Structural Aspects of Polycyclic Aromatic Carcinogen-Damaged DNA and Its Recognition by NER Proteins

[1]  D. Patel,et al.  Conformational searches elucidate effects of stereochemistry on structures of deoxyadenosine covalently bound to tumorigenic metabolites of benzo[C] phenanthrene. , 2004, Frontiers in bioscience : a journal and virtual library.

[2]  F. Hanaoka,et al.  The comings and goings of nucleotide excision repair factors on damaged DNA , 2003, The EMBO journal.

[3]  K. Vasquez,et al.  Critical DNA damage recognition functions of XPC‐hHR23B and XPA‐RPA in nucleotide excision repair , 2003, Molecular carcinogenesis.

[4]  J. Hoeijmakers,et al.  A novel regulation mechanism of DNA repair by damage-induced and RAD23-dependent stabilization of xeroderma pigmentosum group C protein. , 2003, Genes & development.

[5]  Jin Yang,et al.  Defining the function of XPC protein in psoralen and cisplatin-mediated DNA repair and mutagenesis. , 2003, Carcinogenesis.

[6]  D. Patel,et al.  Simulating structural and thermodynamic properties of carcinogen-damaged DNA. , 2003, Biophysical journal.

[7]  J. Hoeijmakers,et al.  Divide and conquer: nucleotide excision repair battles cancer and ageing. , 2003, Current opinion in cell biology.

[8]  T. Buterin,et al.  Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts. , 2003, Biochemistry.

[9]  C. Harris,et al.  Minor groove orientation for the (1S,2R,3S,4R)-N2- [1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyguanosyl adduct in the N-ras codon 12 sequence. , 2003, Biochemistry.

[10]  D. Volk,et al.  Solution structure of a cis-opened (10R)-N6-deoxyadenosine adduct of (9S,10R)-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA duplex. , 2003, Biochemistry.

[11]  P. Hanawalt.  Subpathways of nucleotide excision repair and their regulation , 2002, Oncogene.

[12]  D. Patel,et al.  Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery , 2002, Biopolymers.

[13]  N. Tretyakova,et al.  Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancers , 2002, Oncogene.

[14]  D. Patel,et al.  Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability. , 2002, Nucleic acids research.

[15]  S. Amin,et al.  Synthesis and characterization of site-specific and stereoisomeric fjord dibenzo[a,l]pyrene diol epoxide-N(6)-adenine adducts: unusual thermal stabilization of modified DNA duplexes. , 2002, Chemical research in toxicology.

[16]  K. Sugasawa,et al.  A molecular mechanism for DNA damage recognition by the xeroderma pigmentosum group C protein complex. , 2002, DNA Repair.

[17]  J. Kozelka,et al.  Unrestrained 5 ns molecular dynamics simulation of a cisplatin-DNA 1,2-GG adduct provides a rationale for the NMR features and reveals increased conformational flexibility at the platinum binding site. , 2001, Journal of molecular biology.

[18]  D. Patel,et al.  Cyclohexene ring and Fjord region twist inversion in stereoisomeric DNA adducts of enantiomeric benzo[c]phenanthrene diol epoxides. , 2001, Chemical research in toxicology.

[19]  M. Tang,et al.  Methylated CpG dinucleotides are the preferential targets for G-to-T transversion mutations induced by benzo[a]pyrene diol epoxide in mammalian cells: similarities with the p53 mutation spectrum in smoking-associated lung cancers. , 2001, Cancer research.

[20]  S. Broyde,et al.  Stereochemical, structural, and thermodynamic origins of stability differences between stereoisomeric benzo[a]pyrene diol epoxide deoxyadenosine adducts in a DNA mutational hot spot sequence. , 2001, Journal of the American Chemical Society.

[21]  D. Jerina,et al.  Solution structure of a trans-opened (10S)-dA adduct of (+)-(7S,8R,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully complementary DNA duplex: evidence for a major syn conformation. , 2001, Biochemistry.

[22]  K. Sugasawa,et al.  Diversity of the damage recognition step in the global genomic nucleotide excision repair in vitro. , 2001, Mutation research.

[23]  D. Patel,et al.  Molecular topology of polycyclic aromatic carcinogens determines DNA adduct conformation: a link to tumorigenic activity. , 2001, Journal of molecular biology.

[24]  D. Volk,et al.  NMR evidence for syn-anti interconversion of a trans opened (10R)-dA adduct of benzo[a]pyrene (7S,8R)-diol (9R,10S)-epoxide in a DNA duplex. , 2000, Biochemistry.

[25]  P. Kollman,et al.  Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.

[26]  S. Broyde,et al.  Conformational determinants of structures in stereoisomeric cis-opened anti-benzo[a]pyrene diol epoxide adducts to adenine in DNA. , 2000, Chemical research in toxicology.

[27]  M. Tang,et al.  Targeting of lung cancer mutational hotspots by polycyclic aromatic hydrocarbons. , 2000, Journal of the National Cancer Institute.

