DNA is one of the prime molecules, and its stability is of utmost importance for proper functioning and existence of all living systems. Genotoxic chemicals and radiations exert adverse effects on genome stability. Ultraviolet radiation (UVR) (mainly UV-B: 280–315？nm) is one of the powerful agents that can alter the normal state of life by inducing a variety of mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers as well as DNA strand breaks by interfering the genome integrity. To counteract these lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Additionally, double-strand break repair (by homologous recombination and nonhomologous end joining), SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms with the expense of specific gene products. This review deals with UV-induced alterations in DNA and its maintenance by various repair mechanisms. 1. Introduction The stratospheric ozone layer is continuously depleting due to the release of atmospheric pollutants such as chlorofluorocarbons (CFCs), chlorocarbons (CCs), and organo-bromides (OBs). Consequently there is an increase in the incidence of UV radiation (UVR) on the Earth’s surface [1] which is one of the most effective and carcinogenic exogenous agents that can interact with DNA and alter the genome integrity and may affect the normal life processes of all organisms ranging from prokaryotes to mammals [2–10]. However, wide variations in tolerance to UV-B among species and taxonomic groups have been reported. Moreover, ozone depletion followed by increased UV exposure has been predicted to continue throughout most of this century [11]. In all the groups of UVR (i.e., UV-A: 315–400？nm; UV-B: 280–315？nm; UV-C: <280？nm) UV-B radiation produces adverse effects on diverse habitats, even though most of the extraterrestrial UV-B is absorbed by the stratospheric ozone [12]. UV-A radiation has a poor efficiency in inducing DNA damage, because it is not absorbed by native DNA. UV-A and visible light energy (up to 670–700？nm) are able to generate singlet oxygen (1O2) that can damage DNA via indirect photosensitizing reactions [13]. UV-C radiation is quantitatively absorbed by oxygen and ozone in the Earth’s atmosphere, hence does not show much harmful effects on biota. Solar UV radiation is responsible for a wide range
References
[1]
D. Lubin and E. H. Jensen, “Effects of clouds and stratospheric ozone depletion on ultraviolet radiation trends,” Nature, vol. 377, no. 6551, pp. 710–713, 1995.
[2]
R. P. Sinha, H. D. Kumar, A. Kumar, and D. P. Hader, “Effects of UV-B irradiation on growth, survival, pigmentation and nitrogen metabolism enzymes in cyanobacteria,” Acta Protozoologica, vol. 34, no. 3, pp. 187–192, 1995.
[3]
R. P. Sinha, R. P. Rastogi, N. K. Ambasht, and D.-P. H？der, “Life of wetland cyanobacteria under enhancing solar UV-B radiation,” Proceedings of the National Academy of Sciences, India B, vol. 78, pp. 53–65, 2008.
[4]
D.-P. H？der and R. P. Sinha, “Solar ultraviolet radiation-induced DNA damage in aquatic organisms: potential environmental impact,” Mutation Research, vol. 571, no. 1-2, pp. 221–233, 2005.
[5]
E. C. Friedberg, G. C. Walker, W. Siede, R. D. Wood, R. A. Schultz, and T. Ellenberger, DNA Repair and Mutagenesis, ASM Press, Washington, DC, USA, 2006.
[6]
D.-P. H？der, H. D. Kumar, R. C. Smith, and R. C. Worrest, “Effects of solar UV radiation on aquatic ecosystems and interactions with climate change,” Photochemical and Photobiological Sciences, vol. 6, no. 3, pp. 267–285, 2007.
[7]
M. Norval, A. P. Cullen, F. R. De Gruijl et al., “The effects on human health from stratospheric ozone depletion and its interactions with climate change,” Photochemical and Photobiological Sciences, vol. 6, no. 3, pp. 232–251, 2007.
[8]
K. R. Solomon, “Effects of ozone depletion and UV-B radiation on humans and the environment,” Atmosphere—Ocean, vol. 46, no. 1, pp. 185–202, 2008.
[9]
M. Zeeshan and S. M. Prasad, “Differential response of growth, photosynthesis, antioxidant enzymes and lipid peroxidation to UV-B radiation in three cyanobacteria,” South African Journal of Botany, vol. 75, no. 3, pp. 466–474, 2009.
[10]
M. Llabrés, S. Agustí, P. Alonso-Laita, and G. J. Herndl, “Synechococcus and Prochlorococcus cell death induced by UV radiation and the penetration of lethal UVR in the Mediterranean Sea,” Marine Ecology Progress Series, vol. 399, pp. 27–37, 2010.
[11]
A. Tabazadeh, M. L. Santee, M. Y. Danilin, et al., “Quantifying denitrification and its effect on ozone recovery,” Science, vol. 288, no. 5470, pp. 1407–1411, 2000.
[12]
R. L. McKenzie, L. O. Bj？rn, A. Bais, and M. Ilyasd, “Changes in biologically active ultraviolet radiation reaching the Earth's surface,” Photochemical and Photobiological Sciences, vol. 2, no. 1, pp. 5–15, 2003.
[13]
R. G. Alscher, J. L. Donahue, and C. L. Cramer, “Reactive oxygen species and antioxidants: relationships in green cells,” Physiologia Plantarum, vol. 100, no. 2, pp. 224–233, 1997.
[14]
L. Chalker-Scott, “Survival and sex ratios of the intertidal copepod, Tigriopus californicus, following ultraviolet-B (290–320 nm) radiation exposure,” Marine Biology, vol. 123, no. 4, pp. 799–804, 1995.
[15]
M. J. Peak and J. G. Peak, “Single-strand breaks induced in Bacillus subtilis DNA by ultraviolet light: action spectrum and properties,” Photochemistry and Photobiology, vol. 35, no. 5, pp. 675–680, 1982.
[16]
M. J. Peak, J. G. Peak, M. P. Moehring, and R. B. Webb, “Ultraviolet action spectra for DNA dimer induction, lethality, and mutagenesis in Escherichia coli with emphasis on the UVB region,” Photochemistry and Photobiology, vol. 40, no. 5, pp. 613–620, 1984.
[17]
R. P. Sinha, M. Dautz, and D.-P. H？der, “A simple and efficient method for the quantitative analysis of thymine dimers in cyanobacteria, phytoplankton and macroalgae,” Acta Protozoologica, vol. 40, no. 3, pp. 187–195, 2001.
[18]
A. G. J. Buma, M. K. De Boer, and P. Boelen, “Depth distributions of DNA damage in antarctic marine phyto and bacterioplankton exposed to summertime UV radiation,” Journal of Phycology, vol. 37, no. 2, pp. 200–208, 2001.
[19]
H. Pakker, C. A. C. Beekman, and A. M. Breeman, “Efficient photoreactivation of UVBR-induced DNA damage in the sublittoral macroalga Rhodymenia pseudopalmata (Rhodophyta),” European Journal of Phycology, vol. 35, no. 2, pp. 109–114, 2000.
[20]
F. E. Quaite, B. M. Sutherland, and J. C. Sutherland, “Quantitation of pyrimidine dimers in DNA from UVB-irradiated alfalfa (Medicago sativa L.) seedlings,” Applied and Theoretical Electrophoresis, vol. 2, no. 6, pp. 171–175, 1992.
[21]
B. Stein, H. J. Rahmsdorf, A. Steffen, M. Litfin, and P. Herrlich, “UV-induced DNA damage is an intermediate step in UV-induced expression of human immunodeficiency virus type 1, collagenase, c-fos, and metallothionein,” Molecular and Cellular Biology, vol. 9, no. 11, pp. 5169–5181, 1989.
[22]
R. P. Sinha and D.-P. H？der, “UV-induced DNA damage and repair: a review,” Photochemical and Photobiological Sciences, vol. 1, no. 4, pp. 225–236, 2002.
[23]
K. M. D. Lima-Bessa, M. G. Armelini, V. Chigan？as et al., “CPDs and 6–4PPs play different roles in UV-induced cell death in normal and NER-deficient human cells,” DNA Repair, vol. 7, no. 2, pp. 303–312, 2008.
[24]
K. McAteer, Y. Jing, J. Kao, J.-S. Taylor, and M. A. Kennedy, “Solution-state structure of a DNA dodecamer duplex containing a cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA,” Journal of Molecular Biology, vol. 282, no. 5, pp. 1013–1032, 1998.
[25]
J.-H. Lee, G.-S. Hwang, and B.-S. Choi, “Solution structure of a DNA decamer duplex containing the stable T·G base pair of the pyrimidine(6–4)pyrimidone photoproduct [(6–4) adduct]: implications for the highly specific T → C transition of the (6–4) adduct,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 12, pp. 6632–6636, 1999.
[26]
J.-H. Lee, S.-H. Bae, and B.-S. Choi, “The Dewar photoproduct of thymidylyl( → )-thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 9, pp. 4591–4596, 2000.
[27]
DeLano Scientific LLC, 400 Oyster Point Blvd., Suite 213, South San Francisco, CA 94080-1918, USA. http://www.pymol.org/.
[28]
R. P. Sinha, M. Krywult, and D.-P. H？der, “Effects of ultraviolet, monochromatic and PAR waveband on nitrate reductase activity and pigmentation in a rice field cyanobacterium, Anabaena sp,” Acta Hydrobiologica, vol. 2, pp. 105–112, 1998.
[29]
R. P. Sinha, S. P. Singh, and D.-P. H？der, “Database on mycosporines and mycosporine-like amino acids (MAAs) in fungi, cyanobacteria, macroalgae, phytoplankton and animals,” Journal of Photochemistry and Photobiology B, vol. 89, no. 1, pp. 29–35, 2007.
[30]
A. B. Britt, “Repair of DNA damage induced by solar UV,” Photosynthesis Research, vol. 81, no. 2, pp. 105–112, 2004.
[31]
R. P. Rastogi, Richa, R. P. Sinha, S. P. Singh, and D.-P. H？der, “Photoprotective compounds from marine organisms,” Journal of Industrial Microbiology and Biotechnology, vol. 37, no. 6, pp. 537–558, 2010.
[32]
R. P. Rastogi, Richa, S. P. Singh, D.-P. H？der, and R. P. Sinha, “Mycosporine-like amino acids profile and their activity under PAR and UVR in a hot-spring cyanobacterium Scytonema sp. HKAR-3,” Australian Journal of Botany, vol. 58, no. 4, pp. 286–293, 2010.
[33]
Z. Xie, Y. Wang, Y. Liu, and Y. Liu, “Ultraviolet-B exposure induces photo-oxidative damage and subsequent repair strategies in a desert cyanobacterium Microcoleus vaginatus Gom,” European Journal of Soil Biology, vol. 45, no. 4, pp. 377–382, 2009.
[34]
H. Wiseman and B. Halliwell, “Damage to DNA by reactive oxygen and nitrogen species: role in inflammatory disease and progression to cancer,” Biochemical Journal, vol. 313, no. 1, pp. 17–29, 1996.
[35]
J.-S. Taylor, “DNA, sunlight, and skin cancer,” Journal of Chemical Education, vol. 67, no. 10, pp. 833–841, 1990.
