Base excision repair (BER) is the major pathway for processing of simple lesions in DNA, including single-strand breaks, base damage, and base loss. The scaffold protein XRCC1, DNA polymerase beta, and DNA ligase IIIalpha play pivotal roles in BER. Although all these enzymes are essential for development, their cellular levels must be tightly regulated because increased amounts of BER enzymes lead to elevated mutagenesis and genetic instability and are frequently found in cancer cells. Here we report that BER enzyme levels are linked to and controlled by the level of DNA lesions. We demonstrate that stability of BER enzymes increases after formation of a repair complex on damaged DNA and that proteins not involved in a repair complex are ubiquitylated by the E3 ubiquitin ligase CHIP and subsequently rapidly degraded. These data identify a molecular mechanism controlling cellular levels of BER enzymes and correspondingly the efficiency and capacity of BER.

X-ray repair cross-complementing protein-1 (XRCC1)-deficient cells are sensitive to DNA damaging agents and have delayed processing of DNA base lesions. In support of its role in base excision repair, it was found that XRCC1 forms a tight complex with DNA ligase IIIalpha and also interacts with DNA polymerase beta (Pol beta) and other base excision repair (BER) proteins. We have isolated wild-type XRCC1-DNA ligase IIIalpha heterodimer and mutated XRCC1-DNA ligase IIIalpha complex that does not interact with Pol beta and tested their activities in BER reconstituted with human purified proteins. We find that a point mutation in the XRCC1 protein which disrupts functional interaction with Pol beta, affected the ligation efficiency of the mutant XRCC1-DNA ligase IIIalpha heterodimer in reconstituted BER reactions. We also compared sensitivity to hydrogen peroxide between wild-type CHO-9 cells, XRCC1-deficient EM-C11 cells and EM-C11 cells transfected with empty plasmid vector or with plasmid vector carrying wild-type or mutant XRCC1 gene and find that the plasmid encoding XRCC1 protein, that does not interact with Pol beta has reduced ability to rescue the hydrogen peroxide sensitivity of XRCC1- deficient cells. These data suggest an important role for the XRCC1-Pol beta interaction for coordinating the efficiency of the BER process.

The past decade has seen a surge of interest in the biological effects of UVA exposure as its significance to the process of photo-carcinogenesis has become increasingly evident. However, unpicking the unique complexity of the cellular response to UVA, which is only now becoming apparent, will be a major challenge for the field of photobiology in the 21st century.

The repair of oxidative base lesions in DNA is a coordinated chain of reactions that includes removal of the damaged base, incision of the phosphodiester backbone at the abasic sugar residue, incorporation of an undamaged nucleotide and sealing of the DNA strand break. Although removal of a damaged base in mammalian cells is initiated primarily by a damage-specific DNA glycosylase, several lyases and DNA polymerases may contribute to the later stages of repair. DNA polymerase beta (Pol beta) was implicated recently as the major polymerase involved in repair of oxidative base lesions; however, the identity of the lyase participating in the repair of oxidative lesions is unclear. We studied the mechanism by which mammalian cell extracts process DNA substrates containing a single 8-oxoguanine or 5,6-dihydrouracil at a defined position. We find that, when repair synthesis proceeds through a Pol beta-dependent single nucleotide replacement mechanism, the 5'-deoxyribosephosphate lyase activity of Pol beta is essential for repair of both lesions.

Spontaneously derived DNA lesions, such as base modifications and abasic (AP) sites, and products of base oxidation and alkylation are removed by the base excision repair (BER) pathway [1]. In human cells, BER is initiated by the removal of the damaged base by a DNA glycosylase to generate an AP site that is a substrate for an AP endonuclease (APE1) which cleaves the phosphodiester backbone 5¢ to the lesion, creating a 3¢-OH and 5¢-deoxyribose phosphate (dRP) terminus [2,3]. The majority of the incised AP site proceeds via so-called 'short-patch' repair [4] whereby DNA polymerase b (Pol b) catalyses the removal of the 5¢-dRP lesion through a b-elimination mechanism and also inserts the correct nucleotide to fill the gap [5,6]. The remaining nick in the DNA backbone is then sealed by X-ray cross-complementing gene 1 (XRCC1)-DNA ligase IIIa complex [7][8][9].BER proteins also participate in processing of DNA single-strand breaks (SSB) and one-nucleotide gaps: Pol b is involved in gap filling, XRCC1-DNA ligase IIIa complex is involved in ligation, and APE1 participates in processing of blocked 3¢-ends [10,11]. Furthermore, other proteins, such as polynucleotide kinase and poly(ADP-ribose) polymerase-1 (PARP-1) have been implicated in the repair of SSBs [11][12][13]. PARP-1 is thought to be involved in BER and strand-break processing, as it has a high binding affinity for SSBs [14]. On binding to the strand break, PARP-1 catalytically synthesizes poly(ADP-ribose) polymers from NAD + that covalently modify proteins, of which PARP-1 itself is a target. Subsequently PARP-1 dissociates from the strand break [15]. The importance of PARP-1 in repair is revealed by the fact that PARP-1 knockout mice are hypersensitive to alkylating agents Keywords base excision repair; DNA polymerase b; DNA repair; poly(ADP-ribose) polymerase-1 (PARP-1) Base excision repair (BER), a major pathway for the removal of simple lesions in DNA, requires the co-ordinated action of several repair and ancillary proteins, the impairment of which can lead to genetic instability. We here address the role of poly(ADP-ribose) polymerase-1 (PARP-1) in BER. Using an in vitro cross-linking assay, we reveal that PARP-1 is always involved in repair of a uracil-containing oligonucleotide and that it binds to the damaged DNA during the early stages of repair. Inhibition of PARP-1 poly(ADP-ribosyl)ation by 3-aminobenzamide blocks dissociation of PARP-1 from damaged DNA and prevents further repair. We find that excessive poly(ADP-ribosyl)ation occurs when repair intermediates containing single-strand breaks are in excess of the repair capacity of the cell extract, suggesting that repeated binding of PARP-1 to the nicked DNA occurs. We also find increased sensitivity of repair intermediates to nuclease cleavage in PARP-deficient mouse fibroblasts and after depletion of PARP-1 from HeLa whole cell extracts. Our data support the model in which PARP-1 binding to DNA single-strand breaks or repair intermediates plays a protective role when repair is limited.Abbreviati...

