Encyclopedia of Astrobiology

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DNA Damage

  • Thierry Douki
  • Jean CadetEmail author
Living reference work entry

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DOI: https://doi.org/10.1007/978-3-642-27833-4_451-3
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Keywords

Bipyrimidine photoproducts Cyclobutane pyrimidine dimers DNA oxidation products DNA strand breaks 8-Oxo-7,8-dihydro-2′-deoxyguanosine Pyrimidine (6-4) pyrimidone photoproducts Spore photoproduct 

Synonyms

Definition

DNA damage consists in chemical modifications of the deoxyribonucleic acid components that include alterations of the four main purine (adenine, guanine) and pyrimidine (cytosine, thymine) bases, the relatively minor 5-methylcytosine base and the 2-deoxyribose moiety. According to the damaging agents that may be endogenous (reactive oxygen and nitrogen species such as hydroxyl radical, peroxynitrite, etc.) and exogenous (solar light, ionizing radiation, alkylating compounds, etc.), several classes of DNA lesions may be generated. These include single- and double-strand breaks, normal and oxidized abasic sites, single modified bases (oxidized lesions, alkylated adducts, addition products with reactive aldehyde arising from the breakdown of lipid peroxides, and 2-deoxyribose oxidation), tandem modifications (intrastrand bipyrimidine photoproducts, vicinal oxidized bases), DNA-protein cross-links, interstrand cross-links, and clustered lesions (association of several oxidized bases, single- or double-strand breaks produced within one to two helix turns by several radiation-induced radical hits).

History

The discovery and characterization of cis-syn cyclobutane thymine dimer at the beginning of the 1960s, the main UVB- and UVA-mediated degradation product of isolated and cellular DNA, has provided a strong impetus to investigations in the fields of genotoxicity, mutagenesis, and DNA repair.

Overview

This entry focuses on the two main classes of DNA modifications that may be produced upon exposure of living systems to deleterious space conditions. These conditions comprise high vacuum, wide range of temperature variations, and ionizing and UV radiations that have both galactic and solar origins (Nicholson et al. 2000). These effects include DNA photoproducts that are the main alterations generated upon exposure to solar extraterrestrial UV radiation of resistant microorganisms which may be present in outer space. Under the latter conditions, the contribution of the second class of DNA damage that consists of radiation-induced degradation products involving mostly oxidative reactions is relatively minor. However, the situation is different inside manned space vessels due to an efficient shielding against the UV radiation components involving the vacuum-UV (140 < l < 200 nm), UVC (200 < l < 280 nm), UVB (280 < l < 320 nm), and UVA (320 < l < 400 nm) photons. This protection is much more limited against high-charge (Z) and high-energy (E) (HZE) particles of galactic cosmic radiation (GCR) that, in addition to the HZE particles (1% of the nucleonic component), also include high-energy protons (87%) and α-particles (He ions) (12%) as well as electrons. Of concern are also solar particle radiations that are emitted during solar wind and erratic solar flares, consisting mostly of protons with very small amounts of a-particles and HZE ions (Durante and Cucinotta 2008).

Basic Methodology

Major progress has been made during the last two decades in the development of accurate and sensitive methods aimed at measuring photo- and radiation-induced damage to cellular DNA. This has benefited from the availability of new methodological approaches including high-performance liquid chromatography coupled with electrospray ionization-tandem mass spectrometry detection (HPLC-ESI-MS/MS). Thus, the UV-induced DNA photoproducts that mostly consist of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) at the four main bipyrimidine sequences together with 5,6-dihydro-5-(α-thyminyl)-thymine, the so-called spore photoproduct (SP), can be measured by HPLC-MS/MS (Cadet and Douki 2010, 2018). Polyclonal and monoclonal antibodies are also available for monitoring the formation of bipyrimidine photoproducts in cellular DNA and in tissue in a more semiquantitative way. HPLC-MS/MS is the method of choice for assessing the formation of single and clustered oxidatively generated base damage in cellular DNA at least under acute conditions of ionizing radiation exposure (Cadet et al. 2010). The modified version of the comet assay and the alkaline elution technique that both require the use of DNA repair glycosylases to reveal classes of oxidatively generated damage such as oxidized bases and modified purine bases are suitable alternatives although less specific than HPLC-MS/MS to deal with the detection of low amounts of radiation-induced DNA damage.

