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Douki T, Buhot A. Synergistic or Antagonist Effects of Different UV Ranges Analyzed by the Combination Index: Application to DNA Photoproducts †. Photochem Photobiol 2021; 98:649-661. [PMID: 34555202 DOI: 10.1111/php.13528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022]
Abstract
Photobiological effects are known to greatly depend on the wavelength of the incident photons that define the nature of the activated chromophores. A growing number of experimental data show that considering the effect of complex light sources as a sum of the effects of monochromatic exposures can be misleading. Indeed, the combined exposure to several wavelength ranges may modulate photobiological responses or even induce novel processes. These observations are similar to a well-known topic in chemical toxicology: the nonadditivity of effects in mixtures where either antagonism or synergy are often observed. In the present work, we investigated whether a data analysis tool first developed for studying nonadditivity in mixtures of drugs, the combination index, could be applied to photobiological processes. We chose to work on the formation of UV-induced DNA photoproducts where additive, antagonist, and synergistic effects take place simultaneously. In addition to this application, we worked on the mathematical bases of the concept in order to broaden its applicability to phenomena exhibiting various dose-response patterns. We also addressed the question of the evaluation of the error on the determination of the combination index.
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Affiliation(s)
- Thierry Douki
- Univ. of Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble Cedex 9, France
| | - Arnaud Buhot
- Univ. of Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble Cedex 9, France
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2
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Wu D, Lai W, Lyu C, Hang H, Wang H. UHPLC-Q-TOF/MS detection of UV-induced TpT dimeric lesions in genomic DNA. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1096:135-142. [PMID: 30170291 DOI: 10.1016/j.jchromb.2018.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/21/2018] [Accepted: 08/19/2018] [Indexed: 12/18/2022]
Abstract
Ultraviolet (UV) radiation induces mutagenicity and cytotoxicity in human cells by the formation of DNA lesions, including cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), mainly on thymine-thymine (TpT) dinucleotides. Here, we firstly synthesized the two TpT dimeric lesions with satisfactory yields using a unique UV-irradiated water droplet approach followed by HPLC purification. By the use of purified TpT lesions as standards, we further developed and optimized a quantitative UHPLC-Q-TOF/MS method for the detection of CPDs and 6-4PPs. After the optimization of the enzyme composition and the pH values of hydrolysis solution, a combination of snake venom phosphodiesterase, nuclease P1, and calf intestine alkaline phosphatase can be used for one-step enzymatic digestion to efficiently release the dimeric lesions (CPDs and 6-4PPs) from the genomic DNA. By the use of the one-step digestion and UHPLC-Q-TOF/MS assay for scanning all dimeric lesions, we demonstrate that only are TpT dimeric lesions detectable in genomic DNA of HCT116 cells upon UVC irradiation. The estimated frequency of the CPD of TpT increases from 28.7 to 409 per 106 bases with increasing UVC dosage from 40 J/m2 to 1200 J/m2, while the 6-4PP of TpT increases from 3.7 to 54 per 106 bases. The proposed UHPLC-Q-TOF/MS method is promising for accurate identification and quantitative detection of UV-induced dimeric lesions in cellular DNA.
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Affiliation(s)
- Danni Wu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cong Lyu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiying Hang
- Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Martínez-Fernández L, Improta R. Sequence dependence on DNA photochemistry: a computational study of photodimerization pathways in TpdC and dCpT dinucleotides. Photochem Photobiol Sci 2018; 17:586-591. [PMID: 29624198 DOI: 10.1039/c8pp00040a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The excited states involved in the main photodimerization paths in TpdC and dCpT are mapped by PCM/TD-M052X calculations, considering different dinucleotide conformers. As for TT steps, a cyclobutane pyrimidine dimer (CPD) is formed on the PES of the lowest energy exciton, delocalized over two stacked pyrimidines; 6-4 pyrimidine-pyrimidone (64-PP) adduct's formation involves instead a 5'-ter → 3'-ter charge transfer state. For dCpT, 64-PP dimerization occurs via a two-step reaction, which proceeds through an oxetane intermediate. For TpdC, instead, the final 64-PP product is obtained in a single step and it is as stable as the CPD photoproduct, explaining the relatively large yield of 64-PP found experimentally for TC steps in DNA.