[36]
T. Lindahl, “Instability and decay of the primary structure of DNA,” Nature, vol. 362, no. 6422, pp. 709–715, 1993.
[37]
M. Valko, C. J. Rhodes, J. Moncol, M. Izakovic, and M. Mazur, “Free radicals, metals and antioxidants in oxidative stress-induced cancer,” Chemico-Biological Interactions, vol. 160, no. 1, pp. 1–40, 2006.
[38]
B. Halliwell and J. Gutteridge, Free Radicals in Biology and Medicine, Oxford University Press, Oxford, UK, 4th edition, 2007.
[39]
M. Dizdaroglu, “Oxidative damage to DNA in mammalian chromatin,” Mutation Research, vol. 275, no. 3–6, pp. 331–342, 1992.
[40]
M. Valko, D. Leibfritz, J. Moncol, M. T. D. Cronin, M. Mazur, and J. Telser, “Free radicals and antioxidants in normal physiological functions and human disease,” International Journal of Biochemistry and Cell Biology, vol. 39, no. 1, pp. 44–84, 2007.
[41]
Y.-H. You, P. E. Szabo, and G. P. Pfeifer, “Cyclobutane pyrimidine dimers form preferentially at the major p53 mutational hotspot in UVB-induced mouse skin tumors,” Carcinogenesis, vol. 21, no. 11, pp. 2113–2117, 2000.
[42]
J.-L. Ravanat, T. Douki, and J. Cadet, “Direct and indirect effects of UV radiation on DNA and its components,” Journal of Photochemistry and Photobiology B, vol. 63, no. 1–3, pp. 88–102, 2001.
[43]
J. Cadet, E. Sage, and T. Douki, “Ultraviolet radiation-mediated damage to cellular DNA,” Mutation Research, vol. 571, no. 1-2, pp. 3–17, 2005.
[44]
D. I. Pattison and M. J. Davies, “Actions of ultraviolet light on cellular structures,” in Cancer: Cell Structures, Carcinogens and Genomic Instability, L. P. Bignold, Ed., Birkh？user, Switzerland, 2006.
[45]
J. S. Taylor, H. F. Lu, and J. J. Kotyk, “Quantitative conversion of the (6–4) photoproduct of TpdC to its Dewar valence isomer upon exposure to simulated sunlight,” Photochemistry and Photobiology, vol. 51, no. 2, pp. 161–167, 1990.
[46]
S. Courdavault, C. Baudouin, M. Charveron et al., “Repair of the three main types of bipyrimidine DNA photoproducts in human keratinocytes exposed to UVB and UVA radiations,” DNA Repair, vol. 4, no. 7, pp. 836–844, 2005.
[47]
T. Carell and R. Epple, “Repair of UV light induced DNA lesions: a comparative study with model compounds,” European Journal of Organic Chemistry, no. 7, pp. 1245–1258, 1998.
[48]
T. Douki, A. Reynaud-Angelin, J. Cadet, and E. Sage, “Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar UVA radiation,” Biochemistry, vol. 42, no. 30, pp. 9221–9226, 2003.
[49]
J. E. Donnellan Jr. and R. B. Setlow, “Thymine photoproducts but not thymine dinners found in ultraviolet-irradiated bacterial spores,” Science, vol. 149, no. 3681, pp. 308–310, 1965.
[50]
M. M. Becker and Z. Wang, “Origin of ultraviolet damage in DNA,” Journal of Molecular Biology, vol. 210, no. 3, pp. 429–438, 1989.
[51]
V. Lyamichev, “Unusual conformation of (dA)n.(dT)n-tracts as revealed by cyclobutane thymine-thymine dimer formation,” Nucleic Acids Research, vol. 19, no. 16, pp. 4491–4496, 1991.
[52]
J. R. Pehrson and L. H. Cohen, “Effects of DNA looping on pyrimidine dimer formation,” Nucleic Acids Research, vol. 20, no. 6, pp. 1321–1324, 1992.
[53]
A. Aboussekhra and F. Thoma, “TATA-binding protein promotes the selective formation of UV-induced (6–4)-photoproducts and modulates DNA repair in the TATA box,” EMBO Journal, vol. 18, no. 2, pp. 433–443, 1999.
[54]
T. Douki and J. Cadet, “Individual determination of the yield of the main UV-induced dimeric pyrimidine photoproducts in DNA suggests a high mutagenicity of CC photolesions,” Biochemistry, vol. 40, no. 8, pp. 2495–2501, 2001.
[55]
A. S. Balajee and V. A. Bohr, “Genomic heterogeneity of nucleotide excision repair,” Gene, vol. 250, no. 1-2, pp. 15–30, 2000.
[56]
J. M. Gale, K. A. Nissen, and M. J. Smerdon, “UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 84, no. 19, pp. 6644–6648, 1987.
[57]
R. M. Tyrrell, “Induction of pyrimidine dimers in bacterial DNA by 365 nm radiation,” Photochemistry and Photobiology, vol. 17, no. 1, pp. 69–73, 1973.
[58]
E. Kvam and R. M. Tyrrell, “Induction of oxidative DNA base damage in human skin cells by UV and near visible radiation,” Carcinogenesis, vol. 18, no. 12, pp. 2379–2384, 1997.
[59]
D. Perdiz, P. Gróf, M. Mezzina, O. Nikaido, E. Moustacchi, and E. Sage, “Distribution and repair of bipyrimidine photoproducts in solar UV-irradiated mammalian cells: possible role of dewar photoproducts in solar mutagenesis,” Journal of Biological Chemistry, vol. 275, no. 35, pp. 26732–26742, 2000.
[60]
S. Courdavault, C. Baudouin, M. Charveron, A. Favier, J. Cadet, and T. Douki, “Larger yield of cyclobutane dimers than 8-oxo-7,8-dihydroguanine in the DNA of UVA-irradiated human skin cells,” Mutation Research, vol. 556, no. 1-2, pp. 135–142, 2004.
[61]
D. G. T. Su, J.-S. A. Taylor, and M. L. Gross, “A new photoproduct of 5-methylcytosine and adenine characterized by high-performance liquid chromatography and mass spectrometry,” Chemical Research in Toxicology, vol. 23, no. 3, pp. 474–479, 2010.
[62]
K. L. Wierzchowski and D. Shugar, “Photochemistry of cytosine nucleosides and nucleotides, II,” Acta Biochimica Polonica, vol. 8, pp. 219–234, 1961.
[63]
R. J. Boorstein, T. P. Hilbert, R. P. Cunningham, and G. W. Teebor, “Formation and stability of repairable pyrimidine photohydrates in DNA,” Biochemistry, vol. 29, no. 46, pp. 10455–10460, 1990.
[64]
N. J. Duker and P. E. Gallagher, “Purine photoproducts,” Photochemistry and Photobiology, vol. 48, no. 1, pp. 35–39, 1988.
[65]
S. Kumar, N. D. Sharma, R. J. Davies, D. W. Phillipson, and J. A. McCloskey, “The isolation and characterisation of a new type of dimeric adenine photoproduct in UV-irradiated deoxyadenylates,” Nucleic Acids Research, vol. 15, no. 3, pp. 1199–1216, 1987.
[66]
T. M. G. Koning, R. J. H. Davies, and R. Kaptein, “The solution structure of the intramolecular photoproduct of d(TpA) derived with the use of NMR and a combination of distance geometry and molecular dynamics,” Nucleic Acids Research, vol. 18, no. 2, pp. 277–284, 1990.
[67]
S. N. Bose, R. J. H. Davies, S. K. Sethi, and J. A. McCloskey, “Formation of an adenine-thymine photoadduct in the deoxydinucleoside monophosphate d(TpA) and in DNA,” Science, vol. 220, no. 4598, pp. 723–725, 1983.
[68]
S. N. Bose and R. J. Davies, “The photoreactivity of T-A sequences in oligodeoxyribonucleotides and DNA,” Nucleic Acids Research, vol. 12, no. 20, pp. 7903–7914, 1984.
[69]
P. H. Clingen, R. Jeremy, and H. Davies, “Quantum yields of adenine photodimerization in poly(deoxyadenylic acid) and DNA,” Journal of Photochemistry and Photobiology B, vol. 38, no. 1, pp. 81–87, 1997.
[70]
D. Porschke, “A specific photoreaction in polydeoxyadenylic acid,” Proceedings of the National Academy of Sciences of the United States of America, vol. 70, no. 9, pp. 2683–2686, 1973.
[71]
N. D. Sharma and R. J. H. Davies, “Extent of formation of a dimeric adenine photoproduct in polynucleotides and DNA,” Journal of Photochemistry and Photobiology B, vol. 3, no. 2, pp. 247–258, 1989.
[72]
R. O. Rahn, “Search for an adenine photoproduct in DNA,” Nucleic Acids Research, vol. 3, no. 4, pp. 879–890, 1976.
[73]
P. W. Doetsch, T. H. Zastawny, A. M. Martin, and M. Dizdaroglu, “Monomeric base damage products from adenine, guanine and thymine induced by exposure of DNA to ultraviolet radiation,” Biochemistry, vol. 34, pp. 737–742, 1995.
[74]
D. B. Hall, R. E. Holmlin, and J. K. Barton, “Oxidative DNA damage through long-range electron transfer,” Nature, vol. 382, no. 6593, pp. 731–735, 1996.
[75]
M. Lukin and C. de los Santos, “NMR structures of damaged DNA,” Chemical Reviews, vol. 106, no. 2, pp. 607–686, 2006.
[76]
J.-H. Lee, G.-S. Hwang, J.-K. Kim, and B.-S. Choi, “The solution structure of DNA decamer duplex containing the Dewar product of thymidylyl( → )thymidine by NMR and full relaxation matrix refinement,” FEBS Letters, vol. 428, no. 3, pp. 269–274, 1998.
[77]
S. N. Rao, J. W. Keepers, and P. Kollman, “The structure of d(CGCGAAT[ ]TCGCG)-d(CGCGAATTCGCG): the incorporation of a thymine photodimer into a B-DNA helix,” Nucleic Acids Research, vol. 12, no. 11, pp. 4789–4807, 1984.
[78]
F. E. Hruska, D. J. Wood, K. K. Ogilvie, and J. L. Charlton, “A proton magnetic resonance study of the ultraviolet photoproduct of d(TpT) in aqueous solution,” Canadian Journal of Chemistry, vol. 53, pp. 1193–1203, 1975.
[79]
L.-S. Kan, L. Voituriez, and J. Cadet, “Nuclear magnetic resonance studies of Cis-Syn, Trans-Syn, and 6–4 photodimers of thymidylyl( – )thymidine monophosphate and Cis-Syn photodimers of thymidylyl( – )thymidine cyanoethyl phosphotriester,” Biochemistry, vol. 27, no. 15, pp. 5796–5803, 1988.
[80]
J.-H. Lee, C.-J. Park, J.-S. Shin, T. Ikegami, H. Akutsu, and B.-S. Choi, “NMR structure of the DNA decamer duplex containing double T.G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex,” Nucleic Acids Research, vol. 32, no. 8, pp. 2474–2481, 2004.
[81]
C. Suquet and M. J. Smerdon, “UV damage to DNA strongly influences its rotational setting on the histone surface of reconstituted nucleosomes,” Journal of Biological Chemistry, vol. 268, no. 32, pp. 23755–23757, 1993.
