Repair of oxidized bases in DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2

Purification and characterization of NEIL1 and NEIL2, members of a distinct family of mammalian DNA glycosylases for repair of oxidized bases

NEIL1 and NEIL2 were newly discovered as mammalian orthologs of Escherichia coli Nei and Fpg, oxidized base-specific DNA glycosylases. These are distinct from previously characterized OGG1 and NTH1, the other two glycosylases for repairing oxidatively damaged bases in mammalian cells, in regards to reaction mechanism. Recombinant human NEIL1 and NEIL2 were purified from E. coli and biochemically characterized. Some damaged bases are common substrates for both groups of enzymes. However, in contrast to the lack of activity of NTH1 and OGG1 for substrate lesions in single-stranded DNA, the NEILs have unique preference for bubble or single-stranded DNA substrates, suggesting their preferential involvement in repairing transcribed or replicating DNA sequences.

Oxidative DNA Glycosylases: Recipes from Cloning to Characterization

As new organisms are being sequenced on a daily basis, new DNA glycosylases that recognize DNA damage can be easily identified in an effort to understand both their phylogenetics and substrate specificities. As a practical matter, existing bacterial and human homologs need to be readily available as laboratory reagents in order to compare the activities of the novel enzymes to existing enzymes. This chapter attempts to provide a primer for cloning, expression, and assay procedures for bacterial and human DNA glycosylases that recognize oxidative DNA damages. These methodologies can be translated readily to novel DNA glycosylases or to DNA glycosylases that recognize other types of DNA damages.

Differential modulation of base excision repair activities during brain ontogeny: implications for repair of transcribed DNA

DNA repair sustains fidelity of genomic replication in proliferating cells and integrity of transcribed sequences in postmitotic tissues. The repair process is critical in the brain, because high oxygen consumption exacerbates the risk for accumulation of oxidative DNA lesions in postmitotic neurons. Most oxidative DNA damage is repaired by the base excision repair (BER) pathway, which is initiated by specialized DNA glycosylases. Because the newly discovered Nei-like mammalian DNA glycosylases (NEIL1/2) proficiently excise oxidized bases from bubble structured DNA, it was suggested that NEILs favor repair of transcribed or replicated DNA. In addition, since NEILs generate 3'-phosphate termini, which are poor targets for AP endonuclease (APE1), it was proposed that APE1-dependent and independent BER sub-pathways exist in mammalian cells. We measured expression and activities of BER enzymes during brain ontogeny, i.e., during a physiologic transition from proliferative to postmitotic differentiated state. While a subset of BER enzymes, exhibited declining expression and excision activities, expression of NEIL1 and NEIL2 glycosylases increased during brain development. Furthermore, the capacity for excision of 5-hydroxyuracil from bubble structured DNA was retained in the mature rat brain suggesting a role for NEIL glycosylases in maintaining the integrity of transcribed DNA in postmitotic brain.

To die or not to die: DNA repair in neurons

One of the critical emerging problems in modern pathobiology is how cells govern the decision to live or die, and the cost of making such a decision. Nowhere are these questions more poignant than in deciphering the tissue-specific responses to DNA damage. Mutations in DNA repair enzymes, malfunctions in cell cycle regulation, and genetic instability are associated with most somatic cancers. However, in many hereditary diseases arising from mutations in DNA repair proteins, the same dominant mutations that cause cancer in dividing cells are often associated with cell death in terminally differentiated neurons. Context dependent differences in the response to DNA damage are used to make fundamental choices as to cell fate, and are likely to shed light on the mechanisms underlying human disease.

Transcription arrest at DNA damage sites

Transcription arrest by RNA polymerase II at a DNA damage site on the transcribed strand is considered an essential step in initiation of transcription-coupled repair (TCR), a specialized repair pathway, which specifically removes lesions from transcribed strands of expressed genes. To understand how initiation of TCR occurs, it is necessary to characterize the properties of the transcription complex when it encounters a lesion in its path. The analysis of different types of arrested complexes should help us understand how an arrested RNA polymerase may signal the repair proteins to initiate a repair event. This article will review the recent literature describing how the presence of DNA damage along the DNA affects transcription elongation by RNA polymerase II and its implications for the initial steps of TCR.

