Recognition of DNA Adducts by Human Nucleotide Excision Repair

The mechanism by which mammalian nucleotide excision repair (NER) detects a wide range of base lesions is poorly understood. Here, we tested the ability of human NER to recognize bulky modifications that either destabilize the DNA double helix (acetylaminofluorene (AAF) and benzo[a]pyrene diol-epoxide (BPDE) adducts, UV radiation products) or induce opposite effects by stabilizing the double helix (8-methoxypsoralen (8-MOP), anthramycin, and CC-1065 adducts). We constructed plasmid DNA carrying a defined number of each of these adducts and determined their potential to sequester NER factors contained in a human cell-free extract. For that purpose, we measured the capacity of damaged plasmids to compete with excision repair of a site-directed NER substrate. This novel approach showed differences of more than 3 orders of magnitude in the efficiency by which helix-destabilizing and helix-stabilizing adducts sequester NER factors. For example, AAF modifications were able to compete with the NER substrate ∼1740 times more effectively than 8-MOP adducts. The sequestration potency decreased with the following order of adducts, AAF > UV ≥ BPDE > 8-MOP > anthramycin, CC-1065. A strong preference for helix-destabilizing lesions was confirmed by monitoring the formation of NER patches at site-specific adducts with either AAF or CC-1065. This comparison based on factor sequestration and repair synthesis indicates that human NER is primarily targeted to sites at which the secondary structure of DNA is destabilized. Thus, an early step of DNA damage recognition involves thermodynamic probing of the duplex.

[1]  H. Naegeli,et al.  Site-specific DNA substrates for human excision repair: comparison between deoxyribose and base adducts. , 1996, Chemistry & biology.

[2]  H. Naegeli,et al.  A repair competition assay to assess recognition by human nucleotide excision repair. , 1996, Nucleic acids research.

[3]  B. Van Houten,et al.  Interaction of the UvrABC nuclease system with a DNA duplex containing a single stereoisomer of dG-(+)- or dG-(-)-anti-BPDE. , 1995, Biochemistry.

[4]  J. Hearst,et al.  Solution structures of psoralen monoadducted and cross-linked DNA oligomers by NMR spectroscopy and restrained molecular dynamics. , 1995, Biochemistry.

[5]  D. Phillips,et al.  Formation and persistence of benzo[a]pyrene-DNA adducts in mouse epidermis in vivo: importance of adduct conformation. , 1995, Carcinogenesis.

[6]  R. Legerski,et al.  An interaction between the DNA repair factor XPA and replication protein A appears essential for nucleotide excision repair , 1995, Molecular and cellular biology.

[7]  Dong-Kyoo Kim,et al.  Human Xeroderma Pigmentosum Group A Protein Interacts with Human Replication Protein A and Inhibits DNA Replication (*) , 1995, The Journal of Biological Chemistry.

[8]  D. Mitchell,et al.  Repair of UV-induced) Photoproducts in Nucleosome Core DNA (*) , 1995, The Journal of Biological Chemistry.

[9]  A. Sancar.  Excision Repair in Mammalian Cells (*) , 1995, The Journal of Biological Chemistry.

[10]  C. Ingles,et al.  RPA involvement in the damage-recognition and incision steps of nucleotide excision repair , 1995, Nature.

[11]  R. Wood,et al.  Mammalian DNA nucleotide excision repair reconstituted with purified protein components , 1995, Cell.

[12]  J. K. Kim,et al.  The solution structure of DNA duplex-decamer containing the (6-4) photoproduct of thymidylyl(3'-->5')thymidine by NMR and relaxation matrix refinement. , 1995, European journal of biochemistry.

[13]  D. S. Hsu,et al.  Reconstitution of Human DNA Repair Excision Nuclease in a Highly Defined System (*) , 1995, The Journal of Biological Chemistry.

[14]  P. Hanawalt.  Transcription-coupled repair and human disease. , 1994, Science.

[15]  D. S. Hsu,et al.  Substrate spectrum of human excinuclease: repair of abasic sites, methylated bases, mismatches, and bulky adducts. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[16]  R. Wood,et al.  Xeroderma pigmentosum and nucleotide excision repair of DNA. , 1994, Trends in biochemical sciences.

[17]  J. Hoeijmakers.  Human nucleotide excision repair syndromes: molecular clues to unexpected intricacies. , 1994, European journal of cancer.

[18]  R. Wood,et al.  Repair by human cell extracts of single (6-4) and cyclobutane thymine-thymine photoproducts in DNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[19]  S. Thiagalingam,et al.  Nucleotide excision repair, a tracking mechanism in search of damage. , 1993, The Journal of biological chemistry.

[20]  I. Lambert,et al.  DNA adduct-induced stabilization of slipped frameshift intermediates within repetitive sequences: implications for mutagenesis. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[21]  D. Patel,et al.  Solution conformation of the (+)-cis-anti-[BP]dG adduct in a DNA duplex: intercalation of the covalently attached benzo[a]pyrenyl ring into the helix and displacement of the modified deoxyguanosine. , 1993, Biochemistry.