[82]
A. E. Rumora, K. M. Kolodziejczak, A. M. Wagner, and M. E. Nú？ez, “Thymine dimer-induced structural changes to the DNA duplex examined with reactive probes,” Biochemistry, vol. 47, no. 49, pp. 13026–13035, 2008.
[83]
J.-K. Kim and B.-S. Choi, “The solution structure of DNA duplex-decamer containing the (6–4) photoproduct of thymidylyl( → )thymidine by NMR and relaxation matrix refinement,” European Journal of Biochemistry, vol. 228, no. 3, pp. 849–854, 1995.
[84]
G.-S. Hwang, J.-K. Kim, and B.-S. Choi, “NMR structural studies of DNA decamer duplex containing the Dewar photoproduct of thymidylyl( → )thymidine: conformational changes of the oligonucleotide duplex by photoconversion of a (6–4) adduct to its Dewar valence isomer,” European Journal of Biochemistry, vol. 235, no. 1-2, pp. 359–365, 1996.
[85]
D. A. Pearlman, S. R. Holbrook, D. H. Pirkle, and S.-H. Kim, “Molecular models for DNA damaged by photoreaction,” Science, vol. 227, no. 4692, pp. 1304–1308, 1985.
[86]
T. V. Wang and K. C. Smith, “Postreplication repair in ultraviolet-irradiated human fibroblasts: formation and repair of DNA double-strand breaks,” Carcinogenesis, vol. 7, no. 3, pp. 389–392, 1986.
[87]
T. A. Slieman and W. L. Nicholson, “Artificial and solar UV radiation induces strand breaks and cyclobutane pyrimidine dimers in Bacillus subtilis spore DNA,” Applied and Environmental Microbiology, vol. 66, no. 1, pp. 199–205, 2000.
[88]
C. Baumstark-Khan, U. Hentschel, Y. Nikandrova, J. Krug, and G. Horneck, “Fluorometric analysis of DNA unwinding (FADU) as a method for detecting repair-induced DNA strand breaks in UV-irradiated mammalian cells,” Photochemistry and Photobiology, vol. 72, no. 4, pp. 477–484, 2000.
[89]
R. P. Rastogi, S. P. Singh, D.-P. H？der, and R. P. Sinha, “Detection of reactive oxygen species (ROS) by the oxidant-sensing probe , -dichlorodihydrofluorescein diacetate in the cyanobacterium Anabaena variabilis PCC 7937,” Biochemical and Biophysical Research Communications, vol. 397, no. 3, pp. 603–607, 2010.
[90]
C. L. Limoli, E. Giedzinski, W. M. Bonner, and J. E. Cleaver, “UV-induced replication arrest in the xeroderma pigmentosum variant leads to DNA doublestrand breaks, γ-H2AX formation, and Mre11 relocalization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 1, pp. 233–238, 2002.
[91]
L. F. Z. Batista, B. Kaina, R. Meneghini, and C. F. M. Menck, “How DNA lesions are turned into powerful killing structures: insights from UV-induced apoptosis,” Mutation Research, vol. 681, no. 2-3, pp. 197–208, 2009.
[92]
T. R. Dunkern and B. Kaina, “Cell proliferation and DNA breaks are involved in ultraviolet light-induced apoptosis in nucleotide excision repair-deficient Chinese hamster cells,” Molecular Biology of the Cell, vol. 13, no. 1, pp. 348–361, 2002.
[93]
W. P. Roos and B. Kaina, “DNA damage-induced cell death by apoptosis,” Trends in Molecular Medicine, vol. 12, no. 9, pp. 440–450, 2006.
[94]
M. M. Vilenchik and A. G. Knudson, “Endogenous DNA double-strand breaks: production, fidelity of repair, and induction of cancer,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 22, pp. 12871–12876, 2003.
[95]
A. Takahashi and T. Ohnishi, “Does γH2AX foci formation depend on the presence of DNA double strand breaks?” Cancer Letters, vol. 229, no. 2, pp. 171–179, 2005.
[96]
G. Wang, L. M. Hallberg, E. Saphier, and E. W. Englander, “Short interspersed DNA element-mediated detection of UVB-induced DNA damage and repair in the mouse genome, in vitro, and in vivo in skin,” Mutation Research, vol. 433, no. 3, pp. 147–157, 1999.
[97]
G. Wang, L. M. Hallberg, E. Saphier, and E. W. Englander, “Pyrimidine (6–4) pyrimidone photoproduct mapping after sub-lethal UVC doses: nucleotide resolution using terminal transferase-dependent PCR,” Photochemistry and Photobiology, vol. 82, pp. 1370–1376, 2006.
[98]
A. Kumar, M. B. Tyagi, and P. N. Jha, “Evidences showing ultraviolet-B radiation-induced damage of DNA in cyanobacteria and its detection by PCR assay,” Biochemical and Biophysical Research Communications, vol. 318, no. 4, pp. 1025–1030, 2004.
[99]
A. Karakoula, M. D. Evans, I. D. Podmore, P. E. Hutchinson, J. Lunec, and M. S. Cooke, “Quantification of UVR-induced DNA damage: global- versus gene-specific levels of thymine dimers,” Journal of Immunological Methods, vol. 277, no. 1-2, pp. 27–37, 2003.
[100]
P. L. Olive, J. P. Banath, and R. E. Durand, “Heterogeneity in radiation-induced DNA damage and repair in tumor and normal cells measured using the 'comet' assay,” Radiation Research, vol. 122, no. 1, pp. 86–94, 1990.
[101]
N. Morley, A. Rapp, H. Dittmar et al., “UVA-induced apoptosis studied by the new apo/necro-Comet-assay which distinguishes viable, apoptotic and necrotic cells,” Mutagenesis, vol. 21, no. 2, pp. 105–114, 2006.
[102]
J. L. R. Roti and W. D. Wright, “Visualization of DNA loops in nucleoids from HeLa cells: assays for DNA damage and repair,” Cytometry, vol. 8, no. 5, pp. 461–467, 1987.
[103]
P. Sestili, C. Martinelli, and V. Stocchi, “The fast halo assay: an improved method to quantify genomic DNA strand breakage at the single-cell level,” Mutation Research, vol. 607, no. 2, pp. 205–214, 2006.
[104]
J. Chen, K. Jin, M. Chen et al., “Early detection of DNA strand breaks in the brain after transient focal ischemia: implications for the role of DNA damage in apoptosis and neuronal cell death,” Journal of Neurochemistry, vol. 69, no. 1, pp. 232–245, 1997.
[105]
C. Stecco, A. Porzionato, V. Macchi et al., “Detection of apoptosis in human brainstem by TUNEL assay,” Italian Journal of Anatomy and Embryology, vol. 110, no. 4, pp. 255–260, 2005.
[106]
F. Xu, J. M. Vlak, A. P .M. Eker, and M. M. van Oers, “DNA photolyases of Chrysodeixis chalcites nucleopolyhedrovirus target to the nucleus and interact with chromosomes and mitotic spindle structures,” Journal of General Virology, vol. 91, pp. 907–914, 2010.
[107]
S. K. Murthy and D. J. Demetrick, “New approaches to fluorescence in situ hybridization,” Methods in Molecular Biology, vol. 319, pp. 237–259, 2006.
[108]
S. Kumari, R. P. Rastogi, K. L. Singh, S. P. Singh, and R. P. Sinha, “DNA damage: detection strategies,” EXCLI Journal, vol. 7, pp. 44–62, 2008.
[109]
G. Koopman, C. P. Reutelingsperger, G. A. Kuiiten, R. M. Keehnen, and S. T. Pals, “Annexin V for flow cytometric detection of phosphotidylserine expression on B cells undergoing apoptosis,” Blood, vol. 4, pp. 1415–1420, 1994.
[110]
J. W. Bickham, “Flow cytometry as a technique to monitor the effects of environmental genotoxins on wild life populations,” in In Situ Evaluation of Biological Hazards of Environmental Pollutants, S. S. Sandhu, W. R. Lower, F. J. de Serres, W. A. Suk, and R. R. Tice, Eds., pp. 97–108, Plenum Press, New York, NY, USA, 1990.
[111]
H. Watanabe, Y. Murata, M. Miura, M. Hasegawa, T. Kawamoto, and H. Shibuya, “In-vivo visualization of radiation-induced apoptosis using 125I-annexin V,” Nuclear Medicine Communications, vol. 27, no. 1, pp. 81–89, 2006.
[112]
M. Klisch, R. P. Sinha, E. W. Helbling, and D.-P. H？der, “Induction of thymine dimers by solar radiation in natural freshwater phytoplankton assemblages in Patagonia, Argentina,” Aquatic Sciences, vol. 67, no. 1, pp. 72–78, 2005.
[113]
S. Otero, E. Nú？ez-Olivera, J. Martínez-Abaigar, R. Tomás, M. Arróniz-Crespo, and N. Beaucourt, “Effects of cadmium and enhanced UV radiation on the physiology and the concentration of UV-absorbing compounds of the aquatic liverwort Jungermannia exsertifolia subsp. cordifolia,” Photochemical and Photobiological Sciences, vol. 5, no. 8, pp. 760–769, 2006.
[114]
D. L. Mitchell, C. A. Haipek, and J. M. Clarkson, “(6–4)photoproducts are removed from the DNA of UV-irradiated mammalian cells more efficiently than cyclobutane pyrimidine dimers,” Mutation Research, vol. 143, no. 3, pp. 109–112, 1985.
[115]
W. H. Jeffrey, P. Aas, M. M. Lyons, R. B. Coffin, R. J. Pledger, and D. L. Mitchell, “Ambient solar radiation-induced photodamage in marine bacterioplankton,” Photochemistry and Photobiology, vol. 64, no. 3, pp. 419–427, 1996.
[116]
H. C. Birnboim and J. J. Jevcak, “Fluorometric method for rapid detection of DNA strand breaks in human white blood cells produced by low doses of radiation,” Cancer Research, vol. 41, no. 5, pp. 1889–1892, 1981.
[117]
T. Iwasa, S. Tokutomi, and F. Tokunaga, “Photoreactivation of Halobacterium halobium: action spectrum and role of pigmentation,” Photochemistry and Photobiology, vol. 47, pp. 267–270, 1988.
[118]
A. Yasui, A. P. M. Eker, S. Yasuhira et al., “A new class of DNA photolyases present in various organisms including aplacental mammals,” EMBO Journal, vol. 13, no. 24, pp. 6143–6151, 1994.
[119]
A. Kiener, I. Husain, A. Sancar, and C. Walsh, “Purification and properties of Methanobacterium thermoautotrophicum DNA photolyase,” Journal of Biological Chemistry, vol. 264, no. 23, pp. 13880–13887, 1989.
[120]
M. Fujihashi, N. Numoto, Y. Kobayashi et al., “Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor,” Journal of Molecular Biology, vol. 365, no. 4, pp. 903–910, 2007.
[121]
K. Malhotra, S.-T. Kim, and A. Sancar, “Characterization of a medium wavelength type DNA photolyase: purification and properties of photolyase from Bacillus firmus,” Biochemistry, vol. 33, no. 29, pp. 8712–8718, 1994.