Base excision repair is a major pathway for the removal of simple lesions in DNA including base damage and base loss (abasic site). Base excision repair requires the coordinated action of several repair and ancillary proteins, the impairment of which can lead to genetic instability. Using a protein-DNA cross-linking assay during repair in human whole cell extracts, we monitored proteins involved in the initial steps of repair of a substrate containing a site-specific abasic site to address the molecular events following incision of the abasic site by AP endonuclease. We find that after dissociation of AP endonuclease from the incised abasic site, both DNA polymerase beta (Pol beta) and the DNA ligase IIIalpha-XRCC1 heterodimer efficiently bind/cross-link to the substrate DNA. We also find that the cross-linking efficacy of the DNA ligase IIIalpha-XRCC1 heterodimer was decreased about 2-fold in the Pol beta-deficient cell extract but was rescued by addition of purified wild type but not a mutant Pol beta protein that does not interact with the DNA ligase IIIalpha-XRCC1 heterodimer. We further demonstrate that Pol beta and the DNA ligase IIIalpha-XRCC1 heterodimer are present at equimolar concentrations in whole cell extracts and that Pol beta has a 7-fold higher affinity to the incised abasic site containing substrate than DNA ligase IIIalpha. Using gel filtration of whole cell extracts prepared at physiological salt conditions (0.15 M NaCl), we find no evidence for a stable preexisting complex of DNA Pol beta with the DNA ligase IIIalpha-XRCC1 heterodimer. Taken together, these data suggest that following incision by AP endonuclease, DNA Pol beta recognizes and binds to the incised abasic site and promotes recruitment of the DNA ligase IIIalpha-XRCC1 heterodimer through its interaction with XRCC1.

To investigate the potential role of the hydroxyl radical (•OH) in cold atmospheric plasma (CAP) jet treatment, two fluorescence-based methodologies are utilised to measure DNA strand breaks. The first comprises a model system of a double-stranded DNA oligomer, where the respective strand ends are tagged with fluorophore and quencher molecules; and the second, a cell culture system reporting DNA strand breaks using the γ-H2AX assay. During the various CAP jet treatments, optical emission spectroscopy is used to detect the •OH in the gas phase and electron spin resonance is used to detect the •OH in solution. The CAP jet production of the •OH is shown to correlate to CAP jet induced DNA damage both with the DNA model and in biological cells. Results indicate that the CAP jet induces a higher degree of DNA damage when the CAP plume is in contact with the target solution. The potential of a ‘plasma screen’ based upon a hydrogel film, as a method to remove the DNA-damaging •OH species from reaching skin cells, is shown to significantly reduce DNA damage whilst facilitating the delivery of hydrogen peroxide. These findings could aid in the development of CAP jet-based applications where DNA damage is the objective (e.g. in cancer treatment) and others where it is to be avoided, e.g. in open-wound treatment and dermatology.

Pharmacological inhibition of DNA-repair pathways as an approach for the potentiation of chemo- and radio-therapeutic cancer treatments has attracted increasing levels of interest in recent years. Inhibitors of several enzymes involved in the repair of DNA strand breaks are currently at various stages of the drug development process. Polynucleotide kinase (PNK), a bifunctional DNA-repair enzyme that possesses both 3'-phosphatase and 5'-kinase activities, plays an important role in the repair of both single strand and double strand breaks and as a result, RNAi-mediated knockdown of PNK sensitizes cells to a range of DNA-damaging agents. Recently, a small molecule inhibitor of PNK has been developed that is able to sensitize cells to ionizing radiation and the topoisomerase I poison, camptothecin. Although still in the early stages of development, PNK inhibition represents a promising means of enhancing the efficacy of existing cancer treatments.