Solution-state structure of the Dewar pyrimidinone photoproduct of thymidylyl-(3' .fwdarw. 5')-thymidine

Taylor, John‐Stephen; Garrett, Daniel S.; Cohrs, Michael P.

doi:10.1021/bi00419a007

Cited by 92 publications

(74 citation statements)

References 31 publications

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“…We analyzed sequences directly and avoided reporter genes or sequences not only because all changes can be detected but because the normal sequence is also identified, which allows estimates to be made of the error frequency of translesion synthesis. Oligomer containing isomer 2 of the T-T (6-4) adduct, the Dewar valence isomer (13,14), was produced by irradiating li-mer containing isomer 1 with =11 MJ/m2 of filtered 0. 20 (1).…”

Section: Resultsmentioning

confidence: 99%

The thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct is highly mutagenic and specifically induces 3' thymine-to-cytosine transitions in Escherichia coli.

LeClerc

Borden

Lawrence

1991

Proc. Natl. Acad. Sci. U.S.A.

207

147

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We have constructed single-stranded, M13-based vectors that contain a specifically located thyminethymine pyrimidine-pyrimidone(6-4) UV photoproduct and have used these to estimate the frequency and accuracy of DNA replication past this adduct in uvrA6 cells of Escherichia coli. Both the normal and the Dewar valence photoisomer of the (6-4) adduct were studied. In the absence of SOS induction, vectors carrying the photoproducts were rarely replicated; relative to the lesion-free control, 1.9% of vectors carrying the normal (6-4) isomer produced plaques, and with the Dewar valence isomer the proportion was 0.4%. In SOS-induced cells, these frequencies rose to 22.1% and 12.3%, respectively. The error frequency of replication past the normal isomer in SOS-induced cells was high; in a random sample of 185 progeny phage analyzed, 169 (91%) contained mutations, all of which were targeted. Equally striking, a high proportion of the mutations (158/169; 93%) were of only one type, namely 3' T C transitions. Both the error frequency and the specificity were much reduced with the Dewar valence isomer; overall, 74/140 (53%) of the phage analyzed were mutant, and of these only 34 (46%) entailed the 3' T -+ C transition. We speculate that the high error frequency and specificity arise from the formation of a stable TOG base pair, involving hydrogen bonds at 0-2 and N-3 in the pyrimidone ring. Potential hydrogen bonds at these sites are coplanar in the normal but not in the Dewar isomer, perhaps explaining the reduced specificity of mutagenesis with the latter adduct.Irradiation of DNA with germicidal UV light produces a variety of photoproducts, the chief of which are the cyclobutyl dipyrimidines (dimers) and the pyrimidine-pyrimidone(6-4) adducts (1, 2). We were interested in studying the thymine-thymine (6-4) adduct [5-hydroxy-6-4'-(5'-methylpyrimidin-2'-one)-thymine] as an example of the latter type of photoproduct, for two reasons. (i) We anticipated that it might provide insights into the mechanism determining base selection during translesion synthesis-that is, during chain elongation past the site of a template lesion-and, in general, help in understanding the relation between the structure of a lesion and its mutagenic potential. Previous experiments with cis-syn (3, 4) and trans-syn (5) cyclobutane dimers, and also with abasic sites (6), each located at a T-T site in the same sequence context, suggested that the UV photoproducts often form correct A'T base pairs during translesion synthesis, and that when mutations occur, they might result from base mispairing. We were therefore interested to examine other lesions for evidence of such correct or aberrant base pairing.(ii) We wished to study the T-T (6-4) adduct because ofconflicting conclusions concerning the relative proportions of mutations induced by dimers and adducts in Escherichia coli. Although adducts are collectively 5-to 10-fold less abundant than dimers in UV-irradiated DNA, some evidence (7-9, 25) suggests that they are responsible for the majorit...

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Section: Resultsmentioning

confidence: 99%

The thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct is highly mutagenic and specifically induces 3' thymine-to-cytosine transitions in Escherichia coli.