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Affiliation(s)
- Lara Martínez-Fernández
- Consiglio Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134 Naples, Italy. and LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Roberto Improta
- Consiglio Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134 Naples, Italy. and LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
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Pulschen AA, Rodrigues F, Duarte RTD, Araujo GG, Santiago IF, Paulino-Lima IG, Rosa CA, Kato MJ, Pellizari VH, Galante D. UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology. Microbiologyopen 2015; 4:574-88. [PMID: 26147800 PMCID: PMC4554453 DOI: 10.1002/mbo3.262] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 03/18/2015] [Accepted: 03/27/2015] [Indexed: 11/17/2022] Open
Abstract
The Sairecabur volcano (5971 m), in the Atacama Desert, is a high-altitude extreme environment with high daily temperature variations, acidic soils, intense UV radiation, and low availability of water. Four different species of yeasts were isolated from this region using oligotrophic media, identified and characterized for their tolerance to extreme conditions. rRNA sequencing revealed high identity (>98%) to Cryptococcus friedmannii, Exophiala sp., Holtermanniella watticus, and Rhodosporidium toruloides. To our knowledge, this is the first report of these yeasts in the Atacama Desert. All isolates showed high resistance to UV-C, UV-B and environmental-UV radiation, capacity to grow at moderate saline media (0.75–2.25 mol/L NaCl) and at moderate to cold temperatures, being C. friedmannii and H. watticus able to grow in temperatures down to −6.5°C. The presence of pigments, analyzed by Raman spectroscopy, correlated with UV resistance in some cases, but there is evidence that, on the natural environment, other molecular mechanisms may be as important as pigmentation, which has implications for the search of spectroscopic biosignatures on planetary surfaces. Due to the extreme tolerances of the isolated yeasts, these organisms represent interesting eukaryotic models for astrobiological purposes.
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Affiliation(s)
- André A Pulschen
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Rodrigues
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Rubens T D Duarte
- Microbiology, Immunology and Parasitology Department, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Gabriel G Araujo
- Interunities Graduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil.,Brazilian Synchrotron Light Laboratory, Campinas, Brazil
| | - Iara F Santiago
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ivan G Paulino-Lima
- NASA Postdoctoral Program Fellow at NASA Ames Research Center, Moffett Field, California
| | - Carlos A Rosa
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Massuo J Kato
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
| | | | - Douglas Galante
- Interunities Graduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil.,Brazilian Synchrotron Light Laboratory, Campinas, Brazil
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Nováková E, Vyšín L, Burian T, Juha L, Davídková M, Múčka V, Čuba V, Grisham ME, Heinbuch S, Rocca JJ. Breaking DNA strands by extreme-ultraviolet laser pulses in vacuum. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:042718. [PMID: 25974538 DOI: 10.1103/physreve.91.042718] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Indexed: 06/04/2023]
Abstract
Ionizing radiation induces a variety of DNA damages including single-strand breaks (SSBs), double-strand breaks (DSBs), abasic sites, modified sugars, and bases. Most theoretical and experimental studies have been focused on DNA strand scissions, in particular production of DNA double-strand breaks. DSBs have been proven to be a key damage at a molecular level responsible for the formation of chromosomal aberrations, leading often to cell death. We have studied the nature of DNA damage induced directly by the pulsed 46.9-nm (26.5 eV) radiation provided by an extreme ultraviolet (XUV) capillary-discharge Ne-like Ar laser (CDL). Doses up to 45 kGy were delivered with a repetition rate of 3 Hz. We studied the dependence of the yield of SSBs and DSBs of a simple model of DNA molecule (pBR322) on the CDL pulse fluence. Agarose gel electrophoresis method was used for determination of both SSB and DSB yields. The action cross sections of the single- and double-strand breaks of pBR322 plasmid DNA in solid state were determined. We observed an increase in the efficiency of strand-break induction in the supercoiled DNA as a function of laser pulse fluence. Results are compared to those acquired at synchrotron radiation facilities and other sources of extreme-ultraviolet and soft x-ray radiation.