DNA base damage recognition and removal: new twists and grooves

The discoveries of nucleotide excision repair and transcription-coupled repair led by Phil Hanawalt and a few colleagues sparked a dramatic evolution in our understanding of DNA and molecular biology by revealing the intriguing systems of DNA repair essential to life. In fact, modifications of the cut-and-patch principles identified by Phil Hanawalt and colleagues underlie many of the common themes for the recognition and removal of damaged DNA bases outlined in this review. The emergence of these common themes and a unified understanding have been greatly aided from the direct visualizations of repair proteins and their interactions with damaged DNA by structural biology. These visualizations of DNA repair structures have complemented the increasing wealth of biochemical and genetic information on DNA base damage responses by revealing general themes for the recognition of damaged bases, such as sequence-independent DNA recognition motifs, minor groove reading heads for initial damage recognition, and nucleotide flipping from the major groove into active-site pockets for high specificity of base damage recognition and removal. We know that repair intermediates are as harmful as the initial damage itself, and that these intermediates are protected from one repair step to the next by the enzymes involved, such that pathway-specific handoffs must be efficiently coordinated. Here we focus on the structural biology of the repair enzymes and proteins that recognize specific base lesions and either initiate the base excision repair pathway or directly repair the damage in one step. This understanding of the molecular basis for DNA base integrity is fundamental to resolving key scientific, medical, and public health issues, including the evaluation of the risks from inherited repair protein mutations, environmental toxins, and medical procedures.

No Major Role for 7,8-Dihydro-8-oxoguanine in Ultraviolet Light-Induced Mutagenesis

Oxidative DNA damage, in particular 7,8-dihydro-8-oxoguanine (8-oxoG), has been suggested to mediate mutation formation and malignant transformation after exposure of the skin to long-wave ultraviolet (UVA) light. It is processed primarily by the base excision repair (BER) pathway. The initial step of BER is the removal of the damaged base by a damage-specific DNA-glycosylase, which is 8-oxoG DNA glycosylase (OGG1) for 8-oxoG. To study the contribution of 8-oxoG to UVA-light mutagenesis, we compared UVA- and UVB-light-induced mutation frequencies in mouse embryonal fibroblasts from OGG1 knockout mice and their OGG1-intact littermates using the ouabain mutagenesis assay. After irradiation with various doses of UVA or UVB radiation, mutations in the Na,K-ATPase gene of single cells were detected by testing for colony-forming ability in a selective medium. OGG1-/- cells did not exhibit an increased frequency of UV-light-induced mutations compared to OGG1+/+ cells after exposure to either UVA or UVB radiation. This indicates that 8-oxoG, which is processed by OGG1, does not contribute significantly to either UVA- or UVB-light-induced mutagenesis.

NEIL1 excises 3' end proximal oxidative DNA lesions resistant to cleavage by NTH1 and OGG1

Base excision repair is the major pathway for the repair of oxidative DNA damage in human cells that is initiated by a damage-specific DNA glycosylase. In human cells, the major DNA glycosylases for the excision of oxidative base damage are OGG1 and NTH1 that excise 8-oxoguanine and oxidative pyrimidines, respectively. We find that both enzymes have limited activity on DNA lesions located in the vicinity of the 3′ end of a DNA single-strand break, suggesting that other enzymes are involved in the processing of such lesions. In this study, we identify and characterize NEIL1 as a major DNA glycosylase that excises oxidative base damage located in close proximity to the 3′ end of a DNA single-strand break.

Induction of the human oxidized base-specific DNA glycosylase NEIL1 by reactive oxygen species

NEIL1, a mammalian DNA glycosylase and ortholog of Escherichia coli Nei/Fpg, is involved in the repair of oxidatively damaged bases in mammalian cells. Exposure of HCT116 human colon carcinoma cells to reactive oxygen species, generated by glucose oxidase (GO), enhanced the levels of NEIL1 mRNA and polypeptide by 2-4-fold by 6 h after GO treatment. A similar oxidative stress-induced increase in human NEIL1 (hNEIL1) promoter-dependent luciferase expression in HCT116 cells indicates that reactive oxygen species activates NEIL1 transcription. The transcriptional start site of hNEIL1 was mapped, and the upstream promoter sequence was characterized via luciferase reporter assay. Two identical CRE/AP-1-binding sites were identified in the promoter that binds transcription factors c-Jun and CREB/ATF2. This binding was significantly enhanced in extracts of cells treated with GO. Furthermore, a simultaneous increase in the level of phosphorylated c-Jun suggests its involvement in up-regulating the NEIL1 promoter. Oxidative stress-induced activation of NEIL1 appears to be involved in the feedback regulation of cellular repair activity needed to handle an increase in the level of oxidative base damage.