[28]  T. Buterin,et al.  Unrepaired fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots. , 2000, Cancer research.

[29]  S. Broyde,et al.  Principles Governing Conformations in Stereoisomeric Adducts of Bay Region Benzo[a]pyrene Diol Epoxides to Adenine in DNA: Steric and Hydrophobic Effects Are Dominant , 2000 .

[30]  T. Cheatham,et al.  Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise * , 2000, Biopolymers.

[31]  A. Luch,et al.  Cancer initiation by polycyclic aromatic hydrocarbons results from formation of stable DNA adducts rather than apurinic sites. , 1999, Carcinogenesis.

[32]  D. Patel,et al.  Solution conformation of the (+)-trans-anti-benzo[g]chrysene-dA adduct opposite dT in a DNA duplex. , 1999, Journal of molecular biology.

[33]  D. Patel,et al.  Solution structure of the (+)-cis-anti-benzo[a]pyrene-dA ([BP]dA) adduct opposite dT in a DNA duplex. , 1999, Biochemistry.

[34]  S. Broyde,et al.  Origins of conformational differences between cis and trans DNA adducts derived from enantiomeric anti-benzo[a]pyrene diol epoxides. , 1999, Chemical research in toxicology.

[35]  M. Missura,et al.  Recognition of nonhybridizing base pairs during nucleotide excision repair of DNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[36]  S. Broyde,et al.  Stereochemical origin of opposite orientations in DNA adducts derived from enantiomeric anti-benzo[a]pyrene diol epoxides with different tumorigenic potentials. , 1999, Biochemistry.

[37]  Z. Wang,et al.  Repair of DNA lesions: mechanisms and relative repair efficiencies. , 1999, Mutation research.

[38]  S. Nesnow,et al.  Polycyclic aromatic hydrocarbons: correlations between DNA adducts and ras oncogene mutations. , 1999, Mutation research.

[39]  P. Kollman,et al.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. , 1999, Journal of biomolecular structure & dynamics.

[40]  S. Amin,et al.  Total Synthesis, Mass Spectrometric Sequencing, and Stabilities of Oligonucleotide Duplexes with Single trans-anti-BPDE-N 6-dA Lesions in the N-ras codon 61 and Other Sequence Contexts , 1999 .

[41]  A. Sancar,et al.  Nucleotide excision repair: from E. coli to man. , 1999, Biochimie.

[42]  R. Wood,et al.  DNA damage recognition during nucleotide excision repair in mammalian cells. , 1999, Biochimie.

[43]  R. Lloyd,et al.  Multiple conformations of an intercalated (-)-(7S,8R,9S, 10R)-N6-[10-(7,8,9,10-tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct in the N-ras codon 61 sequence. , 1998, Biochemistry.

[44]  H. Naegeli,et al.  Stereoselectivity of Human Nucleotide Excision Repair Promoted by Defective Hybridization* , 1998, The Journal of Biological Chemistry.

[45]  Bhyravabhotla Jayaram,et al.  Free Energy Analysis of the Conformational Preferences of A and B Forms of DNA in Solution , 1998 .

[46]  H. L. Carrell,et al.  Dibenzo[a,l]pyrene (dibenzo[def,p]chrysene): fjord-region distortions. , 1998, Carcinogenesis.

[47]  P. Kollman,et al.  Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices , 1998 .

[48]  P. J. van der Spek,et al.  Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. , 1998, Molecular cell.

[49]  H. Bartsch,et al.  Polycyclic aromatic hydrocarbon-DNA adducts in humans: relevance as biomarkers for exposure and cancer risk. , 1998, Mutation research.

[50]  E Westhof,et al.  Simulations of the molecular dynamics of nucleic acids. , 1998, Current opinion in structural biology.

[51]  P A Kollman,et al.  Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. , 1998, Journal of biomolecular structure & dynamics.

[52]  A. Dipple,et al.  DNA adduct formation by polycyclic aromatic hydrocarbon dihydrodiol epoxides. , 1998, Chemical research in toxicology.

[53]  H. Naegeli,et al.  Base pair conformation-dependent excision of benzo[a]pyrene diol epoxide-guanine adducts by human nucleotide excision repair enzymes , 1997, Molecular and cellular biology.

[54]  R. Wood,et al.  Two human homologs of Rad23 are functionally interchangeable in complex formation and stimulation of XPC repair activity , 1997, Molecular and cellular biology.

[55]  D. Gorenstein,et al.  Solution structure of the minor conformer of a DNA duplex containing a dG mismatch opposite a benzo[a]pyrene diol epoxide/dA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine. , 1997, Biochemistry.

[56]  Tami I. Spector,et al.  Unrestrained Molecular Dynamics of Photodamaged DNA in Aqueous Solution , 1997 .

[57]  H. Naegeli,et al.  Bipartite substrate discrimination by human nucleotide excision repair. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[58]  D. Patel,et al.  NMR solution structures of stereoisometric covalent polycyclic aromatic carcinogen-DNA adduct: principles, patterns, and diversity. , 1997, Chemical research in toxicology.