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Affiliation(s)
- Eva Nováková
- Department of Radiation and Chemical Physics, Institute of Physics CAS, Na Slovance 2, Prague 8, 182 21, Czech Republic
| | - Luděk Vyšín
- Department of Radiation and Chemical Physics, Institute of Physics CAS, Na Slovance 2, Prague 8, 182 21, Czech Republic
- Department of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, Prague 1, 115 19, Czech Republic
| | - Tomáš Burian
- Department of Radiation and Chemical Physics, Institute of Physics CAS, Na Slovance 2, Prague 8, 182 21, Czech Republic
| | - Libor Juha
- Department of Radiation and Chemical Physics, Institute of Physics CAS, Na Slovance 2, Prague 8, 182 21, Czech Republic
| | - Marie Davídková
- Department of Radiation Dosimetry, Institute of Nuclear Physics CAS, Na Truhlářce 39/64, Prague 8, 180 86, Czech Republic
| | - Viliam Múčka
- Department of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, Prague 1, 115 19, Czech Republic
| | - Václav Čuba
- Department of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, Prague 1, 115 19, Czech Republic
| | - Michael E Grisham
- NSF ERC for Extreme Ultraviolet Science and Technology, Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523-1373, USA
| | - Scott Heinbuch
- NSF ERC for Extreme Ultraviolet Science and Technology, Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523-1373, USA
| | - Jorge J Rocca
- NSF ERC for Extreme Ultraviolet Science and Technology, Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523-1373, USA
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Douki T. The variety of UV-induced pyrimidine dimeric photoproducts in DNA as shown by chromatographic quantification methods. Photochem Photobiol Sci 2014; 12:1286-302. [PMID: 23572060 DOI: 10.1039/c3pp25451h] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Induction of DNA damage is one of the major consequences of exposure to solar UV radiation in living organisms. UV-induced DNA photoproducts are mostly pyrimidine dimers, including cyclobutane pyrimidine dimers, pyrimidine (6-4) pyrimidone photoproducts and Dewar valence isomers. In the last few decades, a large number of methods have been developed for the quantification of these pyrimidine dimers. The present review emphasizes the contribution of chromatographic techniques to our better understanding of the basic DNA photochemistry and the better description of damage in cells.
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Affiliation(s)
- Thierry Douki
- Laboratoire 'Lésions des Acides Nucléiques', Université Joseph Fourier - Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France.
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7
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Peyrane F, Clivio P. Sensitized photochemistry of di(4-tetrazolouracil) dinucleoside monophosphate as a route to dicytosine cyclobutane photoproduct precursors. Photochem Photobiol Sci 2014; 12:1366-74. [PMID: 23572020 DOI: 10.1039/c3pp25402j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The DNA cis-syn cyclobutane photoproduct formed between two adjacent cytosine residues is highly mutagenic and responsible for the tandem CC to TT transition. However, its instability has prevented its in vitro study, so far. With a view to prepare oligodeoxynucleotides containing the CC cyclobutane lesion, we have synthesized in good yield a ditetrazolouracil cyclobutane dinucleotide photoproduct as a stable precursor of this photoproduct. Our approach also overcomes the low photochemical reactivity of the cytosine-cytosine deoxydinucleoside monophosphate.
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Affiliation(s)
- Frédéric Peyrane
- Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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Baggesen LM, Hoffmann SV, Nielsen SB. On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA. Photochem Photobiol 2013; 90:99-106. [PMID: 24117460 DOI: 10.1111/php.12183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/01/2013] [Indexed: 01/25/2023]
Abstract
Solar light leads to thymine dimers that are mutagenic and primary cause of skin cancer. Here, we report absorption and synchrotron radiation circular dichroism (CD) spectra of Tn single strands with different number n of bases (n = 2-7, 10, 11) recorded after various 254 nm irradiation times. From a principal component analysis of the CD spectra, we extract fingerprint spectra of both the cyclobutane pyrimidine dimer (CPD) and the pyrimidine (6-4) pyrimidone photoadduct (64PP). Extending the CD measurements to the vacuum ultraviolet region in combination with systematic examinations of size effects is a new approach to gain insight on the dimeric photoproducts. We find a simple linear correlation between n and average number of dimers formed after 1 h of irradiation. The probability for a thymine to engage in a dimer increases from 32% for n = 2 to 41% for n = 11, which implies limited effects of terminal thymines, i.e., the reaction does not occur preferentially at the extremities of the single strands as previously stated. It is even possible to form two dimers with only two bridging thymines. Finally, experiments conducted on calf thymus DNA provided a similar signature of the photodimer, but differences are also evident.