[122]
J. L. Johnson, S. Hamm-Alvarez, G. Payne, G. B. Sancar, K. V. Rajagopalan, and A. Sancar, “Identification of the second chromophore of Escherichia coli and yeast DNA photolyases as 5,10-methenyltetrahydrofolate,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 7, pp. 2046–2050, 1988.
[123]
G. B. Sancar, F. W. Smith, M. C. Lorence, C. S. Rupert, and A. Sancar, “Sequences of the Escherichia coli photolyase gene and protein,” Journal of Biological Chemistry, vol. 259, no. 9, pp. 6033–6038, 1984.
[124]
A. P. M. Eker, P. Kooiman, J. K. C. Hessels, and A. Yasui, “DNA photoreactivating enzyme from the cyanobacterium Anacystis nidulans,” Journal of Biological Chemistry, vol. 265, no. 14, pp. 8009–8015, 1990.
[125]
W.-O. Ng, R. Zentella, Y. Wang, J.-S. A. Taylor, and H. B. Pakrasi, “phrA, the major photoreactivating factor in the cyanobacterium Synechocystis sp. strain PCC 6803 codes for a cyclobutane-pyrimidine-dimer- specific DNA photolyase,” Archives of Microbiology, vol. 173, no. 5-6, pp. 412–417, 2000.
[126]
A. P. Eker, R. H. Dekker, and W. Berends, “Photoreactivating enzyme from Streptomyces griseus-IV. On the nature of the chromophoric cofactor in Streptomyces griseus photoreactivating enzyme,” Photochemistry and Photobiology, vol. 33, no. 1, pp. 65–72, 1981.
[127]
K. A. O'Connor, M. J. McBride, M. West et al., “Photolyase of Myxococcus xanthus, a Gram-negative eubacterium, is more similar to photolyases found in archaea and "higher" eukaryotes than to photolyases of other eubacteria,” Journal of Biological Chemistry, vol. 271, no. 11, pp. 6252–6259, 1996.
[128]
E. N. Worthington, I. H. Kavakli, G. Berrocal-Tito, B. E. Bondo, and A. Sancar, “Purification and characterization of three members of the photolyase/cryptochrome family blue-light photoreceptors from Vibrio cholerae,” Journal of Biological Chemistry, vol. 278, no. 40, pp. 39143–39154, 2003.
[129]
H. Yajima, H. Inoue, A. Oikawa, and A. Yasui, “Cloning and functional characterization of a eucaryotic DNA photolyase gene from Neurospora crassa,” Nucleic Acids Research, vol. 19, no. 19, pp. 5359–5362, 1991.
[130]
A. P. M. Eker, H. Yajima, and A. Yasui, “DNA photolyase from the fungus Neurospora crassa. Purification, characterization and comparison with other photolyases,” Photochemistry and Photobiology, vol. 60, no. 2, pp. 125–133, 1994.
[131]
T. Todo, H. Takemori, H. Ryo et al., “A new photoreactivating enzyme that specifically repairs ultraviolet light-induced (6–4)photoproducts,” Nature, vol. 361, no. 6410, pp. 371–374, 1993.
[132]
A. Sancar, “No "End of history" for photolyases,” Science, vol. 272, no. 5258, pp. 48–49, 1996.
[133]
S. Yasuhira and A. Yasui, “Visible light-inducible photolyase gene from the goldfish Carassius auratus,” Journal of Biological Chemistry, vol. 267, no. 36, pp. 25644–25647, 1992.
[134]
T. S. Mikkelsen, M. J. Wakefield, B. Aken et al., “Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences,” Nature, vol. 447, no. 7141, pp. 167–177, 2007.
[135]
T. Todo, S.-T. Kim, K. Hitomi et al., “Flavin adenine dinucleotide as a chromophore of the Xenopus (6–4)photolyase,” Nucleic Acids Research, vol. 25, no. 4, pp. 764–768, 1997.
[136]
Q. Pang and J. B. Hays, “UV-B-inducible and temperature-sensitive photoreactivation of cyclobutane pyrimidine dimers in Arabidopsis thaliana,” Plant Physiology, vol. 95, no. 2, pp. 536–543, 1991.
[137]
J. L. Petersen, D. W. Lang, and G. D. Small, “Cloning and characterization of a class II DNA photolyase from Chlamydomonas,” Plant Molecular Biology, vol. 40, no. 6, pp. 1063–1071, 1999.
[138]
S. Takahashi, N. Nakajima, H. Saji, and N. Kondo, “Diurnal changes of cucumber CPD photolyase gene (CsPHR) expression and its physiological role in growth under UV-B irradiation,” Plant and Cell Physiology, vol. 43, pp. 342–349, 2002.
[139]
Y. Takeuchi, T. Inoue, K. Takemura, et al., “Induction and inhibition of cyclobutane pyrimidine dimer photolyase in etiolated cucumber (Cucumis sativus) cotyledons after ultraviolet irradiation depends on wavelength,” Journal of Plant Research, vol. 120, pp. 365–374, 2007.
[140]
J. E. Trosko and V. H. Mansour, “Photoreactivation of ultraviolet light-induced pyrimidine dimers in Ginkgo cells grown in vitro,” Mutation Research, vol. 7, no. 1, pp. 120–121, 1969.
[141]
R. Taylor, A. Tobin, and C. Bray, “Nucleotide sequence of an Arabidopsis cDNA At-phrII encoding a protein with high homology to the class II CPD photolyases present in higher eukaryotes,” Plant Physiology, vol. 112, pp. 862–863, 1996.
[142]
V. Srinivasan, W. M. Schnitzlein, and D. N. Tripathy, “Fowlpox virus encodes a novel DNA repair enzyme, CPD-photolyase, that restores infectivity of UV light-damaged virus,” Journal of Virology, vol. 75, no. 4, pp. 1681–1688, 2001.
[143]
C. L. Afonso, E. R. Tulman, Z. Lu, E. Oma, G. F. Kutish, and D. L. Rock, “The genome of Melanoplus sanguinipes entomopoxvirus,” Journal of Virology, vol. 73, no. 1, pp. 533–552, 1999.
[144]
T. Ohnishi, E. Mori, and A. Takahashi, “DNA double-strand breaks: their production, recognition, and repair in eukaryotes,” Mutation Research, vol. 669, no. 1-2, pp. 8–12, 2009.
[145]
D. Strumberg, A. A. Pilon, M. Smith, R. Hickey, L. Malkas, and Y. Pommier, “Conversion of topoisomerase I cleavage complexes on the leading strand of ribosomal DNA into 5'-phosphorylated DNA double-strand breaks by replication runoff,” Molecular and Cellular Biology, vol. 20, no. 11, pp. 3977–3987, 2000.
[146]
H. C. Box, J. B. Dawidzik, and E. E. Budzinski, “Free radical-induced double lesions in DNA,” Free Radical Biology and Medicine, vol. 31, no. 7, pp. 856–868, 2001.
[147]
J. P. Banáth and P. L. Olive, “Expression of phosphorylated histone H2AX as a surrogate of cell killing by drugs that create DNA double-strand breaks,” Cancer Research, vol. 63, no. 15, pp. 4347–4350, 2003.
[148]
J. V. Harper, J. A. Anderson, and P. O’Neill, “Radiation induced DNA DSBs: contribution from stalled replication forks?” DNA Repair, vol. 9, pp. 907–913, 2010.
[149]
S. E. Freeman, A. D. Blackett, and D. C. Monteleone, “Quantitation of radiation-, chemical-, or enzyme-induced single strand breaks in nonradioactive DNA by alkaline gel electrophoresis: application to pyrimidine dimers,” Analytical Biochemistry, vol. 158, no. 1, pp. 119–129, 1986.
[150]
D. L. Mitchell, J. Jen, and J. E. Cleaver, “Relative induction of cyclobutane dimers and cytosine photohydrates in DNA irradiated in vitro and in vivo with ultraviolet-C and ultraviolet-B light,” Photochemistry and Photobiology, vol. 54, no. 5, pp. 741–746, 1991.
[151]
B. Thyagarajan, K. E. Anderson, C. J. Lessard et al., “Alkaline unwinding flow cytometry assay to measure nucleotide excision repair,” Mutagenesis, vol. 22, no. 2, pp. 147–153, 2007.
[152]
P. Kara, K. Da？deviren, and M. ？zs？z, “An electrochemical DNA biosensor for the detection of DNA damage caused by radioactive iodine and technetium,” Turkish Journal of Chemistry, vol. 31, no. 3, pp. 243–249, 2007.
[153]
A. Hollaender and J. T. Curtis, “Effects of sublethal doses of monochromatic ultraviolet radiation on bacteria in liquid suspension,” Proceedings of the Society for Experimental Biology and Medicine, vol. 33, pp. 61–62, 1935.
[154]
A. Kelner, “Effects of visible light on the recovery of Streptomyces griseus conidia from ultraviolet irradiation injury,” Proceedings of the National Academy of Sciences of the Unites States of America, vol. 35, pp. 73–79, 1949.
[155]
R. Dulbecco, “Reactivation of ultra-violet-inactivated bacteriophage by visible light,” Nature, vol. 163, no. 4155, pp. 949–950, 1949.
[156]
J. Essers, W. Vermeulen, and A. B. Houtsmuller, “DNA damage repair: anytime, anywhere?” Current Opinion in Cell Biology, vol. 18, no. 3, pp. 240–246, 2006.
[157]
S.-T. Kim, P. F. Heelis, and A. Sancar, “Energy transfer (deazaflavin → FADH2) and electron transfer (FADH2 → T<>T) kinetics in Anacystis nidulans photolyase,” Biochemistry, vol. 31, no. 45, pp. 11244–11248, 1992.
[158]
L. O. Essen and T. Klar, “Light-driven DNA repair by photolyases,” Cellular and Molecular Life Sciences, vol. 63, no. 11, pp. 1266–1277, 2006.
[159]
A. B. Britt, “DNA damage and repair in plants,” Annual Review of Plant Physiology and Plant Molecular Biology, vol. 47, no. 1, pp. 75–100, 1996.
[160]
T. Todo, “Functional diversity of the DNA photolyase/blue light receptor family,” Mutation Research, vol. 434, no. 2, pp. 89–97, 1999.
[161]
B. M. Sutherland, “Photoreactivating enzyme from human leukocytes,” Nature, vol. 248, no. 5444, pp. 109–112, 1974.
[162]
B. M. Sutherland and P. V. Bennett, “Human white blood cells contain cyclobutyl pyrimidine dimer photolyase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 21, pp. 9732–9736, 1995.
[163]
H. Harm, “Damage and repair in mammalian cells after exposure to non-ionizing radiations. III. Ultraviolet and visible light irradiation of cells of placental mammals, including humans, and determination of photorepairable damage in vitro,” Mutation Research, vol. 69, no. 1, pp. 167–176, 1980.
[164]
D. S. Hsu, X. Zhao, S. Zhao et al., “Putative human blue-light photoreceptors hCRY1 and hCRY2 are flavoproteins,” Biochemistry, vol. 35, no. 44, pp. 13871–13877, 1996.
