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Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here we introduce a model of thymine dimers in the oxDNA forcefield, parametrised by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.

The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged β-hairpin able to protrude into the major groove of DNA., Ahmadi et al. use a single-molecule tracking method to describe the DNA scanning mode of AlkD, a HEAT-like repeat DNA glycosylase. They show that, contrary to other glycosylases that use a base-flipping mechanism, AlkD scans the DNA without forming a stable interrogation complex.

The α-ketoglutarate-dependent (AlkB) superfamily of FeII/2-oxoglutarate (2-OG)-dependent dioxygenases consists of a unique class of nucleic acid repair enzymes that reversibly remove alkyl substitu...

During the last 30 years, the comet assay has become widely used for the measurement of DNA damage and repair in cells and tissues. A landmark achievement was reached in 2016 when the Organization for Economic Co-operation and Development adopted a comet assay guideline for in vivo testing of DNA strand breaks in animals. However, the comet assay has much more to offer than being an assay for testing DNA strand breaks in animal organs. The use of repair enzymes increases the range of DNA lesions that can be detected with the assay. It can also be modified to measure DNA repair activity. Still, despite the long-term use of the assay, there is a need for studies that assess the impact of variation in specific steps of the procedure. This is particularly important for the on-going efforts to decrease the variation between experiments and laboratories. The articles in this Special Issue of Mutagenesis cover important technical issues of the comet assay procedure, nanogenotoxicity and ionising radiation sensitivity on plant cells. The included biomonitoring studies have assessed seasonal variation and certain predictors for the basal level of DNA damage in white blood cells. Lastly, the comet assay has been used in studies on genotoxicity of environmental and occupational exposures in human biomonitoring studies and animal models. Overall, the articles in this Special Issue demonstrate the versatility of the comet assay and they hold promise that the assay is ready for the next 30 years.

Viral enteric disease imposes a considerable public health and economic burden globally in both humans and livestock. Because enteric viruses are highly transmissible and resistant to numerous control strategies, making early in-field or point-of-care detection is important. There are problems with ligand-based detection strategies (e.g., sensitivity, false positive/negatives) for virus detection. Traditional amplification-based strategies are sensitive, but not as portable or rapid. Recombinase polymerase amplification is a new isothermal technique that utilizes bacterial genome repair enzymes to rapidly amplify target sequences. This report reviews the use of recombinase polymerase amplification for virus detection, showing that the method has favorable fundamental properties supporting its promise for rapid point-of-care detection of enteric viruses.

Tomas Lindahl completed his medical studies at Karolinska Institute in 1970. Yet, his work has always been dedicated to unraveling fundamental mechanisms of DNA decay and DNA repair. His research is characterized with groundbreaking discoveries on the instability of our genome, the identification of novel DNA repair activities, the characterization of DNA repair pathways, and the association to diseases, throughout his 40 years of scientific career.

The global burden of cardiovascular disease is increasing despite therapeutic advances in medication and interventional technologies. Accumulated deoxyribonucleic acid (DNA) damage and subsequent repair pathways are now increasingly recognised as a causal factor in the initiation and progression of atherosclerosis. These molecular alterations have been shown to occur within affected vasculature, plaque microenvironment as well as in circulating cells. The DNA damage response (DDR) pathway is reliant on post-translational modification of sensing proteins which activate a signalling cascade to repair, if possible, DNA damaged sites in response to various environmental and physiological insults. This review summarises the current evidence for DNA damage in atherosclerosis, the key steps involved in the DDR pathway, DNA repair and their subsequent effects on atherosclerotic plaques, as well as the therapeutic options in managing DNA damage-induced atherosclerosis.

Our cells contain common molecules, such as water or oxygen, that can damage DNA. In his studies Tomas Lindahl has shown how specific repair enzymes remove and replace damaged parts of DNA in a process of vital importance.