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Bortolato SA, Thomas KE, McDonough K, Gurney RW, Martino DM. Evaluation of photo-induced crosslinking of thymine polymers using FT-IR spectroscopy and chemometric analysis. POLYMER 2012. [DOI: 10.1016/j.polymer.2012.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Douki T, Ravanat JL, Angelov D, Wagner JR, Cadet J. Effects of Duplex Stability on Charge-Transfer Efficiency within DNA. Top Curr Chem (Cham) 2012. [DOI: 10.1007/b94409] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Gudnason H, Dufva M, Duong Bang D, Wolff A. An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes. Biotechniques 2008; 45:261-71. [PMID: 18778250 DOI: 10.2144/000112905] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Microarrays printed on glass slides are often constructed by covalently linking modified oligonucleotide probes to a derivatized surface at considerable expense. In this article, we demonstrate that 14-base oligonucleotides with a poly(T)10 - poly(C)10 tail (TC tag), but otherwise unmodified, can be linked by UV light irradiation onto a plain, unmodified glass surface. Probes immobilized onto unmodified glass microscope slides performed similarly to probes bound to commercial amino-silane-coated slides and had comparable detection limits. The TC-tagged probes linked to unmodified glass did not show any significant decrease in hybridization performance after a 20 min incubation in water at 100 degrees C prior to rehybridization, indicating a covalent bond between the TC tag and unmodified glass. The probes were used in thermal minisequencing cycling reactions. Furthermore, the TC tag improved the hybridization performance of the immobilized probes on the amino-silane surface, indicating a general benefit of adding a TC tag to DNA probes. In conclusion, our results show that using TC-tagged DNA probes immobilized on an unmodified glass surface is a robust, heat-stable, very simple, and inexpensive method for manufacturing DNA microarrays.
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Affiliation(s)
- Haukur Gudnason
- DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby
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12
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Abstract
It was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)(18) are fully formed in <1 ps after ultraviolet excitation. The speed and low quantum yield of this reaction suggest that only a small fraction of the conformers of this structurally disordered oligonucleotide are in a position to react at the instant of photon absorption. In this work, we explore the hypothesis that conventional molecular dynamics simulations can be used to predict the yield of cyclobutane pyrimidine dimers in DNA. Conformations obtained from simulations of thymidylyl-(3'-5')-thymidine in various cosolvents were classified as dimerizable or nondimerizable depending on the distance between the C5-C6 double bonds of the adjacent thymine bases and the torsion angle between them. The quantum yield of cyclobutane pyrimidine dimer formation was calculated as the number of dimerizable conformations divided by the total number of conformations. The experimental quantum yields measured in the different solvents were satisfactorily reproduced using physically reasonable values for the two parameters. The mean dimerizable structure computed by averaging all of the dimerizable cis-syn conformations is structurally similar to the actual cis-syn dimer. Compared to the canonical B-form TT step, the most important structural property of a dimerizable conformation is its reduced helical twist angle of 22 degrees.
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13
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Douki T. UV-induced DNA Damage. BIOPHYSICAL AND PHYSIOLOGICAL EFFECTS OF SOLAR RADIATION ON HUMAN SKIN 2007. [DOI: 10.1039/9781847557957-00225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Thierry Douki
- Laboratoire “Lésions des Acides Nucléiques” Service de Chimie Inorganique et Biologique Grenoble France
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14
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Emanuele E, Zakrzewska K, Markovitsi D, Lavery R, Millié P. Exciton states of dynamic DNA double helices: alternating dCdG sequences. J Phys Chem B 2007; 109:16109-18. [PMID: 16853047 DOI: 10.1021/jp051833k] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present communication deals with the excited states of the alternating DNA oligomer (dCdG)5.(dCdG)5 which correspond to the UV absorption band around 260 nm. Their properties are studied in the frame of the exciton theory, combining molecular dynamics simulations and quantum chemistry data. It is shown that the dipolar coupling undergoes important variations with the site and the helix geometry. In contrast, the energy of the monomer transitions within the double helix is not sensitive to the local environment. It is thus considered to be distributed over Gaussian curves whose maximum and width are derived from the experimental absorption spectra of nucleosides in aqueous solution. The influence of the spectral width on the excited state delocalization and the absorption spectra is much stronger than that of the oligomer plasticity. About half of the excited states are delocalized over at least two bases. Many of them result from the mixing of different monomer states and extend on both strands. The trends found in the simulated spectra, when going from non-interacting monomers to the duplex, are in agreement with experimental observations. Conformational changes enhance the diversity of the states which can be populated upon excitation at a given energy. The states with larger spatial extent are located close to the maximum of the absorption spectrum.