[165]
T. Ueda, A. Kato, S. Kuramitsu, H. Terasawa, and I. Shimada, “Identification and characterization of a second chromophore of DNA photolyase from Thermus thermophilus HB27,” Journal of Biological Chemistry, vol. 280, no. 43, pp. 36237–36243, 2005.
[166]
C. Saxena, A. Sancar, and D. Zhong, “Femtosecond dynamics of DNA photolyase: energy transfer of antenna initiation and electron transfer of cofactor reduction,” Journal of Physical Chemistry B, vol. 108, no. 46, pp. 18026–18033, 2004.
[167]
Y.-T. Kao, C. Saxena, L. Wang, A. Sancar, and D. Zhong, “Direct observation of thymine dimer repair in DNA by photolyase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 45, pp. 16128–16132, 2005.
[168]
A. E. Stapleton and V. Walbot, “Flavonoids can protect maize DNA from the induction of ultraviolet radiation damage,” Plant Physiology, vol. 105, no. 3, pp. 881–889, 1994.
[169]
R. Schmitz-Hoerner and G. Weissenbock, “Contribution of phenolic compounds to the UV-B screening capacity of developing barley primary leaves in relation to DNA damage and repair under elevated UV-B levels,” Phytochemistry, vol. 64, pp. 243–255, 2003.
[170]
G. Kaiser, O. Kleiner, C. Beisswenger, and A. Batschauer, “Increased DNA repair in Arabidopsis plants overexpressing CPD photolyase,” Planta, vol. 230, no. 3, pp. 505–515, 2009.
[171]
N. Tuteja, M. B. Singh, M. K. Misra, P. L. Bhalla, and R. Tuteja, “Molecular mechanisms of DNA damage and repair: progress in plants,” Critical Reviews in Biochemistry and Molecular Biology, vol. 36, no. 4, pp. 337–397, 2001.
[172]
S. Kimura, Y. Tahira, T. Ishibashi, et al., “DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells,” Nucleic Acids Research, vol. 32, pp. 2760–2767, 2004.
[173]
J. J. Chen, D. L. Mitchell, and A. B. Britt, “A light-dependent pathway for the elimination of UV-induced pyrimidine (6–4) pyrimidinone photoproducts in Arabidopsis,” Plant Cell, vol. 6, no. 9, pp. 1311–1317, 1994.
[174]
H.-S. Kang, J. Hidema, and T. Kumagai, “Effects of light environment during culture on UV-induced cyclobutyl pyrimidine dimers and their photorepair in rice (Oryza sativa L.),” Photochemistry and Photobiology, vol. 68, no. 1, pp. 71–77, 1998.
[175]
A. Mees, T. Klar, P. Gnau et al., “Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair,” Science, vol. 306, no. 5702, pp. 1789–1793, 2004.
[176]
T. Torizawa, T. Ueda, S. Kuramitsu et al., “Investigation of the cyclobutane pyrimidine dimer (CPD) photolyase DNA recognition mechanism by NMR analyses,” Journal of Biological Chemistry, vol. 279, no. 31, pp. 32950–32956, 2004.
[177]
P. F. Heelis, R. F. Hartman, and S. D. Rose, “Photoenzymic repair of UV-damaged DNA—a chemist's perspective,” Chemical Society Reviews, vol. 24, no. 4, pp. 289–297, 1995.
[178]
A. W. MacFarlane and R. J. Stanley, “Cis-Syn thymidine dimer repair by DNA photolyase in real time,” Biochemistry, vol. 42, no. 28, pp. 8558–8568, 2003.
[179]
I. H. Kavakli and A. Sancar, “Analysis of the role of intraprotein electron transfer in photoreactivation by DNA photolyase in vivo,” Biochemistry, vol. 43, no. 48, pp. 15103–15110, 2004.
[180]
E. Schleicher, B. He？ling, V. Illarionova et al., “Light-induced reactions of Escherichia coli DNA photolyase monitored by Fourier transform infrared spectroscopy,” FEBS Journal, vol. 272, no. 8, pp. 1855–1866, 2005.
[181]
G. B. Sancar and F. W. Smith, “Interactions between yeast photolyase and nucleotide excision repair proteins in Saccharomyces cerevisiae and Escherichia coli,” Molecular and Cellular Biology, vol. 9, no. 11, pp. 4767–4776, 1989.
[182]
E. Seeberg, L. Eide, and M. Bj？r？s, “The base excision repair pathway,” Trends in Biochemical Sciences, vol. 20, no. 10, pp. 391–397, 1995.
[183]
J. H. Houtgraaf, J. Versmissen, and W. J. van der Giessen, “A concise review of DNA damage checkpoints and repair in mammalian cells,” Cardiovascular Revascularization Medicine, vol. 7, no. 3, pp. 165–172, 2006.
[184]
K. H. Almeida and R. W. Sobol, “A unified view of base excision repair: lesion-dependent protein complexes regulated by post-translational modification,” DNA Repair, vol. 6, no. 6, pp. 695–711, 2007.
[185]
K. Hitomi, S. Iwai, and J. A. Tainer, “The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair,” DNA Repair, vol. 6, no. 4, pp. 410–428, 2007.
[186]
A. B. Robertson, A. Klungland, T. Rognes, and I. Leiros, “Base excision repair: the long and short of it,” Cellular and Molecular Life Sciences, vol. 66, no. 6, pp. 981–993, 2009.
[187]
D. E. Barnes and T. Lindahl, “Repair and genetic consequences of endogenous DNA base damage in mammalian cells,” Annual Review of Genetics, vol. 38, pp. 445–476, 2004.
[188]
J. L. Parsons, P. S. Tait, D. Finch, I. I. Dianova, S. L. Allinson, and G. L. Dianov, “CHIP-mediated degradation and DNA damage-dependent stabilization regulate base excision repair proteins,” Molecular Cell, vol. 29, no. 4, pp. 477–487, 2008.
[189]
K. W. Caldecott, “XRCC1 and DNA strand break repair,” DNA Repair, vol. 2, no. 9, pp. 955–969, 2003.
[190]
L. Lan, S. Nakajima, Y. Oohata et al., “In situ analysis of repair processes for oxidative DNA damage in mammalian cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 38, pp. 13738–13743, 2004.
[191]
K. Sakumi and M. Sekiguchi, “Structures and functions of DNA glycosylases,” Mutation Research, vol. 236, no. 2-3, pp. 161–172, 1990.
[192]
Y. Matsumoto and K. Kim, “Excision of deoxyribose phosphate residues by DNA polymerase β during DNA repair,” Science, vol. 269, no. 5224, pp. 699–702, 1995.
[193]
B. Demple and L. Harrison, “Repair of oxidative damage to DNA: enzymology and biology,” Annual Review of Biochemistry, vol. 63, pp. 915–948, 1994.
[194]
L. Gros, A. A. Ishchenko, H. Ide, R. H. Elder, and M. K. Saparbaev, “The major human AP endonuclease (Ape1) is involved in the nucleotide incision repair pathway,” Nucleic Acids Research, vol. 32, no. 1, pp. 73–81, 2004.
[195]
P. Fortini and E. Dogliotti, “Base damage and single-strand break repair: mechanisms and functional significance of short- and long-patch repair subpathways,” DNA Repair, vol. 6, no. 4, pp. 398–409, 2007.
[196]
U. Sattler, P. Frit, B. Salles, and P. Calsou, “Long-patch DNA repair synthesis during base excision repair in mammalian cells,” EMBO Reports, vol. 4, no. 4, pp. 363–367, 2003.
[197]
W. D. Henner, S. M. Grunberg, and W. A. Haseltine, “Enzyme action at 3' termini of ionizing radiation-induced DNA strand breaks,” Journal of Biological Chemistry, vol. 258, no. 24, pp. 15198–151205, 1983.
[198]
W. D. Henner, L. O. Rodriguez, S. M. Hecht, and W. A. Haseltine, “gamma Ray induced deoxyribonucleic acid strand breaks. Glycolate termini,” Journal of Biological Chemistry, vol. 258, no. 2, pp. 711–713, 1983.
[199]
A. Jilani, D. Ramotar, C. Slack et al., “Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase -phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage,” Journal of Biological Chemistry, vol. 274, no. 34, pp. 24176–24186, 1999.
[200]
R. Gary, K. Kim, H. L. Cornelius, M. S. Park, and Y. Matsumoto, “Proliferating cell nuclear antigen facilitates excision in long-patch base excision repair,” Journal of Biological Chemistry, vol. 274, no. 7, pp. 4354–4363, 1999.
[201]
P. Fortini, B. Pascucci, E. Parlanti, R. W. Sobol, S. H. Wilson, and E. Dogliotti, “Different DNA polymerases are involved in the short- and long-patch base excision repair in mammalian cells,” Biochemistry, vol. 37, no. 11, pp. 3575–3580, 1998.
[202]
A. B. Britt, “Molecular genetics of DNA repair in higher plants,” Trends in Plant Science, vol. 4, no. 1, pp. 20–25, 1999.
[203]
J. B. Hays, “Arabidopsis thaliana, a versatile model system for study of eukaryotic genome-maintenance functions,” DNA Repair, vol. 1, no. 8, pp. 579–600, 2002.
[204]
E. Hefner, S. B. Preuss, and A. B. Britt, “Arabidopsis mutants sensitive to gamma radiation include the homologue of the human repair gene ERCC1,” Journal of Experimental Botany, vol. 54, no. 383, pp. 669–680, 2003.
[205]
A. G. McLennan, “The repair of ultraviolet light-induced DNA damage in plant cells,” Mutation Research, vol. 181, no. 1, pp. 1–7, 1987.
[206]
E. J. Vonarx, H. L. Mitchell, R. Karthikeyan, I. Chatterjee, and B. A. Kunz, “DNA repair in higher plants,” Mutation Research, vol. 400, no. 1-2, pp. 187–200, 1998.
[207]
E. Dandoy, R. Schyns, R. Deltour, and W. G. Verly, “Appearance and repair of apurinic/apyrimidinic sites in DNA during early germination of Zea mays,” Mutation Research, vol. 181, no. 1, pp. 57–60, 1987.
[208]
M. Talpaert-Borlè and M. Liuzzi, “Base-excision repair in carrot cells,” European Journal of Biochemistry, vol. 124, no. 3, pp. 435–440, 1982.
[209]
R. T. Hess, U. Schwitter, M. Petretta, B. Giese, and H. Naegeli, “Bipartite substrate discrimination by human nucleotide excision repair,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 13, pp. 6664–6669, 1997.
[210]
R. M. A. Costa, V. Chigan？as, R. D. S. Galhardo, H. Carvalho, and C. F. M. Menck, “The eukaryotic nucleotide excision repair pathway,” Biochimie, vol. 85, no. 11, pp. 1083–1099, 2003.
[211]
A. Van Hoffen, J. Venema, R. Meschini, A. A. Van Zeeland, and L. H. F. Mullenders, “Tvanscription-coupled repair removes both cyclobutane pyrimidine dimers and 6–4 photoproducts with equal efficiency and in a sequential way from transcribed DNA in xeroderma pigmentosum group C fibroblasts,” EMBO Journal, vol. 14, no. 2, pp. 360–367, 1995.
