Dynamics of a benzo[a]pyrene-derived guanine DNA lesion in TGT and CGC sequence contexts: enhanced mobility in TGT explains conformational heterogeneity, flexible bending, and greater susceptibility to nucleotide excision repair.

[1]  N. Pavletich,et al.  Recognition of DNA damage by the Rad4 nucleotide excision repair protein , 2007, Nature.

[2]  S. Broyde,et al.  The human DNA repair factor XPC‐HR23B distinguishes stereoisomeric benzo[a]pyrenyl‐DNA lesions , 2007, The EMBO journal.

[3]  B. Van Houten,et al.  Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins. , 2007, Biochemistry.

[4]  C. Rizzo,et al.  Conformational differences of the C8-deoxyguanosine adduct of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) within the NarI recognition sequence. , 2007, Chemical research in toxicology.

[5]  D. Patel,et al.  Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context , 2007, Nucleic acids research.

[6]  Y. Zou,et al.  Conformation-specific recognition of carcinogen-DNA adduct in escherichia coli nucleotide excision repair. , 2007, Chemical research in toxicology.

[7]  A. Bishop,et al.  Ultra-violet light induced changes in DNA dynamics may enhance TT-dimer recognition. , 2006, DNA repair.

[8]  B. Van Houten,et al.  Robust incision of Benoz[a]pyrene-7,8-dihyrodiol-9,10-epoxide-DNA adducts by a recombinant thermoresistant interspecies combination UvrABC endonuclease system. , 2006, Biochemistry.

[9]  Wei Yang.  Poor base stacking at DNA lesions may initiate recognition by many repair proteins. , 2006, DNA repair.

[10]  C. Kisker,et al.  Structural basis for DNA recognition and processing by UvrB , 2006, Nature Structural &Molecular Biology.

[11]  M. Lukin,et al.  NMR structures of damaged DNA. , 2006, Chemical reviews.

[12]  Ludovic C. Gillet,et al.  Molecular mechanisms of mammalian global genome nucleotide excision repair. , 2006, Chemical reviews.

[13]  Erik Malta,et al.  Base Flipping in Nucleotide Excision Repair* , 2006, Journal of Biological Chemistry.

[14]  D. Patel,et al.  Structural Aspects of Polycyclic Aromatic Carcinogen-Damaged DNA and Its Recognition by NER Proteins , 2005 .

[15]  T. Buterin,et al.  DNA quality control by conformational readout on the undamaged strand of the double helix. , 2005, Chemistry & biology.

[16]  Andreas Luch,et al.  Nature and nurture – lessons from chemical carcinogenesis , 2005, Nature Reviews Cancer.

[17]  H. Naegeli,et al.  Mechanisms of DNA damage recognition and strand discrimination in human nucleotide excision repair. , 2004, DNA repair.

[18]  R. Isaacs,et al.  A model for initial DNA lesion recognition by NER and MMR based on local conformational flexibility. , 2004, DNA repair.

[19]  B. Coulombe,et al.  Ordered Conformational Changes in Damaged DNA Induced by Nucleotide Excision Repair Factors* , 2004, Journal of Biological Chemistry.

[20]  B. Cho.  Dynamic Conformational Heterogeneities of Carcinogen-DNA Adducts and their Mutagenic Relevance , 2004, Journal of environmental science and health. Part C, Environmental carcinogenesis & ecotoxicology reviews.

[21]  Y. Zou,et al.  Effects of DNA adduct structure and sequence context on strand opening of repair intermediates and incision by UvrABC nuclease. , 2003, Biochemistry.

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

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

[24]  W. Olson,et al.  3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. , 2003, Nucleic acids research.

[25]  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.

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

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

[28]  Richard Lavery,et al.  Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. , 2003, Nucleic acids research.

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

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

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

[32]  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.

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

[34]  K. Sugasawa,et al.  A multistep damage recognition mechanism for global genomic nucleotide excision repair. , 2001, Genes & development.

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

[36]  F. Hanaoka,et al.  Characterization of DNA Recognition by the Human UV-damaged DNA-binding Protein* , 1999, The Journal of Biological Chemistry.

[37]  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.

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

[39]  V. Zhurkin,et al.  DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[40]  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.

[41]  D. Patel,et al.  Nuclear magnetic resonance solution structures of covalent aromatic amine-DNA adducts and their mutagenic relevance. , 1998, Chemical research in toxicology.

[42]  S. Amin,et al.  Sequence dependence and characteristics of bends induced by site-specific polynuclear aromatic carcinogen-deoxyguanosine lesions in oligonucleotides. , 1998, Biochemistry.

[43]  R. Dickerson,et al.  DNA bending: the prevalence of kinkiness and the virtues of normality. , 1998, Nucleic acids research.

[44]  M. Tang,et al.  Rate of incision of N-acetyl-2-aminofluorene and N-2-aminofluorene adducts by UvrABC nuclease is adduct- and sequence-specific: comparison of the rates of UvrABC nuclease incision and protein-DNA complex formation. , 1998, Biochemistry.

[45]  S. Amin,et al.  Bending and circularization of site-specific and stereoisomeric carcinogen-DNA adducts. , 1998, Biochemistry.

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

[47]  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.

[48]  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.

[49]  R. Wood,et al.  Mechanism of open complex and dual incision formation by human nucleotide excision repair factors , 1997, The EMBO journal.

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

[51]  D. Patel,et al.  Solution conformation of the (-)-trans-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the minor groove. , 1994, Biochemistry.

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

[53]  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.

[54]  J. SantaLucia,et al.  Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.

[55]  Peter A. Kollman,et al.  Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins , 1995, J. Comput. Chem..

[56]  V. Zhurkin,et al.  B-DNA twisting correlates with base-pair morphology. , 1995, Journal of molecular biology.

[57]  T. Krugh,et al.  Structural characterization of a (+)-trans-anti-benzo[a]pyrene-DNA adduct using NMR, restrained energy minimization, and molecular dynamics. , 1995, Biochemistry.

[58]  Ron Elber,et al.  MOIL-View - A Program for Visualization of Structure and Dynamics of Biomolecules and STO - A Program for Computing Stochastic Paths , 1995 .

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

[60]  D. Patel,et al.  Solution conformation of the (+)-trans-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the major groove. , 1994, Biochemistry.

[61]  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.

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

[63]  R Lavery,et al.  Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows. , 1989, Journal of biomolecular structure & dynamics.

[64]  H. Blöcker,et al.  Predicting DNA duplex stability from the base sequence. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[65]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[66]  H R Drew,et al.  Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. , 1982, The Journal of biological chemistry.

[67]  A. Conney,et al.  Induction of microsomal enzymes by foreign chemicals and carcinogenesis by polycyclic aromatic hydrocarbons: G. H. A. Clowes Memorial Lecture. , 1982, Cancer research.