrrolo-[1,2-]pyrimidine rings, as well as separately between the pyrrolo and pyrimidine groups [shortest centroid-centroid separation = 3.5758 (14) Å], help to consolidate the packing.
PubMed: 36339475
DOI: 10.1107/S241431462000382X -
Annual Review of Biochemistry Jun 2023Transcription-coupled repair (TCR), discovered as preferential nucleotide excision repair of UV-induced cyclobutane pyrimidine dimers located in transcribed mammalian... (Review)
Review
Transcription-coupled repair (TCR), discovered as preferential nucleotide excision repair of UV-induced cyclobutane pyrimidine dimers located in transcribed mammalian genes compared to those in nontranscribed regions of the genome, is defined as faster repair of the transcribed strand versus the nontranscribed strand in transcribed genes. The phenomenon, universal in model organisms including , yeast, , mice, and humans, involves a translocase that interacts with both RNA polymerase stalled at damage in the transcribed strand and nucleotide excision repair proteins to accelerate repair. , a notable exception, exhibits TCR but lacks an obvious TCR translocase. Mutations inactivating TCR genes cause increased damage-induced mutagenesis in and severe neurological and UV sensitivity syndromes in humans. To date, only TCR has been reconstituted in vitro with purified proteins. Detailed investigations of TCR using genome-wide next-generation sequencing methods, cryo-electron microscopy, single-molecule analysis, and other approaches have revealed fascinating mechanisms.
Topics: Humans; Animals; Mice; Escherichia coli; Transcription, Genetic; Cryoelectron Microscopy; DNA Repair; Receptors, Antigen, T-Cell; Mammals
PubMed: 37001137
DOI: 10.1146/annurev-biochem-041522-034232 -
Biomolecules May 2021Genomic integrity is constantly insulted by solar ultraviolet (UV) radiation. Adaptative cellular mechanisms called DNA damage responses comprising DNA repair, cell... (Review)
Review
Genomic integrity is constantly insulted by solar ultraviolet (UV) radiation. Adaptative cellular mechanisms called DNA damage responses comprising DNA repair, cell cycle checkpoint, and apoptosis, are believed to be evolved to limit genomic instability according to the photoperiod during a day. As seen in many other key cellular metabolisms, genome surveillance mechanisms against genotoxic UV radiation are under the control of circadian clock systems, thereby exhibiting daily oscillations in their catalytic activities. Indeed, it has been demonstrated that nucleotide excision repair (NER), the sole DNA repair mechanism correcting UV-induced DNA photolesions, and ataxia-telangiectasia-mutated and Rad3-related (ATR)-mediated cell cycle checkpoint kinase are subjected to the robust control of the circadian clock. The molecular foundation for the circadian rhythm of UV-induced DNA damage responses in mammalian cells will be discussed.
Topics: Animals; Ataxia Telangiectasia Mutated Proteins; Circadian Rhythm; DNA Damage; DNA Repair; Humans; Ultraviolet Rays
PubMed: 34064641
DOI: 10.3390/biom11050715 -
Molecules (Basel, Switzerland) Sep 2022The photolyase family consists of flavoproteins with enzyme activity able to repair ultraviolet light radiation damage by photoreactivation. DNA damage by the formation... (Review)
Review
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.
Topics: DNA Repair; Deoxyribodipyrimidine Photo-Lyase; Flavoproteins; Pyrimidine Dimers; Pyrimidines; Pyrimidinones; Ultraviolet Rays
PubMed: 36144740
DOI: 10.3390/molecules27185998 -
International Journal of Molecular... Mar 2022Laccases (Lac) and tyrosinases (TYR) are mild oxidants with a great potential in research and industry. In this work, we review recent advances in their use in organic... (Review)
Review
Laccases (Lac) and tyrosinases (TYR) are mild oxidants with a great potential in research and industry. In this work, we review recent advances in their use in organic synthesis. We summarize recent examples of Lac-catalyzed oxidation, homocoupling and heterocoupling, and TYR-catalyzed -hydroxylation of phenols. We highlight the combination of Lac and TYR with other enzymes or chemical catalysts. We also point out the biological and pharmaceutical potential of the products, such as dimers of piceid, lignols, isorhamnetin, rutin, caffeic acid, 4-hydroxychalcones, thiols, hybrid antibiotics, benzimidazoles, benzothiazoles, pyrimidine derivatives, hydroxytyrosols, alkylcatechols, halocatechols, or dihydrocaffeoyl esters, etc. These products include radical scavengers; antibacterial, antiviral, and antitumor compounds; and building blocks for bioactive compounds and drugs. We summarize the available enzyme sources and discuss the scalability of their use in organic synthesis. In conclusion, we assume that the intensive use of laccases and tyrosinases in organic synthesis will yield new bioactive compounds and, in the long-term, reduce the environmental impact of industrial organic chemistry.