[212]
R. P. Boyce and P. Howard-Flanders, “Release of ultraviolet light-induced thymine dimers from DNA in E. coli K-12,” Proceedings of the National Academy of Sciences of the United States of America, vol. 51, pp. 293–300, 1964.
[213]
D. E. Pettijohn and P. C. Hanawalt, “Evidence for repair-replication of ultraviolet damaged DNA in bacteria,” Journal of Molecular Biology, vol. 9, pp. 395–410, 1964.
[214]
J.-J. Lin and A. Sancar, “Reconstitution of nucleotide excision nuclease with UvrA and UvrB proteins from Escherichia coli and UvrC protein from Bacillus subtilis,” Journal of Biological Chemistry, vol. 265, no. 34, pp. 21337–21341, 1990.
[215]
D. K. Orren, P. Selby, J. E. Hearst, and A. Sancar, “Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I,” The Journal of Biological Chemistry, vol. 267, pp. 780–788, 1992.
[216]
T. Nouspikel, “Nucleotide excision repair: variations on versatility,” Cellular and Molecular Life Sciences, vol. 66, no. 6, pp. 994–1009, 2009.
[217]
S. W. Matson, D. W. Bean, and J. W. George, “DNA helicases: enzymes with essential roles in all aspects of DNA metabolism,” BioEssays, vol. 16, no. 1, pp. 13–22, 1994.
[218]
K. A. Henning, L. Li, N. Iyer et al., “The Cockayne syndrome group a gene encodes a WD repeat protein that interacts with CSB protein and a subunit of RNA polymerase II TFIIH,” Cell, vol. 82, no. 4, pp. 555–564, 1995.
[219]
C. P. Selby and A. Sancar, “Human transcription-repair coupling factor CSB/ERCC6 is a DNA-stimulated ATPase but is not a helicase and does not disrupt the ternary transcription complex of stalled RNA polymerase II,” Journal of Biological Chemistry, vol. 272, no. 3, pp. 1885–1890, 1997.
[220]
P. C. Hanawalt, B. A. Donahue, and K. S. Sweder, “Repair and transcription: collision or collusion?” Current Biology, vol. 4, no. 6, pp. 518–522, 1994.
[221]
S. Tornaletti and P. C. Hanawalt, “Effect of DNA lesions on transcription elongation,” Biochimie, vol. 81, no. 1-2, pp. 139–146, 1999.
[222]
J. N. Ratner, B. Balasubramanian, J. Corden, S. L. Warren, and D. B. Bregman, “Ultraviolet radiation-induced ubiquitination and proteasomal degradation of the large subunit of RNA polymerase II: implications for transcription-coupled DNA repair,” Journal of Biological Chemistry, vol. 273, no. 9, pp. 5184–5189, 1998.
[223]
A. Sarasin and A. Stary, “New insights for understanding the transcription-coupled repair pathway,” DNA Repair, vol. 6, no. 2, pp. 265–269, 2007.
[224]
M. Fousteri, W. Vermeulen, A. A. van Zeeland, and L. H. F. Mullenders, “Cockayne syndrome A and B proteins differentially regulate recruitment of chromatin remodeling and repair factors to stalled RNA polymerase II in vivo,” Molecular Cell, vol. 23, no. 4, pp. 471–482, 2006.
[225]
L. Proietti-De-Santis, P. Drané, and J.-M. Egly, “Cockayne syndrome B protein regulates the transcriptional program after UV irradiation,” EMBO Journal, vol. 25, no. 9, pp. 1915–1923, 2006.
[226]
K. Sugasawa, J. M. Y. Ng, C. Masutani et al., “Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair,” Molecular Cell, vol. 2, no. 2, pp. 223–232, 1998.
[227]
W. L. De Laat, N. G. J. Jaspers, and J. H. J. Hoeijmakers, “Molecular mechanism of nucleotide excision repair,” Genes and Development, vol. 13, no. 7, pp. 768–785, 1999.
[228]
L. C. J. Gillet and O. D. Sch？rer, “Molecular mechanisms of mammalian global genome nucleotide excision repair,” Chemical Reviews, vol. 106, no. 2, pp. 253–276, 2006.
[229]
C. Petit and A. Sancar, “Nucleotide excision repair: from E. coli to man,” Biochimie, vol. 81, no. 1-2, pp. 15–25, 1999.
[230]
C. Masutani, K. Sugasawa, J. Yanagisawa et al., “Purification and cloning of a nucleotide excision repair complex involving the xeroderma pigmentosum group C protein and a human homologue of yeast RAD23,” EMBO Journal, vol. 13, no. 8, pp. 1831–1843, 1994.
[231]
M. Araki, C. Masutani, M. Takemura et al., “Centrosome protein centrin 2/caltractin 1 is part of the xeroderma pigmentosum group C complex that initiates global genome nucleotide excision repair,” Journal of Biological Chemistry, vol. 276, no. 22, pp. 18665–18672, 2001.
[232]
L. Schaeffer, R. Roy, S. Humbert, et al., “DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor,” Science, vol. 260, pp. 58–63, 1993.
[233]
F. Coin, V. Oksenych, and J.-M. Egly, “Distinct roles for the XPB/p52 and XPD/p44 subcomplexes of TFIIH in damaged DNA opening during nucleotide excision repair,” Molecular Cell, vol. 26, no. 2, pp. 245–256, 2007.
[234]
L. Schaeffer, V. Moncollin, R. Roy et al., “The ERCC2/DNA repair protein is associated with the class II BTF2/TFIIH transcription factor,” EMBO Journal, vol. 13, no. 10, pp. 2388–2392, 1994.
[235]
J. Chen, S. Larochelle, X. Li, and B. Suter, “Xpd/Ercc2 regulates CAK activity and mitotic progression,” Nature, vol. 424, no. 6945, pp. 228–232, 2003.
[236]
P. Schultz, S. Fribourg, A. Poterszman, V. Mallouh, D. Moras, and J. M. Egly, “Molecular structure of human TFIIH,” Cell, vol. 102, no. 5, pp. 599–607, 2000.
[237]
J. A. Ranish, S. Hahn, Y. Lu et al., “Identification of TFB5, a new component of general transcription and DNA repair factor IIH,” Nature Genetics, vol. 36, no. 7, pp. 707–713, 2004.
[238]
C. J. Jones and R. D. Wood, “Preferential binding of the xeroderma pigmentosum group A complementing protein to damaged DNA,” Biochemistry, vol. 32, no. 45, pp. 12096–12104, 1993.
[239]
T. Matsuda, M. Saijo, I. Kuraoka et al., “DNA repair protein XPA binds replication protein A (RPA),” Journal of Biological Chemistry, vol. 270, no. 8, pp. 4152–4157, 1995.
[240]
E. Stigger, R. Drissi, and S.-H. Lee, “Functional analysis of human replication protein A in nucleotide excision repair,” Journal of Biological Chemistry, vol. 273, no. 15, pp. 9337–9343, 1998.
[241]
Z. He, L. A. Henricksen, M. S. Wold, and C. J. Ingles, “RPA involvement in the damage-recognition and incision steps of nucleotide excision repair,” Nature, vol. 374, no. 6522, pp. 566–569, 1995.
[242]
J. L. Burns, S. N. Guzder, P. Sung, S. Prakash, and L. Prakash, “An affinity of human replication protein A for ultraviolet-damaged DNA: implications for damage recognition in nucleotide excision repair,” Journal of Biological Chemistry, vol. 271, no. 20, pp. 11607–11610, 1996.
[243]
E. Evans, J. G. Moggs, J. R. Hwang, J.-M. Egly, and R. D. Wood, “Mechanism of open complex and dual incision formation by human nucleotide excision repair factors,” EMBO Journal, vol. 16, no. 21, pp. 6559–6573, 1997.
[244]
A. H. Sarker, S. E. Tsutakawa, S. Kostek et al., “Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne syndrome,” Molecular Cell, vol. 20, no. 2, pp. 187–198, 2005.
[245]
K. G. Cloud, B. Shen, G. F. Strniste, and M. S. Park, “XPG protein has a structure-specific endonuclease activity,” Mutation Research, vol. 347, no. 2, pp. 55–60, 1995.
[246]
W. L. De Laat, E. Appeldoorn, N. G. J. Jaspers, and J. H. J. Hoeijmakers, “DNA structural elements required for ERCC1-XPF endonuclease activity,” Journal of Biological Chemistry, vol. 273, no. 14, pp. 7835–7842, 1998.
[247]
J. H. Enzlin and O. D. Sch？rer, “The active site of the DNA repair endonuclease XPF-ERCC1 forms a highly conserved nuclease motif,” EMBO Journal, vol. 21, no. 8, pp. 2045–2053, 2002.
[248]
R. D. Wood, “Nucleotide excision repair in mammalian cells,” Journal of Biological Chemistry, vol. 272, no. 38, pp. 23465–23468, 1997.
[249]
D. Mu, D. S. Hsu, and A. Sancar, “Reaction mechanism of human DNA repair excision nuclease,” Journal of Biological Chemistry, vol. 271, no. 14, pp. 8285–8294, 1996.
[250]
K. Sugasawa, Y. Okuda, M. Saijo et al., “UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex,” Cell, vol. 121, no. 3, pp. 387–400, 2005.
[251]
J. Tang and G. Chu, “Xeroderma pigmentosum complementation group E and UV-damaged DNA-binding protein,” DNA Repair, vol. 1, no. 8, pp. 601–616, 2002.
[252]
O. Maillard, S. Solyom, and H. Naegeli, “An aromatic sensor with aversion to damaged strands confers versatility to DNA repair,” PLoS Biology, vol. 5, no. 4, article no. e79, 2007.
[253]
K. Sugasawa, “UV-induced ubiquitylation of XPC complex, the UV-DDB-ubiquitin ligase complex, and DNA repair,” Journal of Molecular Histology, vol. 37, no. 5-7, pp. 189–202, 2006.
[254]
D. Hoogstraten, S. Bergink, V. H. M. Verbiest et al., “Versatile DNA damage detection by the global genome nucleotide excision repair protein XPC,” Journal of Cell Science, vol. 121, no. 17, pp. 2850–2859, 2008.
[255]
P. J. Van der Spek, A. Eker, S. Rademakers et al., “XPC and human homologs of RAD23: intracellular localization and relationship to other nucleotide excision repair complexes,” Nucleic Acids Research, vol. 24, no. 13, pp. 2551–2559, 1996.
[256]
K. Sugasawa, C. Masutani, A. Uchida et al., “HHR23B, a human Rad23 homolog, stimulates XPC protein in nucleotide excision repair in vitro,” Molecular and Cellular Biology, vol. 16, no. 9, pp. 4852–4861, 1996.
[257]
C. Masutani, M. Araki, K. Sugasawa et al., “Identification and characterization of XPC-binding domain of hHR23B,” Molecular and Cellular Biology, vol. 17, no. 12, pp. 6915–6923, 1997.
[258]
K. Sugasawa, J. M. Y. Ng, C. Masutani et al., “Two human homologs of Rad23 are functionally interchangeable in complex formation and stimulation of XPC repair activity,” Molecular and Cellular Biology, vol. 17, no. 12, pp. 6924–6931, 1997.