Key Research Findings

DNA Photoproducts

The UVC and UVB photochemistry of DNA that is triggered by the direct excitation of the bases is strongly dependent on the water content of the considered microorganisms, with two extreme situations that involve vegetative cells and bacterial spores.

Vegetative Cells

Dimerization of two adjacent pyrimidine bases is the overwhelming reaction induced upon exposure of DNA of vegetative cells to UVC and UVB photons, thus giving rise to two main types of photoproducts, namely, cis-syn cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) (Fig. 1). The formation of CPDs involves a [2 + 2] cycloaddition between the C5–C6 double bonds of the two adjacent pyrimidine bases. The generation of 6-4PPs is rationalized in terms of [2 + 2]
Fig. 1

Photo- and radiation-induced damage in DNA: UVB-induced bipyrimidine photoproducts upon photoexcitation and radiation-induced base and 2-deoxyribose degradation products by hydroxyl radical (OH) and one-electron oxidation (ionization)

Paternò-Büchi cycloaddition between the C5–C6 double bond of the 5′-end pyrimidine to either the C4 carbonyl of a thymine or the imine group of a cytosine in a suitable tautomeric form (Cadet and Vigny 1990; Taylor 1994). The efficiency of bipyrimidine photoproduct formation and the relative yield of CPDs and 6-4PPs are strongly dependent on the primary DNA sequence. Another striking feature is the efficient hydrolytic deamination of cytosine residues in either CPDs or at the 5′-end of 6-4PPs that leads to the formation of mutagenic uracil derivatives. One may add that UVA is able to induce CPDs through a direct excitation mechanism (Banyasz et al. 2011) with an efficiency that is higher than the generation of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) (Cadet et al. 2009) that mostly arises from singlet oxygen oxidation of 2′-deoxyguanosine (Cadet et al. 2017).

Bacterial Spores

The spectrum of DNA photoproducts in UVC- or UVB-irradiated bacterial spores is very different from what is observed in vegetative cells. Thus, the spore photoproduct (SP) that is another bithymine lesion is formed almost exclusively at the expense of CPDs and 6-4PPs in Bacillus subtilis spores (Cadet and Douki 2010). The pronounced changes in DNA photoreactivity have been accounted for by notable structural modifications of DNA molecules that were shown to adopt an A-like conformation. This was found to result from the binding of small acid-soluble proteins (SASP) in a dehydrated environment that is maintained by the presence of a high concentration of calcium dipicolinate (Ca-DPA). It was also shown that Ca-DPA is able to photosensitize the UVC-mediated formation of SP while protecting DNA against the damaging effects of UVB and UVA radiations (Cadet and Douki 2010). It may be added that CPDs and 6-4PPs are formed in significant amounts in spores that lack either SASP or Ca-DPA, showing the major role played by the latter molecules in the generation of SP.

Radiation-Induced DNA Damage

The molecular effects of ionizing radiation on cellular DNA may be rationalized in terms of indirect effects through the generation of hydroxyl radical (OH), the product of water molecule radiolysis (Fig. 1), and direct interaction with the genetic material that leads to ionization of the bases and the 2-deoxyribose moiety (von Sonntag 1987). An important aspect to be considered in the mode of action of ionizing radiation is the multiplicity of radical and excitation hits that follow the energy deposition (Goodhead 1994). As a result, clustered damage, initially called “multiply damage,” consisting of several lesions (modified bases, abasic sites, single- and double-strand breaks), may be generated within one or two helix turns. It may be added that the complexity of the clustered DNA damage increases with the linear energy transfer (LET) value of ionizing radiation and heavy particles. This is particularly of concern for space ionizing radiation that consists of high-energy protons and densely ionizing high-LET HZE particles ranging from helium to uranium, whereas terrestrial radiation is represented mostly by low-LET photons (X-, β-, or γ-rays) (Durante and Cucinotta 2008).