The influence of DNA repair gene polymorphisms (XRCC1: Arg194Trp, Arg280His, Arg399Gln; APE1: Asp148Glu; hOGG1: Ser326Cys) on oxidative DNA damage is controversial and was investigated in 214 German workers with occupational exposure to vapors and aerosols of bitumen,compared to 87 German construction workers without exposure, who were part of the Human Bitumen Study. Genotypes were determined by real-time polymerase chain reaction (PCR), and actual smoking habits by a questionnaire and cotinine analysis. Oxidative DNA damage in white blood cells (WBC) collected pre- and postshift was measured as 8-oxodGuo adducts/10(6) dGuo by a hjigh-performance liquid chromatography electron capture detection (HPLC-ECD) method, followed by calculation of the difference between post- and preshift values (Δ8-oxodGuo/10(6) dGuo). The 214 bitumen exposed workers showed higher median Δ8-oxodGuo values than the 87 references. In the whole study group (n=301) there was a trend for increasing adduct values for XRCC1 Arg(GG)399Gln(AA) during a shift, especially in nonsmokers (n=108. Referents (n=87) displayed a similar trend for hOGG1 Ser(CC)326Cys(GG). In contrast, XRCC1 Arg(GG)280His(AA) showed a decrease of median Δ8-oxodGuo/10(6) dGuo values in workers with exposure to vapors and aerosols of bitumen (n=214), especially in smokers (n=145). XRCC1 Arg194Trp and APE1 Asp148Glu displayed no marked association with Δ8-oxodGuo levels. Data indicate that the combination of different variants in DNA damage repair enzymes may modulate the production of 8-oxoguanine adducts in WBC produced by xenobiotics during a shift.

The kinetics of the search for damaged DNA bases by repair enzymes was theoretically studied. In particular, the characteristic features of the diffusive motion of the enzyme were investigated. Compact analytical expressions for the average search time and its dispersion were obtained for two models of the one-dimensional motion of the enzyme along the DNA fragment: continuous diffusion and stochastic jumps. It was shown that the kinetics of the search is essentially non-exponential due to characteristic features of the diffusive motion.

DNA damage is a hazard all cells must face, and evolution has created a number of mechanisms to repair damaged bases in the chromosome. Paradoxically, many of these repair mechanisms can create double-strand breaks in the DNA molecule which are fatal to the cell. This indicates that the connection between DNA repair and death is far from straightforward, and suggests that the repair mechanisms can be a double-edged sword. In this report, we formulate a mathematical model of the dynamics of DNA damage and repair, and we obtain analytical expressions for the death rate. We predict a counterintuitive relationship between survival and repair. We can discriminate between two phases: below a critical threshold in the number of repair enzymes, the half-life decreases with the number of repair enzymes, but becomes independent of the number of repair enzymes above the threshold. We are able to predict quantitatively the dependence of the death rate on the damage rate and other relevant parameters. We verify our analytical results by simulating the stochastic dynamics of DNA damage and repair. Finally, we also perform an experiment with Escherichia coli cells to test one of the predictions of our model.

The 40th International Symposium of the Princess Takamatsu Cancer Research Fund, entitled “DNA Repair and Human Cancers,” was held on November 10–12, 2009 at Hotel Grand Palace, Tokyo, Japan. The meeting focused on the role of DNA repair in preventing mutations by endogenous and exogenous DNA damage and increasing the efficacy of chemotherapeutic agents by interfering with DNA repair. The 14 presentations by the speakers from the United States, four from the United Kingdom, one each from Italy, The Netherlands, and France, and 13 from Japan, covered most aspects of DNA repair, spanning DNA damage, molecular structures of repair enzymes, and clinical studies on inhibition of DNA repair processes. Extensive time was reserved for discussions with the active participation of the 150 invited Japanese scientists. The choice of a symposium on DNA repair in human cancers resulted in part from the excellent basic and clinical studies that have been carried out for many years in Japan, and the general lack of recognition versus the importance of DNA repair in understanding carcinogenesis. Cancer Res; 70(11); 4269–73. ©2010 AACR.

An investigation of the precise interactions between damaged DNA and DNA repair enzymes is required in order to understand the lesion recognition step, which is one of the most fundamental processes in DNA repair. Most recently, photoaffinity labeling approaches have enabled the analysis of even transient protein-DNA interactions. Here we report the synthesis and evaluation of oligonucleotides that contain two photoaffinity "catcher moieties" next to incorporated DNA lesions. With these DNA constructs it is possible to analyze the interactions between DNA lesions and the appropriate repair enzymes. The probes labeled the repair protein efficiently enough to enable subsequent protein analysis by mass spectrometry.