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Affiliation(s)
- Emanuela Emanuele
- Laboratoire Francis Perrin CEA/DSM/DRECAM/SPAM-CNRS URA 2453, CEA Saclay, 91191 Gif-sur-Yvette, France
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15
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Labiuk SL, Delbaere LTJ, Lee JS. Gamma and Ultraviolet Radiation Cause DNA Crosslinking in the Presence of Metal Ions at High pH¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0730579gaurcd2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Celewicz L, Mayer M, Shetlar MD. The Photochemistry of Thymidylyl-(3′-5′)-5-methyl-2′-deoxycytidine in Aqueous Solution¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb00201.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Celewicz L, Mayer M, Shetlar MD. The photochemistry of thymidylyl-(3'-5')-5-methyl-2'-deoxycytidine in aqueous solution. Photochem Photobiol 2005; 81:404-18. [PMID: 15493957 DOI: 10.1562/2004-06-15-ra-201.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The photochemistry of the dinucleoside monophosphate thymidylyl-(3'-5')-5-methyl-2'-deoxycytidine (Tpm5dC) has been studied in aqueous solution using both 254 nm and UV-B radiation. A variety of dinucleotide photoproducts containing 5-methylcytosine (m5C) have been isolated and characterized. These include two cyclobutane dimers (CBD) (the cis-syn [c,s]and trans-syn forms), a (6-4) adduct and its related Dewar isomer, and two isomers of a product in which the m5C moiety was converted into an acrylamidine. Small amounts of thymidylyl-(3'-5')-thymidine (TpT) were also formed, presumably as a secondary photoreaction product. In addition, a photoproduct was characterized in which the m5C moiety was lost, thus generating 3'-thymidylic acid esterified with 2'-deoxyribose at the 5-hydroxyl on the sugar moiety. The c,s CBD of Tpm5dC readily undergoes deamination to form the corresponding CBD of TpT. The kinetics of this deamination process has been studied; the corresponding enthalpy and entropy of activation for the reaction have been evaluated at pH 7.4 as being, respectively, 73.4 kJ/mol and -103.5 J/K mol. Deamination was not observed for the other characterized photoproducts of Tpm5dC.
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Affiliation(s)
- Lech Celewicz
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143-0446, USA
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18
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Abstract
The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 +/- 0.3) x 10-3, and that of the cyclobutane dimers is (2.8 +/- 0.2) x 10-2. No triplet absorption is detected, showing that either the intersystem crossing yield decreases by 1 order of magnitude upon oligomerization (<1.4 x 10-3) or the triplet state reacts with unit efficiency in less than 200 ns to yield cyclobutane dimers.