[22]  T. Krugh,et al.  Structural characterization of an N-acetyl-2-aminofluorene (AAF) modified DNA oligomer by NMR, energy minimization, and molecular dynamics. , 1993, Biochemistry.

[23]  C. Swenberg,et al.  Differences in unwinding of supercoiled DNA induced by the two enantiomers of anti-benzo[a]pyrene diol epoxide. , 1992, Nucleic acids research.

[24]  M. Tang,et al.  A comparison of the rates of reaction and function of UVRB in UVRABC- and UVRAB-mediated anthramycin-N2-guanine-DNA repair. , 1992, The Journal of biological chemistry.

[25]  A. Sancar,et al.  (A)BC excinuclease: the Escherichia coli nucleotide excision repair enzyme , 1992, Molecular microbiology.

[26]  D. Patel,et al.  Influence of benzo[a]pyrene diol epoxide chirality on solution conformations of DNA covalent adducts: the (-)-trans-anti-[BP]G.C adduct structure and comparison with the (+)-trans-anti-[BP]G.C enantiomer. , 1992, Biochemistry.

[27]  L. Hurley,et al.  Structure-activity relationships of (+)-CC-1065 analogues in the inhibition of helicase-catalyzed unwinding of duplex DNA. , 1992, Journal of medicinal chemistry.

[28]  A. Sancar,et al.  Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5' and the 6th phosphodiester bond 3' to the photodimer. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[29]  S. Skerfving,et al.  Cytogenetic effects in rotogravure printers exposed to toluene (and benzene). , 1991, Mutation research.

[30]  R. Wood,et al.  DNA excision repair in mammalian cell extracts , 1991, BioEssays : news and reviews in molecular, cellular and developmental biology.

[31]  L. Hurley,et al.  Determination of the structural features of (+)-CC-1065 that are responsible for bending and winding of DNA. , 1991, Chemical research in toxicology.

[32]  D. S. Garrett,et al.  1H NMR assignment and melting temperature study of cis-syn and trans-syn thymine dimer containing duplexes of d(CGTATTATGC).d(GCATAATACG). , 1990, Biochemistry.

[33]  B. V. Houten.  Nucleotide excision repair in Escherichia coli. , 1990 .

[34]  T. Krugh,et al.  Two-dimensional NMR studies on the anthramycin-d(ATGCAT)2 adduct. , 1989, Biochemistry.

[35]  R. Wood,et al.  Localization of DNA repair synthesis by human cell extracts to a short region at the site of a lesion. , 1989, Journal of Biological Chemistry.

[36]  D. Bogenhagen,et al.  Repair of a synthetic abasic site in DNA in a Xenopus laevis oocyte extract , 1989, Molecular and cellular biology.

[37]  M. Tang,et al.  Recognition and repair of 2-aminofluorene- and 2-(acetylamino)fluorene-DNA adducts by UVRABC nuclease. , 1989, Biochemistry.

[38]  M. Leng,et al.  The DNA bending by acetylaminofluorene residues and by apurinic sites. , 1989, Journal of molecular biology.

[39]  D. Patel,et al.  NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite acyclic lesions. , 1989, Biochemistry.

[40]  Charles R.scriver,et al.  The Metabolic basis of inherited disease , 1989 .

[41]  J. Hearst,et al.  Evidence for structural deformation of the DNA helix by a psoralen diadduct but not by a monoadduct. , 1988, Nucleic acids research.

[42]  D. Mitchell.  THE RELATIVE CYTOTOXICITY OF(6–4) PHOTOPRODUCTS AND CYCLOBUTANE DIMERS IN MAMMALIAN CELLS * , 1988, Photochemistry and photobiology.

[43]  R. Wood,et al.  Complementation of the xeroderma pigmentosum DNA repair defect in cell-free extracts , 1988, Cell.

[44]  J. Hearst,et al.  Thermostability of double-stranded deoxyribonucleic acids: effects of covalent additions of a psoralen. , 1986, Biochemistry.

[45]  L. Hurley,et al.  The chemistry, mechanism of action and biological properties of CC-1065, a potent antitumor antibiotic. , 1986, The Journal of antibiotics.

[46]  M. Hogan,et al.  Site-specific carcinogen binding to DNA. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[47]  J. Hearst,et al.  The reaction of the psoralens with deoxyribonucleic acid , 1984, Quarterly Reviews of Biophysics.

[48]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[49]  P. Sharp,et al.  In vitro transcription: whole-cell extract. , 1983, Methods in enzymology.

[50]  W. C. Krueger,et al.  Mechanism of interaction of CC-1065 (NSC 298223) with DNA. , 1982, Cancer research.

[51]  R. Rahn,et al.  3 – Photochemistry of DNA; Secondary Structure, Photosensitization, Base Substitution, and Exogenous Molecules∗† , 1976 .

[52]  K. Kohn,et al.  Reaction of anthramycin with deoxyribonucleic acid. , 1970, Journal of molecular biology.

[53]  J. Cleaver.  Defective Repair Replication of DNA in Xeroderma Pigmentosum , 1968, Nature.

[54]  A. George.  The metabolic basis of inherited disease , 1961 .