[259]
J. T. Reardon, D. Mu, and A. Sancar, “Overproduction, purification, and characterization of the XPC subunit of the human DNA repair excision nuclease,” Journal of Biological Chemistry, vol. 271, no. 32, pp. 19451–19456, 1996.
[260]
K. Sugasawa, T. Okamoto, Y. Shimizu, C. Masutani, S. Iwai, and F. Hanaoka, “A multistep damage recognition mechanism for global genomic nucleotide excision repair,” Genes and Development, vol. 15, no. 5, pp. 507–521, 2001.
[261]
A. Aboussekhra, M. Biggerstaff, M. K. K. Shivji et al., “Mammalian DNA nucleotide excision repair reconstituted with purified protein components,” Cell, vol. 80, no. 6, pp. 859–868, 1995.
[262]
F. Tirode, D. Busso, F. Coin, and J.-M. Egly, “Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7,” Molecular Cell, vol. 3, no. 1, pp. 87–95, 1999.
[263]
D. Mu, C.-H. Park, T. Matsunaga, D. S. Hsu, J. T. Reardon, and A. Sancar, “Reconstitution of human DNA repair excision nuclease in a highly defined system,” Journal of Biological Chemistry, vol. 270, no. 6, pp. 2415–2418, 1995.
[264]
M. R. Lieber, “The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair,” BioEssays, vol. 19, no. 3, pp. 233–240, 1997.
[265]
A. Constantinou, D. Gunz, E. Evans et al., “Conserved residues of human XPG protein important for nuclease activity and function in nucleotide excision repair,” Journal of Biological Chemistry, vol. 274, no. 9, pp. 5637–5648, 1999.
[266]
R. Guo, J. Chen, F. Zhu, et al., “E2F1 Localizes to sites of UV-induced DNA damage to enhance nucleotide excision repair,” The Journal of Biological Chemistry, vol. 285, pp. 19308–19315, 2010.
[267]
S. Nocentini, “Rejoining kinetics of DNA single- and double-strand breaks in normal and DNA ligase-deficient cells after exposure to ultraviolet C and gamma radiation: an evaluation of ligating activities involved in different DNA repair processes,” Radiation Research, vol. 151, no. 4, pp. 423–432, 1999.
[268]
J. Moser, H. Kool, I. Giakzidis, K. Caldecott, L. H.F. Mullenders, and M. I. Fousteri, “Sealing of chromosomal DNA nicks during nucleotide excision repair requires XRCC1 and DNA ligase IIIα in a cell-cycle-specific manner,” Molecular Cell, vol. 27, no. 2, pp. 311–323, 2007.
[269]
S. Tornaletti, “Transcription-coupled DNA repair: directing your effort where it's most needed,” Cellular and Molecular Life Sciences, vol. 66, no. 6, pp. 1010–1020, 2009.
[270]
G. R. Harlow, M. E. Jenkins, T. S. Pittalwala, and D. W. Mount, “Isolation of uvh1, an Arabidopsis mutant hypersensitive to ultraviolet light and ionizing radiation,” Plant Cell, vol. 6, no. 2, pp. 227–235, 1994.
[271]
A. L. Fidantsef, D. L. Mitchell, and A. B. Britt, “The Arabidopsis UVH1 gene is a homolog of the yeast repair endonuclease RAD1,” Plant Physiology, vol. 124, no. 2, pp. 579–586, 2000.
[272]
Z. Liu, G. S. Hossain, M. A. Islas-Osuna, D. L. Mitchell, and D. W. Mount, “Repair of UV damage in plants by nucleotide excision repair: Arabidopsis UVH1 DNA repair gene is a homolog of Saccharomyces cerevisiae Rad1,” Plant Journal, vol. 21, no. 6, pp. 519–528, 2000.
[273]
Z. Liu, J. D. Hall, and D. W. Mount, “Arabidopsis UVH3 gene is a homolog of the Saccharomyces cerevisiae RAD2 and human XPG DNA repair genes,” Plant Journal, vol. 26, no. 3, pp. 329–338, 2001.
[274]
G. C. Cannon, L. A. Hedrick, and S. Heinhorst, “Repair mechanisms of UV-induced DNA damage in soybean chloroplasts,” Plant Molecular Biology, vol. 29, no. 6, pp. 1267–1277, 1995.
[275]
J. Hidema, T. Kumagai, J. C. Sutherland, and B. M. Sutherland, “Ultraviolet B-sensitive rice cultivar deficient in cyclobutyl pyrimidine dimer repair,” Plant Physiology, vol. 113, no. 1, pp. 39–44, 1997.
[276]
M. E. Jenkins, G. R. Harlow, Z. Liu, M. A. Shotwell, J. Ma, and D. W. Mount, “Radiation-sensitive mutants of Arabidopsis thaliana,” Genetics, vol. 140, no. 2, pp. 725–732, 1995.
[277]
C.-Z. Jiang, C.-N. Yen, K. Cronin, D. Mitchell, and A. B. Britt, “UV- and gamma-radiation sensitive mutants of Arabidopsis thaliana,” Genetics, vol. 147, no. 3, pp. 1401–1409, 1997.
[278]
S. Kimura and K. Sakaguchi, “DNA repair in plants,” Chemical Reviews, vol. 106, no. 2, pp. 753–766, 2006.
[279]
H. Xu, I. Swoboda, P. L. Bhalla et al., “Plant homologue of human excision repair gene ERCC1 points to conservation of DNA repair mechanisms,” Plant Journal, vol. 13, no. 6, pp. 823–829, 1998.
[280]
E. C. Friedberg, “DNA damage and repair,” Nature, vol. 421, no. 6921, pp. 436–440, 2003.
[281]
J. Wu, L.-Y. Lu, and X. Yu, “The role of BRCA1 in DNA damage response,” Protein Cell, vol. 1, pp. 117–123, 2010.
[282]
P. Sung, K. M. Trujillo, and S. Van Komen, “Recombination factors of Saccharomyces cerevisiae,” Mutation Research, vol. 451, no. 1-2, pp. 257–275, 2000.
[283]
G. A. Cromie, J. C. Connelly, and D. R. F. Leach, “Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans,” Molecular Cell, vol. 8, no. 6, pp. 1163–1174, 2001.
[284]
J. Thacker, “The RAD51 gene family, genetic instability and cancer,” Cancer Letters, vol. 219, no. 2, pp. 125–135, 2005.
[285]
K. McEntee, G. M. Weinstock, and I. R. Lehman, “recA protein-catalyzed strand assimilation: stimulation by Escherichia coli single-stranded DNA-binding protein,” Proceedings of the National Academy of Sciences of the United States of America, vol. 77, no. 2, pp. 857–861, 1980.
[286]
D. K. Bishop, D. Park, L. Xu, and N. Kleckner, “DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression,” Cell, vol. 69, no. 3, pp. 439–456, 1992.
[287]
S. T. Lovett, “Sequence of the RAD5 gene of Saccharomyces cerevisiae: similarity of RAD55 to prokaryotic RecA and other RecA-like proteins,” Gene, vol. 142, no. 1, pp. 103–106, 1994.
[288]
W. Li and H. Ma, “Double-stranded DNA breaks and gene functions in recombination and meiosis,” Cell Research, vol. 16, no. 5, pp. 402–412, 2006.
[289]
M. Kawabata, T. Kawabata, and M. Nishibori, “Role of recA/RAD51 family proteins in mammals,” Acta Medica Okayama, vol. 59, no. 1, pp. 1–9, 2005.
[290]
Y. Aylon and M. Kupiec, “New insights into the mechanism of homologous recombination in yeast,” Mutation Research, vol. 566, no. 3, pp. 231–248, 2004.
[291]
M. S. Park, “Expression of human RAD52 confers resistance to ionizing radiation in mammalian cells,” Journal of Biological Chemistry, vol. 270, no. 26, pp. 15467–15470, 1995.
[292]
Y. Aylon and M. Kupiec, “The checkpoint protein Rad24 of Saccharomyces cerevisiae is involved in processing double-strand break ends and in recombination partner choice,” Molecular and Cellular Biology, vol. 23, no. 18, pp. 6585–6596, 2003.
[293]
S. Palmer, E. Schildkraut, R. Lazarin, J. Nguyen, and J. A. Nickoloff, “Gene conversion tracts in Saccharomyces cerevisiae can be extremely short and highly directional,” Nucleic Acids Research, vol. 31, no. 4, pp. 1164–1173, 2003.
[294]
O. Inbar and M. Kupiec, “Homology search and choice of homologous partner during mitotic recombination,” Molecular and Cellular Biology, vol. 19, no. 6, pp. 4134–4142, 1999.
[295]
Y. Aylon, B. Liefshitz, G. Bitan-Banin, and M. Kupiec, “Molecular dissection of mitotic recombination in the yeast Saccharomyces cerevisiae,” Molecular and Cellular Biology, vol. 23, no. 4, pp. 1403–1417, 2003.
[296]
H. Puchta, P. Swoboda, and B. Hohn, “Induction of intrachromosomal homologous recombination in whole plants,” Plant Journal, vol. 7, no. 2, pp. 203–210, 1995.
[297]
P. A. Jeggo, “Studies on mammalian mutants defective in rejoining double-strand breaks in DNA,” Mutation Research, vol. 239, no. 1, pp. 1–16, 1990.
[298]
G. Ira, A. Pellicioll, A. Balijja et al., “DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1,” Nature, vol. 431, no. 7011, pp. 1011–1017, 2004.
[299]
P. Sung, “Yeast Rad55 and Rad57 proteins form a heterodimer that functions with replication protein A to promote DNA strand exchange by Rad51 recombinase,” Genes and Development, vol. 11, no. 9, pp. 1111–1121, 1997.
[300]
B. Wolner, S. Van Komen, P. Sung, and C. L. Peterson, “Recruitment of the recombinational repair machinery to a DNA double-strand break in yeast,” Molecular Cell, vol. 12, no. 1, pp. 221–232, 2003.
[301]
E. Sonoda, G. Y. Zhao, M. Kohzaki et al., “Collaborative roles of γH2AX and the Rad51 paralog Xrcc3 in homologous recombinational repair,” DNA Repair, vol. 6, no. 3, pp. 280–292, 2007.
[302]
F. Paques and J. E. Haber, “Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae,” Microbiology and Molecular Biology Reviews, vol. 63, no. 2, pp. 349–404, 1999.
[303]
S. E. Critchlow and S. P. Jackson, “DNA end-joining: from yeast to man,” Trends in Biochemical Sciences, vol. 23, no. 10, pp. 394–398, 1998.
[304]
M. L. Hefferin and A. E. Tomkinson, “Mechanism of DNA double-strand break repair by non-homologous end joining,” DNA Repair, vol. 4, no. 6, pp. 639–648, 2005.
[305]
S. A. McElhinny, J. M. Havener, M. Garcia-Diaz et al., “A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining,” Molecular Cell, vol. 19, no. 3, pp. 357–366, 2005.
[306]
J.-P. Capp, F. Boudsocq, P. Bertrand et al., “The DNA polymerase λ is required for the repair of non-compatible DNA double strand breaks by NHEJ in mammalian cells,” Nucleic Acids Research, vol. 34, no. 10, pp. 2998–3007, 2006.