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Affiliation(s)
- Sylvie Marguet
- Laboratoire Francis Perrin, CEA/DSM/DRECAM/SPAM-CNRS, URA 2453, CEA Saclay, 91191 Gif-sur-Yvette, France
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19
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Arndt PF, Hwa T. Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics 2005; 21:2322-8. [PMID: 15769841 DOI: 10.1093/bioinformatics/bti376] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Neighbor-dependent substitution processes generated specific pattern of dinucleotide frequencies in the genomes of most organisms. The CpG-methylation-deamination process is, e.g. a prominent process in vertebrates (CpG effect). Such processes, often with unknown mechanistic origins, need to be incorporated into realistic models of nucleotide substitutions. RESULTS Based on a general framework of nucleotide substitutions we developed a method that is able to identify the most relevant neighbor-dependent substitution processes, estimate their relative frequencies and judge their importance in order to be included into the modeling. Starting from a model for neighbor independent nucleotide substitution we successively added neighbor-dependent substitution processes in the order of their ability to increase the likelihood of the model describing given data. The analysis of neighbor-dependent nucleotide substitutions based on repetitive elements found in the genomes of human, zebrafish and fruit fly is presented. AVAILABILITY A web server to perform the presented analysis is freely available at: http://evogen.molgen.mpg.de/server/substitution-analysis
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Affiliation(s)
- Peter F Arndt
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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20
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Kundu LM, Linne U, Marahiel M, Carell T. RNA Is More UV Resistant than DNA: The Formation of UV-Induced DNA Lesions is Strongly Sequence and Conformation Dependent. Chemistry 2004; 10:5697-705. [PMID: 15472947 DOI: 10.1002/chem.200305731] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA and RNA hairpins, which represent well-folded oligonucleotide structures, were irradiated and the amount of damaged hairpins was directly quantified by using ion-exchange HPLC. The types of photoproducts formed in the hairpins were determined by ESI-HPLC-MS/MS experiments. Irradiation of hairpins with systematically varied sequences and conformations (A versus B) revealed remarkable differences regarding the amount of photolesions formed. UV-damage formation is, therefore, a strongly sequence and conformation dependent process.
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Affiliation(s)
- Lal Mohan Kundu
- Department Chemie, Ludwig-Maximilians University, Butenandtstrasse 5-13, 81377 Munich, Germany
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Douki T, Laporte G, Cadet J. Inter-strand photoproducts are produced in high yield within A-DNA exposed to UVC radiation. Nucleic Acids Res 2003; 31:3134-42. [PMID: 12799441 PMCID: PMC162242 DOI: 10.1093/nar/gkg408] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Far-UV irradiation of DNA leads to the dimerization of pyrimidine bases, resulting in the formation of cyclobutane type dimers and (6-4) photoproducts. In the dry state, an additional thymine dimeric photolesion, the spore photoproduct, is also generated. While most photoproducts are expected to be produced between adjacent pyrimidines, little attention has been paid to lesions involving bases located on different DNA strands. Using HPLC- mass spectrometry analysis of enzymatically digested DNA, we observed that, in the dry state, inter-strand dimeric photoproducts represented 30% of the total yield of dimeric thymine lesions. The major inter-strand damage was found to be the spore photoproduct. Formation of inter-strand lesions in significant yield could be obtained in solution upon modification of the DNA conformation as the result of the addition of large amounts of ethanol. In both cases, DNA is in the A-form, which is characterized by a high compaction, likely to favor inter-strand photoreactions. Since the latter DNA conformation is also predominant in bacterial spores, the formation and repair of dimeric photoproducts involving thymine bases located on different DNA strands may thus be relevant in terms of deleterious effects of UV radiation to the latter microorganisms.
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Affiliation(s)
- Thierry Douki
- Laboratoire 'Lésions des Acides Nucléiques', Service de Chimie Inorganique et Biologique, FRE 2600, CEA/DSM/Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France.
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Douki T, Cadet J. Formation of the spore photoproduct and other dimeric lesions between adjacent pyrimidines in UVC-irradiated dry DNA. Photochem Photobiol Sci 2003; 2:433-6. [PMID: 12760543 DOI: 10.1039/b300173c] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Far-UV irradiation of DNA leads to the formation of several types of dimeric lesions between adjacent pyrimidine bases including cyclobutane dimers, (6-4) photoproducts and Dewar valence isomers In the dry state, an additional specific thymine lesion, the spore photoproduct, is produced. We designed an HPLC-tandem mass spectrometry assay for the detection of the latter lesion. This technique that does not require radio-labelling of DNA allowed the simultaneous quantification of the spore photoproduct and other pyrimidine dimeric photoproducts. Using this approach, the complete distribution of bipyrimidine lesions within UVC-irradiated dry DNA was determined.
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Affiliation(s)
- Thierry Douki
- Laboratoire "Lésions des Acides Nucléiques", Service de Chimie Inorganique et Biologique, FRE 2600, CEA/DSM/Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 38054 Grenoble 9, France.
