High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications

Davies, R. Jeremy H.; Malone, John F.; Gan, Yu; Cardin, C.J.; Lee, Michael P.H.; Neidle, Stephen

doi:10.1093/nar/gkl1101

Cited by 26 publications

(23 citation statements)

References 35 publications

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“…It was also shown that 8-oxoGua and single-strand breaks are generated with a very low efficiency that is about two to three orders of magnitude lower than that of bipyrimidine photoproducts in cells exposed to UVB radiation (Kielbassa et al 1997;Douki et al 1999;Cadet et al 2012c). It remains to be assessed whether adenine-containing interstrand cross-links that have been characterized in model studies (Wang et al 2001;Davies et al 2007;Asgatay et al 2010;Su et al 2010) are formed in cellular DNA. Increasing interest is being devoted to the photoreactions of 5-methylcytosine at CpG sites because of the implication of methylated cytosine in epigenetic regulation.…”

Section: Formation and Repair Of Uvb-induced Dna Photoproductsmentioning

confidence: 99%

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

Cadet

Wagner

2013

Cold Spring Harbor Perspectives in Biology

693

510

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Emphasis has been placed in this article dedicated to DNA damage on recent aspects of the formation and measurement of oxidatively generated damage in cellular DNA in order to provide a comprehensive and updated survey. This includes single pyrimidine and purine base lesions, intrastrand cross-links, purine 5 0 ,8-cyclonucleosides, DNA-protein adducts and interstrand cross-links formed by the reactions of either the nucleobases or the 2-deoxyribose moiety with the hydroxyl radical, one-electron oxidants, singlet oxygen, and hypochlorous acid. In addition, recent information concerning the mechanisms of formation, individual measurement, and repair-rate assessment of bipyrimidine photoproducts in isolated cells and human skin upon exposure to UVB radiation, UVA photons, or solar simulated light is critically reviewed.I n this article, we emphasize recent developments in the formation of damage to cellular DNA mediated by reactive oxygen species (ROS) and oxidizing agents, including singlet oxygen, the hydroxyl radical ( † OH), one-electron oxidants, hypochlorous acid (HOCl), and ten-eleven translocation (TET) oxygenases involved in epigenetic regulation. These advances have been possible because of the development of sensitive and powerful high-performance liquid chromatography-mass spectrometry (HPLC-MS)/ mass spectrometry (MS) methods allowing one to revise previously reported data obtained using methods such as gas chromatographymass spectrometry (GC-MS), immunoassays, and HPLC with single MS detection (Cadet et al. , 2012a. Considerable progress has also been made in the elucidation of oxidative degradation pathways of isolated DNA and related model compounds (for recent comprehensive reviews, see Gimisis and Cismaş 2006;Neeley and Essigmann 2006;Pratviel and Meunier 2006;von Sonntag 2006;Cadet et al. 2008Cadet et al. , 2010Cadet et al. , 2012bDedon 2008;Burrows 2009;Wagner and Cadet 2010). In addition, there is much complementary information on solar-radiation-induced formation of bipyrimidine photoproducts in the DNA of fibroblasts, keratinocytes, and human skin. In particular, the distribution of UVA and UVB photoproducts has been determined, allowing accurate determination of their rates of repair (Cadet et al.

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Section: Formation and Repair Of Uvb-induced Dna Photoproductsmentioning

confidence: 99%

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

Cadet

Wagner

2013

Cold Spring Harbor Perspectives in Biology

693

510

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“…In parallel, we detect the ngerprints of the dimerization reactions. Such reactions are known to occur on the singlet excited state following 254 nm excitation of AT strands, [20][21][22][23] leading to the formation of various photoproducts whose nature is still a matter of debate. 24 Our experimental results are interpreted in the light of quantum mechanical calculations (TD-DFT).…”

Section: Introductionmentioning

confidence: 99%

Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation

et al. 2018

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There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical. The adenine radicals, thus identified in the time-resolved spectra, disappear with a lifetime of 2.5 ms, giving rise to a reaction product that absorbs at 350 nm. In parallel, the fingerprint of reaction intermediates other than radicals, formed directly from singlet excited states and assigned to AT/TA dimers, is detected at shorter wavelengths. PCM/TD-DFT calculations are carried out to map the pathways leading to such species and to characterize their absorption spectra; we find that, in addition to the path leading to the well-known TA* photoproduct, an AT photo-dimerization path may be operative in duplexes.

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“…Previous studies (41,42) have shown that UVC irradiation of DNA strands containing "AATTAA" would produce the AA and TA photoproducts, along with the CPD and PP. However, the AA and TA photochemical yields are at most only 10% of those of TT, making these products much less probable (43,44). The yield of formation of the PP was found to have a sequencedependent photochemistry.…”

Section: Detection Of Uv-induced Dna Photodamage In 96-well Platementioning

confidence: 99%

Multiplexed, UVC‐Induced, Sequence‐Dependent DNA Damage Detection

Nair

Loppnow

2013

Photochem & Photobiology

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The exposure of DNA to ultraviolet (UV) radiation causes sequence-dependent damage. Thus, there is a need for an analytical technique that can detect damage in large numbers of DNA sequences simultaneously. In this study, we have designed an assay for UVC-induced DNA damage in multiple oligonucleotides simultaneously by using a 96-well plate and a novel automated sample mover. The UVC-induced DNA damage is measured using smart probes, analogs of molecular beacons in which guanosine nucleotides act as the fluorescence quencher. Our results show that the oligonucleotide damage constants obtained with this method are reproducible and similar to those obtained in cuvettes. The calibration curve for poly-dT shows good linearity (R(2) = 0.96), with limits of detection (LOD) and quantification (LOQ) equal to 55 and 183 nm, respectively. The results show that the damage kinetics upon irradiation is sensitive to the different types of photoproducts formed in the different sequences used; i.e. poly-A oligonucleotides containing guanine are damaged at a faster rate than poly-A oligonucleotides containing either thymine or cytosine. Thus, detecting DNA damage in a 96-well plate and quantifying the damage with smart probes are a simple, fast and inexpensive mix-and-read technique for multiplexed, sequence-specific DNA damage detection.

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High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications

Cited by 26 publications

References 35 publications

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation

Multiplexed, UVC‐Induced, Sequence‐Dependent DNA Damage Detection

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