[307]
S. Thode, A. Sch？fer, P. Pfeiffer, and W. Vielmetter, “A novel pathway of DNA end-to-end joining,” Cell, vol. 60, no. 6, pp. 921–928, 1990.
[308]
R. B. Cary, S. R. Peterson, J. Wang, D. G. Bear, E. M. Bradbury, and D. J. Chen, “DNA looping by Ku and the DNA-dependent protein kinase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 9, pp. 4267–4272, 1997.
[309]
D. A. Ramsden and M. Geliert, “Ku protein stimulates DNA end joining by mammalian DNA ligases: a direct role for Ku in repair of DNA double-strand breaks,” EMBO Journal, vol. 17, no. 2, pp. 609–614, 1998.
[310]
P. Baumann and S. C. West, “DNA end-joining catalyzed by human cell-free extracts,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 24, pp. 14066–14070, 1998.
[311]
H. Yajima, K.-J. Lee, S. Zhang, J. Kobayashi, and B. P. C. Chen, “DNA double-strand break formation upon UV-induced replication stress activates ATM and DNA-PKcs kinases,” Journal of Molecular Biology, vol. 385, no. 3, pp. 800–810, 2009.
[312]
C. Muller, P. Calsou, P. Frit, C. Cayrol, T. Carter, and B. Salles, “UV sensitivity and impaired nucleotide excision repair in DNA-dependent protein kinase mutant cells,” Nucleic Acids Research, vol. 26, no. 6, pp. 1382–1389, 1998.
[313]
P. Hentges, P. Ahnesorg, R. S. Pitcher et al., “Evolutionary and functional conservation of the DNA non-homologous end-joining protein, XLF/Cernunnos,” Journal of Biological Chemistry, vol. 281, no. 49, pp. 37517–37526, 2006.
[314]
P. Ahnesorg, P. Smith, and S. P. Jackson, “XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining,” Cell, vol. 124, no. 2, pp. 301–313, 2006.
[315]
D. Buck, L. Malivert, R. De Chasseval et al., “Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly,” Cell, vol. 124, no. 2, pp. 287–299, 2006.
[316]
E. Riballo, M. Kühne, N. Rief et al., “A pathway of double-strand break rejoining dependent upon ATM, Artemis, and proteins locating to γ-H2AX foci,” Molecular Cell, vol. 16, no. 5, pp. 715–724, 2004.
[317]
J. Lloyd, J. R. Chapman, J. A. Clapperton et al., “A supramodular FHA/BRCT-repeat architecture mediates Nbs1 adaptor function in response to DNA damage,” Cell, vol. 139, no. 1, pp. 100–111, 2009.
[318]
R. S. Williams, G. E. Dodson, O. Limbo, et al., “Nbs1 is an extended flexible arm binding to Ctp1 and Mre11-Rad50 to coordinate dsDNA break processing,” Cell, vol. 139, pp. 87–99, 2009.
[319]
T. T. Paull and M. Gellert, “A mechanistic basis for Mre11-directed DNA joining at microhomologies,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 12, pp. 6409–6414, 2000.
[320]
L. Chen, K. Trujillo, W. Ramos, P. Sung, and A. E. Tomkinson, “Promotion of Dnl4-Catalyzed DNA end-joining by the Rad50/Mre11/Xrs2 and Hdf1/Hdf2 complexes,” Molecular Cell, vol. 8, no. 5, pp. 1105–1115, 2001.
[321]
L. Aravind, V. M. Dixit, and E. V. Koonin, “Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons,” Science, vol. 291, no. 5507, pp. 1279–1284, 2001.
[322]
M.-P. Doutriaux, F. Couteau, C. Bergounioux, and C. White, “Isolation and characterisation of the RAD51 and DMC1 homologs from Arabidopsis thaliana,” Molecular and General Genetics, vol. 257, no. 3, pp. 283–291, 1998.
[323]
A. C. Vergunst and P. J. J. Hooykaas, “Recombination in the plant genome and its application in biotechnology,” Critical Reviews in Plant Sciences, vol. 18, no. 1, pp. 1–31, 1999.
[324]
M. Majchrzak, R. P. Bowater, P. Staczek, and P. Parniewski, “SOS repair and supercoiling influence the genetic stability of DNA triplet repeats in Escherichia coli,” Journal of Molecular Biology, vol. 364, no. 4, pp. 612–624, 2006.
[325]
J. Courcelle, A. Khodursky, B. Peter, P. O. Brown, and P. C. Hanawalt, “Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli,” Genetics, vol. 58, pp. 41–64, 2001.
[326]
B. Michel, “After 30 years of study, the bacterial SOS response still surprises us,” PLoS Biology, vol. 3, no. 7, pp. 1174–1176, 2005.
[327]
M. Martins-Pinheiro, R. C. P. Marques, and C. F. M. Menck, “Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus,” BMC Microbiology, vol. 7, article no. 17, 2007.
[328]
B. Van Houten, J. A. Eisen, and P. C. Hanawalt, “A cut above: discovery of an alternative excision repair pathway in bacteria,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 5, pp. 2581–2583, 2002.
[329]
R. P. Fuchs, S. Fujii, and J. Wagner, “Properties and functions of Escherichia coli Pol IV and Pol V,” Advances in Protein Chemistry, vol. 69, pp. 229–264, 2004.
[330]
M. F. Goodman, “Coping with replication 'train wrecks' in Escherichia coli using Pol V, Pol II and RecA proteins,” Trends in Biochemical Sciences, vol. 25, no. 4, pp. 189–195, 2000.
[331]
B. S. Strauss, R. Roberts, L. Francis, and P. Pouryazdanparast, “Role of the dinB gene product in spontaneous mutation in Escherichia coli with an impaired replicative polymerase,” Journal of Bacteriology, vol. 182, no. 23, pp. 6742–6750, 2000.
[332]
R. S. Galhardo, R. P. Rocha, M. V. Marques, and C. F. M. Menck, “An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus,” Nucleic Acids Research, vol. 33, no. 8, pp. 2603–2614, 2005.
[333]
L. H. Hartwell and T. A. Weinert, “Checkpoints: controls that ensure the order of cell cycle events,” Science, vol. 246, no. 4930, pp. 629–634, 1989.
[334]
H.-L. Lo, S. Nakajima, L. Ma et al., “Differential biologic effects of CPD and 6–4PP UV-induced DNA damage on the induction of apoptosis and cell-cycle arrest,” BMC Cancer, vol. 5, article no. 135, 2005.
[335]
J. Mercer, M. Mahmoudi, and M. Bennett, “DNA damage, p53, apoptosis and vascular disease,” Mutation Research, vol. 621, no. 1-2, pp. 75–86, 2007.
[336]
J. Lukas, C. Lukas, and J. Bartek, “Mammalian cell cycle checkpoints: signalling pathways and their organization in space and time,” DNA Repair, vol. 3, no. 8-9, pp. 997–1007, 2004.
[337]
Y. Shiloh, “ATM and related protein kinases: safeguarding genome integrity,” Nature Reviews Cancer, vol. 3, no. 3, pp. 155–168, 2003.
[338]
P. A. Jeggo and M. L？brich, “Contribution of DNA repair and cell cycle checkpoint arrest to the maintenance of genomic stability,” DNA Repair, vol. 5, no. 9-10, pp. 1192–1198, 2006.
[339]
S. S. Zinkel, K. E. Hurov, C. Ong, F. M. Abtahi, A. Gross, and S. J. Korsmeyer, “A role for proapoptotic BID in the DNA-damage response,” Cell, vol. 122, no. 4, pp. 579–591, 2005.
[340]
I. Kamer, R. Sarig, Y. Zaltsman et al., “Proapoptotic BID is an ATM effector in the DNA-damage response,” Cell, vol. 122, no. 4, pp. 593–603, 2005.
[341]
J. Jin, T. Shirogane, L. Xu et al., “SCFβ-TRCP links Chk1 signaling to degradation of the Cdc25A protein phosphatase,” Genes and Development, vol. 17, no. 24, pp. 3062–3074, 2003.
[342]
Y. Kanemori, K. Uto, and N. Sagata, “β-TrCP recognizes a previously undescribed nonphosphorylated destruction motif in Cdc25A and Cdc25B phosphatases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 18, pp. 6279–6284, 2005.
[343]
N. Mailand, J. Falck, C. Lukas et al., “Rapid destruction of human Cdc25A in response to DNA damage,” Science, vol. 288, no. 5470, pp. 1425–1429, 2000.
[344]
N. Mailand, A. V. Podtelejnikov, A. Groth, M. Mann, J. Bartek, and J. Lukas, “Regulation of G2/M events by Cdc25A through phosphorylation-dependent modulation of its stability,” EMBO Journal, vol. 21, no. 21, pp. 5911–5920, 2002.
[345]
J. Bartek and J. Lukas, “DNA damage checkpoints: from initiation to recovery or adaptation,” Current Opinion in Cell Biology, vol. 19, no. 2, pp. 238–245, 2007.
[346]
N. Watanabe, H. Arai, Y. Nishihara et al., “M-phase kinases induce phospho-dependent ubiquitination of somatic Wee1 by SCFβ-TrCP,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 13, pp. 4419–4424, 2004.
[347]
N. Mailand, S. Bekker-Jensen, J. Bartek, and J. Lukas, “Destruction of claspin by SCFβTrCP restrains Chk1 activation and facilitates recovery from genotoxic stress,” Molecular Cell, vol. 23, no. 3, pp. 307–318, 2006.
[348]
A. Peschiaroli, N. V. Dorrello, D. Guardavaccaro et al., “SCFβTrCP-mediated degradation of claspin regulates recovery from the DNA replication checkpoint response,” Molecular Cell, vol. 23, no. 3, pp. 319–329, 2006.
[349]
I. Mamely, M. A. van Vugt, V. A. Smits et al., “Polo-like kinase-1 controls proteasome-dependent degradation of Claspin during checkpoint recovery,” Current Biology, vol. 16, no. 19, pp. 1950–1955, 2006.
[350]
L. Busino, M. Donzelli, M. Chiesa et al., “Degradation of Cdc25A by β-TrCP during S phase and in response to DNA damage,” Nature, vol. 426, no. 6962, pp. 87–91, 2003.
[351]
M. B. Kastan and J. Bartek, “Cell-cycle checkpoints and cancer,” Nature, vol. 432, no. 7015, pp. 316–323, 2004.
[352]
C. Masutani, R. Kusumoto, S. Iwai, and F. Hanaoka, “Mechanisms of accurate translesion synthesis by human DNA polymerase η,” EMBO Journal, vol. 19, no. 12, pp. 3100–3109, 2000.
[353]
R. E. Johnson, S. Prakash, and L. Prakash, “Efficient bypass of a thymine—thymine dimer by yeast DNA polymerase, Polη,” Science, vol. 283, no. 5404, pp. 1001–1004, 1999.
[354]
R. P. Rastogi, Richa, and R. P. Sinha, “Apoptosis: molecular mechanisms and pathogenicity,” EXCLI Journal, vol. 8, pp. 155–181, 2009.