As part of the EU-project COMICS, high throughput versions of the comet assay was developed. In order to test the performance of the new formats; the novel 12-gel slide and the 96-minigel film were compared with standard 3-gel slides for their ability to detect effects of genotoxic chemicals on cellular DNA with limited cytotoxicity. Among the chemicals were negative controls, a non-carcinogen that causes DNA damage through cytotoxicity, and carcinogens that are known to be hard to detect by simple DNA strand break analysis. Chemicals requiring metabolic activation were preincubated with rat liver S9 fraction. TK-6 human lymphoblastoid cells were treated with a range of concentrations of each chemical, above and below the expected cytotoxic concentration. Trials were carried out in 3 centres applying all three formats. Results obtained with the three systems (standard, medium- and high-throughput) were essentially the same. The 96-minigel format was analysed with the fully automated scoring system IMSTAR and comparable results were achieved with the semi-automated scoring system from Perceptives. The known genotoxic chemicals MNU, B(a)P, 4-NQO and cyclophosphamide showed little consistent sign of genotoxicity at concentrations causing limited cytotoxicity. D-mannitol and Triton X-100 were, as expected, non-genotoxic (though Triton X-100, at high concentrations, caused DNA breaks as an apparent secondary effect of cytotoxicity). Etoposide and bleomycin gave significant increase in DNA strand break at borderline cytotoxic concentrations. The limitation of the assay to detect damaged bases by known genotoxins may be overcome by incorporating a DNA repair enzyme, such as formamidopyrimidine-DNA-glycosylase (FPG), to convert damaged bases into breaks as shown by Azqueta A et al., Mutagenesis vol. 28 no. 3 pp. 271–277, 2013 .

Molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.

Global DNA topology is sensed locally by enzymes that act on plectonemes in supercoiled DNA. Here we report that the formation and diffusion of plectonemes are determined by the energetic contributions of their tips and tails. First, to systematically vary the geometry and formation energy of plectoneme end-loops, we introduced base-pair defect regions of variable size (1-16 bp) using a cassette based single-strand nicking template generated by PCR. Direct manipulation measurements with magnetic tweezers revealed that even a single mismatch or abasic site is sufficient to nucleate formation of a plectoneme. Presentation of the defect precisely at an extruded plectoneme tip potentially serves as a damage-sensing mechanism and may facilitate the search process of repair enzymes. Second, our measurements unexpectedly revealed that after twisted DNA abruptly buckles into an initial plectoneme loop, further plectoneme extrusion occurs through a cascade of additional buckling steps in which the torque changes by roughly half of the initial overshoot value. These discrete steps do not match any obvious scale of the system but are consistent with discontinuous feed-in of curving plectoneme tails. In light of these results, theoretical models of plectonemes should include their overall structure, including the often neglected tips and tails.

The purpose of the present review is to summarize the data related with the structural features of interaction between the human repair enzyme 8-oxoguanine DNA glycosylase (hOGG1) and DNA. The review covers the questions concerning the role of individual amino acids of hOGG1 in the specific recognition of the oxidized DNA bases, formation of the enzyme–substrate complex, and excision of the lesion bases from DNA. Attention is also focused upon conformational changes in the enzyme active site and disruption of enzyme activity as a result of amino acid mutations. The mechanism of damaged bases release from DNA induced by hOGG1 is discussed in the context of structural dynamics.

DNA photolyases are repair enzymes which split (repair) UV-induced cyclobutane DNA lesions. Critical steps in the light-driven repair reaction are the absorption of light by a deazaflavin or methen...

Purpose: To investigate whether it is possible to explain doseresponse plateaus for in-vitro X-ray irradiation of different cell lines with radioprotective mechanisms such as radiologically induced expression of scavengers and repair enzymes. Materials and methods: A biomathematical model was developed based on a previous state-vector model. New features of the model are a mathematical description of enhanced repair and radical scavenging as a result of irradiation. Results: The model produces a plateau in the dose-response for in-vitro tranformations between 0.5 and 1Gy and for chromosome aberrations and it predicts an inverse-fractionation effect within a selected range of doses. Conclusions: Adaptive response mechanisms within a state-vector model provide a coherent explanation of the dose-response characteristics for in-vitro transformations and chromosomal aberrations. These results suggest the need for new experimental studies described in the paper.

Recent crystallographic studies of DNA-repair enzymes have provided the structural basis for the recognition of damaged DNA. The results imply that flipping out of the base is a common and crucial event in DNA repair. Two classes of repair enzymes that recognize distinct types of damage may exist. DNA-repair enzymes that share similar folds and DNA binding motifs have been proposed to belong to a superfamily.