[59]  H. Naegeli,et al.  Recognition of DNA Adducts by Human Nucleotide Excision Repair , 1996, The Journal of Biological Chemistry.

[60]  D. Patel,et al.  Solution conformation of the (-)-cis-anti-benzo[a]pyrenyl-dG adduct opposite dC in a DNA duplex: intercalation of the covalently attached BP ring into the helix with base displacement of the modified deoxyguanosine into the major groove. , 1996, Biochemistry.

[61]  C. Harris,et al.  Adduction of the human N-ras codon 61 sequence with (-)-(7S,8R,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a] pyrene: structural refinement of the intercalated SRSR(61,2) (-)-(7S,8R,9S,10R)-N6-[10-(7,8,9,10- tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct from 1H NMR. , 1996, Biochemistry.

[62]  L. Marky,et al.  Differential Hydration Thermodynamics of Stereoisomeric DNA−Benzo[a]pyrene Adducts Derived from Diol Epoxide Enantiomers with Different Tumorigenic Potentials , 1996 .

[63]  P. Sung,et al.  Nucleotide Excision Repair in Yeast Is Mediated by Sequential Assembly of Repair Factors and Not by a Pre-assembled Repairosome (*) , 1996, The Journal of Biological Chemistry.

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

[65]  L. Zhou,et al.  Major groove (S)-alpha-(N6-adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the S(61,2) and S(61,3) sequence isomers from 1H NMR. , 1995, Biochemistry.

[66]  D. Gorenstein,et al.  NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene: an unusual syn glycosidic torsion angle at the modified dA. , 1995, Biochemistry.

[67]  S. Amin,et al.  Mammary carcinogenicity in female CD rats of fjord region diol epoxides of benzo[c]phenanthrene, benzo[g]chrysene and dibenzo[a,l]pyrene. , 1995, Carcinogenesis.

[68]  D. Gorenstein,et al.  Nuclear magnetic resonance solution structure of an undecanucleotide duplex with a complementary thymidine base opposite a 10R adduct derived from trans addition of a deoxyadenosine N6-amino group to (-)-(7R,8S,9R,10S)-7,8-dihydroxy- 9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. , 1995, Biochemistry.

[69]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[70]  S. Amin,et al.  Direct synthesis and characterization of site-specific adenosyl adducts derived from the binding of a 3,4-dihydroxy-1,2-epoxybenzo[c]phenanthrene stereoisomer to an 11-mer oligodeoxyribonucleotide. , 1995, Chemical research in toxicology.

[71]  N. Geacintov,et al.  Synthesis and characterization of covalent adducts derived from the binding of benzo[a]pyrene diol expoxide to a -GGG- sequence in a deoxyoligonucleotide. , 1995, Carcinogenesis.

[72]  D. Patel,et al.  Solution conformation of the (-)-trans-anti-benzo[c]phenanthrene-dA ([BPh]dA) adduct opposite dT in a DNA duplex: intercalation of the covalently attached benzo[c]phenanthrenyl ring to the 3'-side of the adduct site and comparison with the (+)-trans-anti-[BPh]dA opposite dT stereoisomer. , 1995, Biochemistry.

[73]  C. Harris,et al.  Mutations in the p53 tumor suppressor gene: clues to cancer etiology and molecular pathogenesis. , 1994, Cancer research.

[74]  S. Amin,et al.  Potent mammary carcinogenicity in female CD rats of a fjord region diol-epoxide of benzo[c]phenanthrene compared to a bay region diol-epoxide of benzo[a]pyrene. , 1994, Cancer research.

[75]  D. Patel,et al.  Solution conformation of the (+)-trans-anti-[BPh]dA adduct opposite dT in a DNA duplex: intercalation of the covalently attached benzo[c]phenanthrene to the 5'-side of the adduct site without disruption of the modified base pair. , 1993, Biochemistry.

[76]  S. Amin,et al.  Tumor-initiating activity on mouse skin of bay region diol-epoxides of 5,6-dimethylchrysene and benzo[c]phenanthrene. , 1993, Carcinogenesis.

[77]  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.

[78]  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.

[79]  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.

[80]  D. Patel,et al.  Solution conformation of the major adduct between the carcinogen (+)-anti-benzo[a]pyrene diol epoxide and DNA. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[81]  N. V. Ramakrishna,et al.  Comparative dose-response tumorigenicity studies of dibenzo[a,l]pyrene versus 7, 12-dimethylbenz[a]anthracene, benzo[a and two dibenzo[a,l]pyrene dihydrodiols in mouse skin and rat mammary gland , 1991 .

[82]  T. Hayden,et al.  Prediction of DNA structure from sequence: A build‐up technique , 1989, Biopolymers.

[83]  K. Breslauer,et al.  Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves , 1987, Biopolymers.

[84]  F. L. Hirshfeld.  399. The structure of overcrowded aromatic compounds. Part VII. Out-of-plane deformation in benzo[c]phenanthrene and 1,12-dimethylbenzo[c]phenanthrene , 1963 .