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Ravanat JL, Douki T, Cadet J. Direct and indirect effects of UV radiation on DNA and its components. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2001; 63:88-102. [PMID: 11684456 DOI: 10.1016/s1011-1344(01)00206-8] [Citation(s) in RCA: 598] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In this survey, emphasis was placed on the main photoreactions of nucleic acid components, involving both direct and indirect effects. The main UVB- and UVA-induced DNA photoproducts, together with the mechanisms of their formation, are described. Information on the photoproduct distribution within cellular DNA is also provided, taking into account the limitations of the different analytical methods applied to monitor the formation of the DNA damage. Thus, the formation of the main DNA dimeric pyrimidine lesions produced by direct absorption of UVB photons was assessed using a powerful HPLC-tandem mass spectrometry assay. In addition, it was found that UVA photooxidation damage mostly involves the guanine residues of cellular DNA as the result of singlet oxygen generation by still unknown endogenous photosensitizers.
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Affiliation(s)
- J L Ravanat
- Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR 5046, Département de Recherche Fondamentale sur la Matière Condensée, CEA Grenoble, 17 Avenue des Martyrs, F-38054 Grenoble Cedex 9, France
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Labiuk SL, Delbaere LT, Lee JS. Gamma and ultraviolet radiation cause DNA crosslinking in the presence of metal ions at high pH. Photochem Photobiol 2001; 73:579-84. [PMID: 11421062 DOI: 10.1562/0031-8655(2001)073<0579:gaurcd>2.0.co;2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
M-DNA is a novel duplex conformation in which metal ions such as Co2+, Ni2+ or Zn2+ replace the imino protons of every base pair. An ethidium fluorescence assay was used to estimate lesions in M-DNA induced by gamma- and UV radiation. General damage to DNA was assessed from the loss of ethidium fluorescence after irradiation of calf thymus DNA. Crosslinks were measured from the return of ethidium fluorescence after a heating and cooling step. Strand breaks were estimated from the loss of fluorescence in covalently closed circular plasmid DNA after a heating and cooling step. For the Co2+ form of M-DNA, gamma-radiation caused the very efficient formation of crosslinks which was not observed with B-DNA nor with the Ni2+ or Zn2+ forms of M-DNA. The crosslinks occurred in both A-T and G-C base pairs but did not form in the presence of a free radical scavenger. Crosslinks induced by UV radiation also formed at a faster rate in the Co2+, Ni2+ and Zn2+ forms of M-DNA compared to B-DNA; crosslinking occurred in all DNA but was more prominent in AT-rich sequences and was not inhibited by a free radical scavenger. Therefore, the presence of certain metal ions may lead to large increases in the formation of radiation-induced crosslinks in DNA.
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Affiliation(s)
- S L Labiuk
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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UV damage to nucleic acid components. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1568-461x(01)80045-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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Distribution and Repair of Bipyrimidine Photoproducts in Solar UV-irradiated Mammalian Cells. J Biol Chem 2000. [DOI: 10.1016/s0021-9258(19)61437-7] [Citation(s) in RCA: 185] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Douki T, Court M, Sauvaigo S, Odin F, Cadet J. Formation of the main UV-induced thymine dimeric lesions within isolated and cellular DNA as measured by high performance liquid chromatography-tandem mass spectrometry. J Biol Chem 2000; 275:11678-85. [PMID: 10766787 DOI: 10.1074/jbc.275.16.11678] [Citation(s) in RCA: 175] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
UVB radiation-induced formation of dimeric photoproducts at bipyrimidine sites within DNA has been unambiguously associated with the lethal and mutagenic properties of sunlight. The main lesions include the cyclobutane pyrimidine dimers and the pyrimidine (6-4) pyrimidone adducts. The latter compounds have been shown in model systems to be converted into their Dewar valence isomers upon exposure to UVB light. A new direct assay, based on the use of liquid chromatography coupled to tandem mass spectrometry, is now available to simultaneously detect each of the thymine photoproducts. It was applied to the determination of the yields of formation of the thymine lesions within both isolated and cellular DNA exposed to either UVC or UVB radiation. The cis-syn cyclobutane thymine dimer was found to be the major photoproduct within cellular DNA, whereas the related (6-4) adduct was produced in an approximately 8-fold lower yield. Interestingly, the corresponding Dewar valence isomer could not be detected upon exposure of human cells to biologically relevant doses of UVB radiation.