Defects in DNA, e.g., unpaired/bulged nucleotides, are repaired by specific repair enzymes. Understanding the dynamics and structure of DNA defects is important. Two DNA heptamers, CTb-GTACG and CGTACTbG, each containing a bulged T nucleotide embedded in the CpG step, have been studied by NMR. Both duplexes are significantly destabilized, and the bulged T remains intrahelical. Binding of the anthracycline antitumor antibiotic nogalamycin (Ng) to these two heptamers stabilizes the duplex structure. The solution structures of the 2:1 complexes of Ng-d(CTbGTACG) and Ng-d(CGTACTbG) have been determined by the NOE-restrained refinement procedure. In both structures the elongated aglycon of Ng is intercalated between base pairs, and the nogalose and aminoglucose lie in the minor and major grooves, respectively. The bulged T behaves differently upon the binding of Ng. In Ng-CTbGTACG wobble G6:Tb base pairs are formed, leaving two dangling 5'-C1 nucleotides; whereas in Ng-CGTACTbG weak C1:Tb base pairs are formed, leaving two dangling 3'-G6 nucleotides. Thus Ng induces the bulged T and the opposing base in the duplex to stack on the aglycon and causes the base next to Tb to unpair, mimicking a "frame-shift". Such structural rearrangement of a bulged DNA site due to the binding of an intercalator drug may perturb the recognition of DNA defects by repair enzymes or may cause mutation during replication.

The biological efficacy of oxidants is based on a highly regulated equilibrium between the production of oxygen radicals and the counteracting defense mechanisms of antioxidant scavenging systems and repair enzymes for the elimination of the degraded bioproducts. Imbalance of this finely tuned, sophisticated equilibrium can result in oxidative stress unleashing a cascade of pathological processes. This review summarizes the general aspects of the analytical methods used for the detection of an excess of free radicals together with a critical evaluation of the results obtained by their application. Free radicals are very reactive, short-lived and react in a non-specific way. In spite of the broad array of existing analytical methods no routine diagnostic in vivo procedures are available to date. The development of more site-specific in vivo methods will enable the elucidation of the exact role of these very reactive radicals and molecular species. For the time being, the most important task of physicians and surgeons is to prevent all catalytic reactions known to initiate pro-oxidative stress and counteract the absolute or relative lack of antioxidants.

Adequate photoprotection is essential to control UV-related disorders, including sunburn, photoaging and photocarcinogenisis. Sun avoidance, protection of skin with clothing, and sunscreens are presently the best way of photoprotection, assuming that they are used properly. However, new strategies, which are based on or make use of the endogenous protective response to UV light, may further improve currently used photoprotective means. The addition of repair enzymes and/or antioxidants has a positive effect on skin's recovery from UV-induced DNA-damage. Several botanical agents, mainly vitamins and polyphenols, have shown to influence signal transduction pathways leading to photoprotective effects. Also stimulation of endogenous UV-response pathways via irradiation with a low UV dose or via simulation of UV-induced DNA-damage results in photoprotective effects. Future research in this field and combination of different photoprotective strategies will hopefully lead to improved photoprotection.

Repair mechanisms for alkylation damage are described. Similarities and differences of repair enzymes in different groups of organisms are discussed with respect to the evolution of these proteins. Some aspects of DNA repair in plants are described.

The human genome is divided into isochores, large stretches (much greater than 300 kb) of genomic DNA with more or less consistent GC content. Mutational/neutralist and selectionist models have been put forward to explain their existence. A major criticism of the mutational models is that they cannot account for the higher GC content at fourfold-redundant silent sites within exons (GC4) than in flanking introns (GCi). Indeed, it has been asserted that it is hard to envisage a mutational bias explanation, as it is difficult to see how repair enzymes might act differently in exons and their flanking introns. However, this rejection, we note, ignores the effects of transposable elements (TEs), which are a major component of introns and tend to cause them to have a GC content different from (usually lower than) that dictated by point mutational processes alone. As TEs tend not to insert at the extremities of introns, this model predicts that GC content at the extremities of introns should be more like that at GC4 than are the intronic interiors. This we show to be true. The model also correctly predicts that small introns should have a composition more like that at GC4 than large introns. We conclude that the logic of the previous rejection of neutralist models is unsafe.

SummaryThe Rad9–Hus1–Rad1 checkpoint clamp (9-1-1) is a central player in the cellular response to DNA damage; three groups have determined the crystal structure of 9-1-1, providing new insight into its loading mechanism and association with DNA damage checkpoint and repair enzymes.

Recent work on Drosophila oogenesis has uncovered connections between cell-cycle checkpoints and pattern formation. Genes of the spindle class, which encode double-strand break repair enzymes and RNA helicases, affect oocyte polarity and the decision whether to differentiate as an oocyte or a nurse cell.

DNA-protein cross-link (DPC) damage is produced by varieties of genotoxic agents such as ionizing radiation, UV light, aldehydes, and some chemotherapeutic compounds. DPCs would be harmful to cells since proteins immobilized on DNA strands could hamper DNA transactions in cells. However, it has not been clarified how DPCs are repaired in cells. In the present study, we prepared DNA substrates containing defined DPCs and tested them for repair enzymes. We also examined the sensitivity of Escherichia coli to DPC-inducing agents.