LeClerc

Borden

Lawrence

1991

Proc. Natl. Acad. Sci. U.S.A.

207

147

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“…The observation that the rate of 6-4PP removal from nontranscribed DNA exceeds the rate of CPD removal suggests a higher affinity of DNA-recognizing proteins towards this type of lesion that distorts the helical structure of the DNA duplex more profoundly: adjacent pyrimidine rings in cis-syn CPDs are believed to be nearly coplanar (2), whereas the pyrimidine planes within the 6-4PP are almost perpendicular, and for them a more-pronounced bending angle (44°) of the DNA has been observed (8,20). Alternatively, induction of 6-4PPs might lead to an enhanced destabilization of nucleosomes (12), thereby rendering lesions more accessible to repair proteins.…”

Section: Discussionmentioning

confidence: 99%

RNA Polymerase II Transcription Suppresses Nucleosomal Modulation of UV-Induced (6-4) Photoproduct and Cyclobutane Pyrimidine Dimer Repair in Yeast

Tijsterman

Pril

Jong

et al. 1999

Molecular and Cellular Biology

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The nucleotide excision repair (NER) pathway is able to remove a wide variety of structurally unrelated lesions from DNA. NER operates throughout the genome, but the efficiencies of lesion removal are not the same for different genomic regions. Even within a single gene or DNA strand repair rates vary, and this intragenic heterogeneity is of considerable interest with respect to the mutagenic potential of carcinogens. In this study, we have analyzed the removal of the two major types of genotoxic DNA adducts induced by UV light, i.e., the pyrimidine (6-4)-pyrimidone photoproduct (6-4PP) and the cyclobutane pyrimidine dimer (CPD), from the Saccharomyces cerevisiae URA3 gene at nucleotide resolution. In contrast to the fast and uniform removal of CPDs from the transcribed strand, removal of lesions from the nontranscribed strand is generally less efficient and is modulated by the chromatin environment of the damage. Removal of 6-4PPs from nontranscribed sequences is also profoundly influenced by positioned nucleosomes, but this type of lesion is repaired at a much higher rate. Still, the transcribed strand is repaired preferentially, indicating that, as in the removal of CPDs, transcription-coupled repair predominates in the removal of 6-4PPs from transcribed DNA. The hypothesis that transcription machinery operates as the rate-determining damage recognition entity in transcriptioncoupled repair is supported by the observation that this pathway removes both types of UV photoproducts at equal rates without being profoundly influenced by the sequence or chromatin context. UV light induces two major classes of genotoxic lesions in DNA, i.e., cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4)-pyrimidone photoproducts (6-4PPs). Both lesions are repaired by the nucleotide excision repair (NER) pathway, in which incision of the damaged strand on both sides of the lesion is followed by resynthesis of excised DNA with the undamaged strand as a template (reviewed in reference 2). Although the molecular mechanism of the NER reaction has become increasingly clear as it has been reconstituted in vitro by using purified components of either yeast or human origin (1,4,15), the mechanism of damage recognition in the nucleus where DNA is folded into chromatin with different levels of complexity is largely unknown. One possible way by which cells sense DNA damage is lesion interference with essential cellular DNA metabolic processes, like transcription, replication, or even recombination. This is exemplified by the intimate link found for the process of NER and mRNA transcription: UVinduced CPDs introduced in sequences transcribed by RNA polymerase or RNA polymerase II, respectively, in pro-and eukaryotes, are repaired preferentially to CPDs induced in nontranscribed DNA (13,14). The molecular basis for this enhanced strand-specific repair, more commonly termed transcription-coupled repair (TCR) since it is dependent upon ongoing transcription (10, 18), is thought to originate from efficient recruitment of repair proteins to...