OH and One-Electron Oxidation Products as One-Hit Lesions

A large body of information is available on the OH and one-electron oxidation of the purine and pyrimidine bases of DNA, thanks to comprehensive and detailed studies on model compounds Cadet et al. 2009; Wagner and Cadet 2010). Thus, the 4 cis and trans diastereomers of 5,6-dihydroxy-5,6-dihydrothymidine, 5-(hydroxymethyl)-2′-deoxyuridine, and 5-formyl-2′-deoxyuridine have been characterized as the main OH-mediated degradation products of thymidine in cellular DNA (Cadet et al. 2008). Other pyrimidine base oxidation products including 5-hydroxy-5-methylhydantoin, 5-hydroxyhydantoin, 1-carbamoyl-4,5-dihydroxy-2-oxoimidazolidine, 5-hydroxymethylcytosine and 5-formylcytosine have been identified in gamma-irradiated human cells (Madugundu et al. 2014). In addition, 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fig. 2) have been shown to arise from one-electron oxidation and one-electron reduction, respectively, of 8-hydroxy-7,8-dihydroguanyl radical, the initial OH addition product to guanine (Cadet et al. 2010). Similar degradation products are generated by OH addition to adenine, however, with an efficiency that is about tenfold lower than for guanine degradation products. One-electron oxidation of nucleobases in cells gives rise to the same pattern of degradation products as those induced by OH. However, one may note a different product distribution since 8-oxodGuo is formed predominantly upon ionization of the bases as the result of positive hole migration along the DNA chain with preferential trapping of the radical cation at guanine sites (Genereux and Barton 2010; Kanvah et al. 2010). It is well documented that DNA single-strand breaks (SSBs) are generated by OH-mediated hydrogen abstraction from the 2-deoxyribose moiety (von Sonntag 2006; Dedon 2008). Ionization reactions are also likely to be involved in the formation of SSBs although there is still a lack of mechanistic information.
Fig. 2

Radiation-induced formation of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) and N(2-deoxy-β-D-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapydGuo) as the result of either OH addition or electron abstraction

Specific Radiation-Induced Clustered Damage

DNA double-strand breaks (DSBs) that consist of two closely spaced and opposed single-strand breaks (SSBs) separated by less than 15 base pairs are the most representative radiation-induced DNA clustered damage. It has been predicted by Monte Carlo calculations that the frequency of complex DSBs that contain at least one additional nick/or modified base increases up to 70% for 2 MeV particles, while the proportion was only 20% for low-LET 4.5 keV electrons. Experimental support for the induction of a higher density of DSBs with the increase in LET of incident HZE particles was provided by the observation of a larger frequency of fluorescent γ-H2AX foci (i.e., 1 of the eukaryotic histones that becomes phosphorylated on serine 139 as a reaction to DNA DSBs formation). It has also been shown that the DSBs generated with high-LET radiation are more difficult to be repaired likely due to an increase in the complexity of the clustered lesions.

A second class of complex DNA damage consists in non-double-strand break clustered damage that may comprise at least one strand break together with one or several base lesions and/or apurinic sites on the two complementary DNA strands within one or two DNA helix turns (Hada and Georgakilas 2008). Attempts have been made using a DNA repair-based assay to monitor the formation of these lesions. However, it was found that the yield of clustered lesions, thus measured, is only slightly lower to those of single oxidized bases in irradiated cells, a rather surprising finding. At this point it may be stressed that further work is required to better assess the formation of clustered DNA modifications.

Applications

The measurement of CPDs, 6-4PPS, and SP photoproducts has been made in the DNA of several microorganisms allowing detailed studies of their repair. The yields of bipyrimidine photoproducts vary according to the microorganisms due to the presence in some cases of photoprotective compounds and differences in the membrane composition. One may also note that the radiation-induced formation of 8-oxodGuo in cellular DNA was found to decrease with the increase in LET of the radiation. This is indirectly indicative of the major deleterious role played by complex clustered DNA damage in radiation biology.

Future Directions

Efforts should be made to better ascertain the effects of vacuum-UV light on the DNA of resistant microorganisms including bacterial spores when exposed to outer space conditions in terms of photoproduct distribution. Another major topic to be further investigated concerns the detection and quantification of radiation-induced clustered damage whose identification remains a challenging issue due to the complexity of the analytical problem thus addressed and the oneness of each of the damage.

See Also

References and Further Reading

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Laboratoire Lésions des Acides NucléiquesInsitut Nanosciences et Cryogénie/CEAGrenobleFrance
  2. 2.Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la SantéUniversité de SherbrookeSherbrookeCanada