Product inhibition and magnesium modulate the dual reaction mode of hOgg1

8-Oxoguanine (8-oxoG) is a major mutagenic DNA base damage corrected by the base excision repair (BER) pathway, which is initiated by lesion specific DNA glycosylases. The human DNA glycosylase hOgg1 catalyses excision of 8-oxoG followed by strand incision 3' to the abasic site if cytosine is positioned in the complementary strand. Unlike most bifunctional glycosylases, hOgg1 uncouples base removal and strand cleavage. This paper addresses the significance of product inhibition and magnesium for the non-concerted action of hOgg1 activities. The enzymatic activities of hOgg1 were analysed on duplex DNA containing a single 8-oxoG or abasic site opposite cytosine. AP-lyase cleavage of abasic sites was inhibited in the presence of free 8-oxoG, indicating that the product of base excision inhibits the subsequent strand incision step. Assays with DNA containing 8-oxoG showed that free 8-oxoG also inhibited the glycosylase activity. This result suggests that the free 8-oxoG base may retain in the recognition site following N-glycosylic cleavage, implying that product inhibition contribute to uncoupling the activities of hOgg1. Magnesium reduced the efficiency of base excision and strand incision on DNA containing 8-oxoG under single turnover conditions; however, the reduction was more pronounced for the AP-lyase activity. Furthermore, Shiff-base formation between hOgg1 and 8-oxoG containing DNA was abrogated in the presence of magnesium. These results suggest that hOgg1 mainly operates as a monofunctional glycosylase under physiological concentrations of magnesium.

Substantial decrease of urinary 8-oxo-7,8-dihydroguanine, a product of the base excision repair pathway, in DNA glycosylase defective mice

Genome integrity is maintained via removal (repair) of DNA lesions and an increased load of such DNA damage has been linked to numerous pathological conditions, including carcinogenesis and ageing. 8-Oxo-7,8-dihydroguanine is one of the most critical lesions of this type. The free 8-oxo-7,8-dihydroguanine produced by the action of a specific DNA glycosylase is a potential source of this compound in urine. To date, there has been no direct, experimental evidence demonstrating that urinary 8-oxo-7,8-dihydroguanine is produced by the base excision repair pathway. For clarification of this issue, we applied a recently developed methodology which involved high performance liquid chromatography pre-purification followed by gas chromatography with isotope dilution mass spectrometric detection to compare the urinary excretion rate of 8-oxo-7,8-dihydroguanine in wild type and OGG1 glycosylase knock out mice. Our study revealed a 26% reduction in urinary level of 8-oxo-7,8-dihydroguanine in OGG1 deficient mice in comparison with the wild type strain. This clearly indicates that the mouse OGG1 glycosylase contributes significantly to the generation of urinary 8-oxo-7,8-dihydroguanine. Therefore, urinary measurements of 8-oxo-7,8-dihydroguanine may be attributed to DNA damage and repair, which in turn suggests that they may be useful in studying associations between DNA repair and disease.

Recognition of the oxidized lesions spiroiminodihydantoin and guanidinohydantoin in DNA by the mammalian base excision repair glycosylases NEIL1 and NEIL2

8-Oxoguanine (8-oxoG) is an unstable mutagenic DNA lesion that is prone to further oxidation. High valent metals such as Cr(V) and Ir(IV) readily oxidize 8-oxoG to form guanidinohydantoin (Gh), its isomer iminoallantoin (Ia), and spiroiminodihydantoin (Sp). When present in DNA, these lesions show enhanced base misincorporation over the parent 8-oxoG lesion leading to G --> T and G --> C transversion mutations and polymerase arrest. These findings suggested that further oxidized lesions of 8-oxoG are more mutagenic and toxic than 8-oxoG itself. Repair of oxidatively damaged bases, including Sp and Gh/Ia, are initiated by the base excision repair (BER) system that involves the DNA glycosylases Fpg, Nei, and Nth in E. coli. Mammalian homologs of two of these BER enzymes, OGG1 and NTH1, have little or no affinity for Gh/Ia and Sp. Herein we report that two recently identified mammalian glycosylases, NEIL1 and NEIL2, showed a high affinity for recognition and cleavage of DNA containing Gh/Ia and Sp lesions. NEIL1 and NEIL2 recognized both of these lesions in single-stranded DNA and catalyzed the removal of the lesions through a beta- and delta-elimination mechanism. NEIL1 and NEIL2 also recognized and excised the Gh/Ia lesion opposite all four natural bases in double-stranded DNA. NEIL1 was able to excise the Sp lesion opposite the four natural bases in double-stranded DNA, however, NEIL2 showed little cleavage activity against the Sp lesion in duplex DNA although DNA trapping studies show recognition and binding of NEIL2 to this lesion. This work suggests that NEIL1 and NEIL2 are essential in the recognition of further oxidized lesions arising from 8-oxoG and implies that these BER glycosylases may play an important role in the repair of DNA damage induced by carcinogenic metals.