Topics: Chemistry Techniques, Synthetic; Laccase; Monophenol Monooxygenase; Oxidation-Reduction; Phenols
PubMed: 35408822
DOI: 10.3390/ijms23073462 -
Journal of Traditional and... May 2020Skin is the largest human organ that shields the inner body from contact with xenobiotic and genotoxic agents, and in this process, the skin's cellular genome faces... (Review)
Review
Skin is the largest human organ that shields the inner body from contact with xenobiotic and genotoxic agents, and in this process, the skin's cellular genome faces continuous stress due to direct exposure to these noxious factors. Accumulation of genetic stress results in genomic alterations leading to undesirable gene or protein alteration/expression in skin cells, which eventually causes the formation of non-melanoma skin cancers (NMSCs). Ultraviolet B (UVB) radiation from sun is the most prominent factor contributing to ∼5 million skin cancer cases (which are mostly NMSCs) in the United States (US) and western countries. UVB exposure causes aberrations in a range of biochemical and molecular pathways such as: thymine dimer formation, DNA damage, oxidative stress, inflammatory responses, altered cellular signaling, which ultimately contribute to the development of NMSCs. The focus of this review is to summarize the protective and preventive potential of silymarin and/or silibinin against UVB-induced NMSC in pre-clinical skin cancer studies. Over two decades of research has shown the strong potential of silibinin, a biologically active flavonolignan (crude form Silymarin) derived from milk thistle plant, against a wide range of cancers, including NMSCs. Silibinin protects against UVB-induced thymine dimer formation and in turn promotes DNA repair and/or initiates apoptosis in damaged cells via an increase in p53 levels. Additionally, silibinin has shown strong efficacy against NMSCs via its potential to target aberrant signaling pathways, and induction of anti-inflammatory responses. Overall, completed comprehensive studies suggest the potential use of silibinin to prevent and/or manage NMSCs in humans.
PubMed: 32670818
DOI: 10.1016/j.jtcme.2020.02.003 -
Journal of Biological Rhythms Feb 2020CRYPTOCHROMES (CRYs) are structurally related to ultraviolet (UV)/blue-sensitive DNA repair enzymes called photolyases but lack the ability to repair pyrimidine dimers... (Review)
Review
CRYPTOCHROMES (CRYs) are structurally related to ultraviolet (UV)/blue-sensitive DNA repair enzymes called photolyases but lack the ability to repair pyrimidine dimers generated by UV exposure. First identified in plants, CRYs have proven to be involved in light detection and various light-dependent processes in a broad range of organisms. In , CRY's best understood role is the cell-autonomous synchronization of circadian clocks. However, CRY also contributes to the amplitude of circadian oscillations in a light-independent manner, controls arousal and UV avoidance, influences visual photoreception, and plays a key role in magnetic field detection. Here, we review our current understanding of the mechanisms underlying CRY's various circadian and noncircadian functions in fruit flies.
Topics: Animals; Circadian Clocks; Circadian Rhythm; Cryptochromes; Drosophila; Drosophila Proteins; Light; Photoreceptor Cells, Invertebrate
PubMed: 31599203
DOI: 10.1177/0748730419878290 -
Genes Jul 2021The nucleotide excision repair (NER) is essential for the repair of ultraviolet (UV)-induced DNA damage, such as cyclobutane pyrimidine dimers (CPDs) and... (Review)
Review
The nucleotide excision repair (NER) is essential for the repair of ultraviolet (UV)-induced DNA damage, such as cyclobutane pyrimidine dimers (CPDs) and 6,4-pyrimidine-pyrimidone dimers (6,4-PPs). Alterations in genes of the NER can lead to DNA damage repair disorders such as Xeroderma pigmentosum (XP). XP is a rare autosomal recessive genetic disorder associated with UV-sensitivity and early onset of skin cancer. Recently, extensive research has been conducted on the functional relevance of splice variants and their relation to cancer. Here, we focus on the functional relevance of alternative splice variants of XP genes.
Topics: DNA Damage; DNA Repair; Humans; Mutation; Pyrimidine Dimers; RNA Splicing; Xeroderma Pigmentosum
PubMed: 34440347
DOI: 10.3390/genes12081173