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Affiliation(s)
- T Douki
- Commissariat à l'Energic Aromique/Grenoble, DRFMC/Service de Chimie Inorganique et Biologique, Laboratoire Lésions des Acides Nucléiques, 17 Ave. des Martyrs, F-38054 Grenoble, Cedex 9, France
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Douki T, Court M, Cadet J. Electrospray-mass spectrometry characterization and measurement of far-UV-induced thymine photoproducts. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2000; 54:145-54. [PMID: 10836545 DOI: 10.1016/s1011-1344(00)00009-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Far-UV-induced formation of dimeric pyrimidine photoproducts within DNA is a major cause of the carcinogenic effects of solar light. The chemical structure of this class of lesion has been mostly determined by studies on model compounds. The present work is aimed at providing mass spectrometry data on the thymine-thymine photoproducts, including the diastereoisomers of the cyclobutane dimer, the (6-4) adduct, the related Dewar valence isomer and the spore photoproduct. Fragmentation mass spectra of the modified bases, nucleosides, dinucleoside monophosphates and dinucleotides were recorded following electrospray ionization with either triple-quadrupolar or ion-trap detection. The results showed differences in fragmentation pattern between the different types of photoproducts. In addition, a drastic effect of the diastereoisometry was observed for the cyclobutane dimers. A sensitive detection technique has been developed for the analysis of dinucleoside monophosphate photoproducts by high-performance liquid chromatography associated with mass spectrometry in the negative mode with multiple reaction-monitoring detection.
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Affiliation(s)
- T Douki
- Département de Recherche Fondamentale sur la Matière Condensée, CEA/Grenoble, France
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Mizukoshi T, Hitomi K, Todo T, Iwai S. Studies on the Chemical Synthesis of Oligonucleotides Containing the (6−4) Photoproduct of Thymine−Cytosine and Its Repair by (6−4) Photolyase. J Am Chem Soc 1998. [DOI: 10.1021/ja982004y] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toshimi Mizukoshi
- Contribution from the Department of Bioorganic Chemistry, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan, and Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenichi Hitomi
- Contribution from the Department of Bioorganic Chemistry, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan, and Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takeshi Todo
- Contribution from the Department of Bioorganic Chemistry, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan, and Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shigenori Iwai
- Contribution from the Department of Bioorganic Chemistry, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan, and Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Ramaiah D, Koch T, Orum H, Schuster GB. Detection of thymine [2+2] photodimer repair in DNA: selective reaction of KMnO4. Nucleic Acids Res 1998; 26:3940-3. [PMID: 9705501 PMCID: PMC147792 DOI: 10.1093/nar/26.17.3940] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The specific reaction of potassium permanganate with thymine in single-stranded DNA was employed to analyze thymine [2+2] dimer repair in DNA and in DNA/peptide nucleic acid hybrid duplexes. This simple and highly sensitive chemical assay is convenient for monitoring repair of thymine dimers in oligonucleotides.
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Affiliation(s)
- D Ramaiah
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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31
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Herrlich P, Blattner C, Knebel A, Bender K, Rahmsdorf HJ. Nuclear and non-nuclear targets of genotoxic agents in the induction of gene expression. Shared principles in yeast, rodents, man and plants. Biol Chem 1997; 378:1217-29. [PMID: 9426181 DOI: 10.1515/bchm.1997.378.11.1217] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interplay between environmental cues and the genetic response is decisive for the development, health and well-being of an organism. For some environmental factors a narrow margin separates beneficial and toxic impacts. With the increasing exposure to UV-B this dichotomy has reached public attention. This review will be concerned with the mechanisms that mediate a cellular genetic response to noxious agents. The toxic stimuli find access to the regulatory network inside cells by interacting at several points with cellular molecules - a process that converts the 'outside information' into 'cellular language'. As a consequence of such interactions, many adverse agents cause massive signal transduction and changes of gene expression. There is an interesting conservation of the mechanisms from yeast to man. An understanding of the genetic programs and of their phenotypic consequences is lagging behind.
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Affiliation(s)
- P Herrlich
- Forschungszentrum Karlsruhe, Institut für Genetik and Universität Karlsruhe, Germany
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