Transcription activities at 8-oxoG lesions in DNA

7,8-Dihydro-8-oxoguanine (8-oxoG) is the most frequent mutagenic lesion caused by oxidative stress. Eukaryotic cells use a specific DNA glycosylase, OGG1, to excise 8-oxoG from DNA. The mild phenotype of OGG1 null mice has been attributed to the existence of alternative pathways, including Cockayne syndrome B (CSB)-dependent transcription coupled repair (TCR), for removal of 8-oxoG. We have studied repair and transcription activities at 8-oxoG lesions with a reconstituted transcription system (RTS; RNA polymerase II, TBP, TFIIA, TFIIB, TFIIE, TFIIF and TFIIH), as well as in cellular extracts and in vivo. All measurable repair activity at 8-oxoG lesions takes place in the 3'-direction from the lesion, indicating base excision repair (BER) activity and negligible role of nucleotide excision repair (NER). Although 8-oxoG has been shown to be preferentially removed from the transcribed strand, in vitro experiments with purified transcription factors failed to identify a definite block for RNA polymerase II at the lesion. However, a weak block was observed at the lesion during transcription carried out with RTS as well as with cellular extracts. RNA polymerase II was identified at the site of the lesion on obstructed templates. Wild-type cells, as well as cells carrying targeted mutations of genes required for removal of 8-oxoG, were transfected with a luciferase expression vector containing an 8-oxoG lesion. No significant obstruction at 8-oxoG lesions was observed by this in vivo approach. In control experiments transcription elongation was completely blocked by cisplatin.

Ape1 abasic endonuclease activity is regulated by magnesium and potassium concentrations and is robust on alternative DNA structures

Abasic lesions are common mutagenic or cytotoxic DNA damages. Ape1 is the major human apurinic/apyrimidinic (AP) endonuclease and initiates repair of abasic sites by catalyzing strand cleavage at the lesion. I show here that Ape1 single-stranded (ss) AP site incision activity prefers 0.5 mM or 2 mM MgCl(2) and low concentrations (< or =50 mM) of KCl, whereas its double-stranded (ds) activity favors 10 mM MgCl(2) and 50 mM KCl or 2 mM MgCl(2) and 200 mM KCl. Both activities favor a pH between 7.0 and 7.5, suggesting a common catalytic mechanism. In conditions designed to mimic the intracellular environment (pH 7.2; 100 mM KCl; 1 mM MgCl(2)), Ape1 ssAP site incision activity is either about fivefold more active or approximately 20-fold less efficient than its ds activity, depending on the oligonucleotide employed. Secondary structure predictions suggest a role for the DNA conformational state in determining the effectiveness of Ape1. Ape1 complex stability in the presence of EDTA (non-incising conditions) is significantly weaker for ssDNA than dsDNA, regardless of the AP substrate. Duplexes where the AP site is positioned opposite the 3' terminus of a complementary primer strand are incised with an efficiency similar (less than twofold difference) to that of the ssAP substrate alone. Moreover, Ape1 cleaved AP sites in fork-like and bubble DNA structures with an efficiency that is identical or up to sevenfold higher than ssAP-DNA. The findings here suggest that Ape1 ssAP and dsAP endonuclease activities are regulated by sequence context and the relative concentrations of certain chemical elements in vivo, and that Ape1 incision activity occurs on complex replication, recombination, and/or transcription DNA intermediates.