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“…Near a cyclobutane DP, the DNA is unwound and kinked by about 300 relative to B-form DNA (27,36). <6-4> DPs probably produce even more distortion because the pyrimidine planes within the <6-4> photodimer are almost perpendicular (15,43). DNA-protein contacts inhibit photoproduct formation presumably by inhibiting rotation of pyrimidines.…”

Section: Discussionmentioning

confidence: 99%

Binding of transcription factors creates hot spots for UV photoproducts in vivo.

Pfeifer¹,

Drouin²,

Riggs³

et al. 1992

Mol. Cell. Biol.

154

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Cyclobutane dipyrimidines and <6-4> dipyrimidines are the two major classes of mutagenic DNA photoproducts produced by UV irradiation of cells. We developed a method to map cyclobutane dipyrimidines at the DNA sequence level in mammalian cells. The frequency of this class of photoproducts was determined at every dipyrimidine along the human phosphoglycerate kinase-1 (PGKI) promoter sequence and was compared to the UV-induced frequency distribution of <6-4> dipyrimidines. The formation of DNA photoproducts by UV light is implicated in induction of mutations and the development of skin cancer (1,10,16,24,32,33). Because of a lack of sufficiently sensitive techniques, the susceptibility of specific DNA sequences to form photoproducts has heretofore been analyzed almost exclusively with cloned DNA, and very little is known about the effects of DNA sequence and chromatin structure on photoproduct formation in mammalian cells. Becker and Wang introduced a NaBH4-aniline technique to break DNA at virtually all classes of UVinduced photoproducts (4, 5). These photoproduct classes are, in order of their relative frequency, (i) cyclobutane dipyrimidines (cyclobutane DPs), which involve two covalent bonds between adjacent pyrimidines; (ii) pyrimidine <6-4> pyrimidone photoproducts (<6-4> dipyrimidines [<6-4> DPs]), which involve a single covalent bond between positions 6 and 4 of adjacent pyrimidines; (iii) rare monoadducts, usually involving photoaddition of H-or HO-to the double bonds at positions 5 and 6 of pyrimidines (6); and (iv) rare TpA and ApA dimers (7,8,19,20,28). End-labeled DNA was size fractionated on sequencing gels to reveal the sequence position of these photoproducts. Selleck and Majors (42) used the Church and Gilbert (14) genomic sequencing technique on in vivo UV-irradiated yeast DNA to reveal the sequence positions of NaBH4-aniline labile photoproducts. Subsequently, they used end-labeled primers for multiple primer extensions with Taq polymerase (2).The polymerase stopped almost exclusively at dipyrimidine photoproducts yielding a sequence ladder reflecting photoproduct frequency of both cyclobutane DPs and <6-4> DPs along the UV-irradiated yeast genome. We recently used an exponential amplification method, the ligation-mediated polymerase chain reaction (LM-PCR) (35, 39), to map photoproducts which can be converted into ligatable DNA breaks (37). Pyrimidine <6-4> pyrimidone photoproducts were specifically cleaved with alkaline piperidine (29 The frequency with which a particular nucleotide or dinucleotide will be involved in a particular class of photoreaction may be affected by flanking sequence, methylation state of cytidines, and bound proteins. These factors are expected to combine to produce photoproduct hot spots and cold spots along the genome. In previous studies, we determined the sequence, cytidine methylation status, and DNase I footprints due to transcription factors or nucleosomes along the promoter of active and inactive PGKJ genes (38)(39)(40). Here, we have determined the influence of...

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Solution-state structure of the Dewar pyrimidinone photoproduct of thymidylyl-(3' .fwdarw. 5')-thymidine

Cited by 92 publications

References 31 publications

The thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct is highly mutagenic and specifically induces 3' thymine-to-cytosine transitions in Escherichia coli.

The thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct is highly mutagenic and specifically induces 3' thymine-to-cytosine transitions in Escherichia coli.

RNA Polymerase II Transcription Suppresses Nucleosomal Modulation of UV-Induced (6-4) Photoproduct and Cyclobutane Pyrimidine Dimer Repair in Yeast

Binding of transcription factors creates hot spots for UV photoproducts in vivo.

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