Human DNA glycosylases involved in the repair of oxidatively damaged DNA

Reactive oxygen species from endogenous and environmental sources induce oxidative damage to DNA, and hence pose an enormous threat to the genetic integrity of cells. Such oxidative DNA damage is restored by the base excision repair (BER) pathway that is conserved from bacteria to humans and is initiated by DNA glycosylases, which simply remove the aberrant base from the DNA backbone by hydrolyzing the N-glycosidic bond (monofunctional DNA glycosylase), or further catalyze the incision of a resulting abasic site (bifunctional DNA glycosylase). In human cells, oxidative pyrimidine lesions are generally removed by hNTH1, hNEIL1, or hNEIL2, whereas oxidative purine lesions are removed by hOGG1. hSMUG1 excises a subset of oxidative base damage that is poorly recognized by the above enzymes. Unlike these enzymes, hMYH removes intact A misincorporated opposite template 8-oxoguanine during DNA replication. Although hNTH1, hOGG1, and hMYH account for major cellular glycosylase activity for inherent substrate lesions, mouse models deficient in the enzymes exhibit no overt phenotypes such as the development of cancer, implying backup mechanisms. Contrary to the mouse model, hMYH mutations have been shown to lead to a multiple colorectal adenoma syndrome and high colorectal cancer risk. For cleavage of the N-glycosidic bond, bifunctional DNA glycosylases (hNTH1, hNEIL1, hNEIL2, and hOGG1) use Lys or Pro for direct attack on sugar C1', whereas monofunctional DNA glycosylases (hSMUG1 and hMYH) use an activated water molecule. DNA glycosylases for oxidative damage, if not all, are covalently trapped by DNA containing 2-deoxyribonolactone or oxanine. Thus, the depletion of functional DNA glycosylases using covalent trapping may reduce the BER capacity of cancer cells, hence potentiating the efficacy of anticancer drugs or radiation therapy.

Identification of a zinc finger domain in the human NEIL2 (Nei-like-2) protein

The recently identified human NEIL2 (Nei-like-2) protein, a DNA glycosylase/AP lyase specific for oxidatively damaged bases, shares structural features and reaction mechanism with the Escherichia coli DNA glycosylases, Nei and Fpg. Amino acid sequence analysis of NEIL2 suggested it to have a zinc finger-like Nei/Fpg. However, the Cys-X2-His-X16-Cys-X2-Cys (CHCC) motif present near the C terminus of NEIL2 is distinct from the zinc finger motifs of Nei/Fpg, which are of the C4 type. Here we show the presence of an equimolar amount of zinc in NEIL2 by inductively coupled plasma mass spectrometry. Individual mutations of Cys-291, His-295, Cys-315, and Cys-318, candidate residues for coordinating zinc, inactivated the enzyme by abolishing its DNA binding activity. H295A and C318S mutants were also shown to lack bound zinc, and a significant change in their secondary structure was revealed by CD spectra analysis. Molecular modeling revealed Arg-310 of NEIL2 to be a critical residue in its zinc binding pocket, which is highly conserved throughout the Fpg/Nei family. A R310Q mutation significantly reduced the activity of NEIL2. We thereby conclude that the zinc finger motif in NEIL2 is essential for its structural integrity and enzyme activity.

The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity

In prokaryotes, two DNA glycosylases recognize and excise oxidized pyrimidines: endonuclease III (Nth) and endonuclease VIII (Nei). The oxidized purine 8-oxoguanine, on the other hand, is recognized by Fpg (also known as MutM), a glycosylase that belongs to the same family as Nei. The recent availability of the human genome sequence allowed the identification of three human homologs of Escherichia coli Nei. We report here the crystal structure of a human Nei-like (NEIL) enzyme, NEIL1. The structure of NEIL1 exhibits the same overall fold as E. coli Nei, albeit with an unexpected twist. Sequence alignments had predicted that NEIL1 would lack a zinc finger, and it was therefore expected to use a different DNA-binding motif instead. Our structure revealed that, to the contrary, NEIL1 contains a structural motif composed of two antiparallel beta-strands that mimics the antiparallel beta-hairpin zinc finger found in other Fpg/Nei family members but lacks the loops that harbor the zinc-binding residues and, therefore, does not coordinate zinc. This "zincless finger" appears to be required for NEIL1 activity, because mutating a very highly conserved arginine within this motif greatly reduces the glycosylase activity of the enzyme.

AP Endonuclease-Independent DNA Base Excision Repair in Human Cells

The paradigm for repair of oxidized base lesions in genomes via the base excision repair (BER) pathway is based on studies in Escherichia coli, in which AP endonuclease (APE) removes all 3' blocking groups (including 3' phosphate) generated by DNA glycosylase/AP lyases after base excision. The recently discovered mammalian DNA glycosylase/AP lyases, NEIL1 and NEIL2, unlike the previously characterized OGG1 and NTH1, generate DNA strand breaks with 3' phosphate termini. Here we show that in mammalian cells, removal of the 3' phosphate is dependent on polynucleotide kinase (PNK), and not APE. NEIL1 stably interacts with other BER proteins, DNA polymerase beta (pol beta) and DNA ligase IIIalpha. The complex of NEIL1, pol beta, and DNA ligase IIIalpha together with PNK suggests coordination of NEIL1-initiated repair. That NEIL1/PNK could also repair the products of other DNA glycosylases suggests a broad role for this APE-independent BER pathway in mammals.

Acetylation of the human DNA glycosylase NEIL2 and inhibition of its activity

Post-translational modifications of proteins, including acetylation, modulate their cellular functions. Several human DNA replication and repair enzymes have recently been shown to be acetylated, leading to their inactivation in some cases. Here we show that the transcriptional coactivator p300 stably interacts with, and acetylates, the recently discovered human DNA glycosylase NEIL2, involved in the repair of oxidized bases both in vivo and in vitro. Lys49 and Lys153 were identified as the major acetylation sites in NEIL2. Acetylation of Lys49, conserved among Nei orthologs, or its mutation to Arg inactivates both base excision and AP lyase activities, while acetylation of Lys153 has no effect. Reversible acetylation of Lys49 could thus regulate the repair activity of NEIL2 in vivo.

Differential Specificity of Human and Escherichia coli Endonuclease III and VIII Homologues for Oxidative Base Lesions

In human cells, oxidative pyrimidine lesions are restored by the base excision repair pathway initiated by homologues of Endo III (hNTH1) and Endo VIII (hNEIL1 and hNEIL2). In this study we have quantitatively analyzed and compared their activity toward nine oxidative base lesions and an apurinic/apyrimidinic (AP) site using defined oligonucleotide substrates. hNTH1 and hNEIL1 but not hNEIL2 excised the two stereoisomers of thymine glycol (5R-Tg and 5S-Tg), but their isomer specificity was markedly different: the relative activity for 5R-Tg:5S-Tg was 13:1 for hNTH1 and 1.5:1 for hNEIL1. This was also the case for their Escherichia coli homologues: the relative activity for 5R-Tg:5S-Tg was 1:2.5 for Endo III and 3.2:1 for Endo VIII. Among other tested lesions for hNTH1, an AP site was a significantly better substrate than urea, 5-hydroxyuracil (hoU), and guanine-derived formamidopyrimidine (mFapyG), whereas for hNEIL1 these base lesions and an AP site were comparable substrates. In contrast, hNEIL2 recognized an AP site exclusively, and the activity for hoU and mFapyG was marginal. hNEIL1, hNEIL2, and Endo VIII but not hNTH1 and Endo III formed cross-links to oxanine, suggesting conservation of the -fold of the active site of the Endo VIII homologues. The profiles of the excision of the Tg isomers with HeLa and E. coli cell extracts closely resembled those of hNTH1 and Endo III, confirming their major contribution to the repair of Tg isomers in cells. However, detailed analysis of the cellular activity suggests that hNEIL1 has a significant role in the repair of 5S-Tg in human cells.

Single-Stranded Breaks in DNA but Not Oxidative DNA Base Damages Block Transcriptional Elongation by RNA Polymerase II in HeLa Cell Nuclear Extracts

Transcription and repair of many DNA helix-distorting lesions such as cyclobutane pyrimidine dimers have been shown to be coupled in cells across phyla from bacteria to humans. The signal for transcription-coupled repair appears to be a stalled transcription complex at the lesion site. To determine whether oxidative DNA lesions can block correctly initiated human RNA polymerase II, we examined the effect of site-specifically introduced oxidative damages on transcription in HeLa cell nuclear extracts. We found that transcription was blocked by single-stranded breaks, common oxidative DNA lesions, when present in the transcribed strand of the transcription template. Cyclobutane pyrimidine dimers, which have been previously shown to block transcription both in vitro and in vivo, also blocked transcription in the HeLa cell nuclear transcription assay. In contrast, the oxidative DNA base lesions, 8-oxoguanine, 5-hydroxycytosine, and thymine glycol did not inhibit transcription, although pausing was observed with the thymine glycol lesion. Thus, DNA strand breaks but not oxidative DNA base damages blocked transcription by RNA polymerase II.