Toward understanding the mutagenicity of an environmental carcinogen: structural insights into nucleotide incorporation preferences.

[1]  Yanbin Zhang,et al.  trans-Lesion Synthesis Past Bulky Benzo[a]pyrene Diol Epoxide N 2-dG and N 6-dA Lesions Catalyzed by DNA Bypass Polymerases* , 2002, The Journal of Biological Chemistry.

[2]  Samuel H. Wilson,et al.  Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. , 2002, Journal of molecular biology.

[3]  M. Radman,et al.  Specialized DNA Polymerases, Cellular Survival, and the Genesis of Mutations , 2002, Science.

[4]  A. Grollman,et al.  Translesion synthesis by human DNA polymerase kappa on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-N(2)-BPDE (7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene). , 2002, Biochemistry.

[5]  D. Jerina,et al.  Preferential Misincorporation of Purine Nucleotides by Human DNA Polymerase η Opposite Benzo[a]pyrene 7,8-Diol 9,10-Epoxide Deoxyguanosine Adducts* , 2002, The Journal of Biological Chemistry.

[6]  D. Jerina,et al.  Efficiency and Accuracy of SOS-induced DNA Polymerases Replicating Benzo[a]pyrene-7,8-diol 9,10-Epoxide A and G Adducts* , 2002, The Journal of Biological Chemistry.

[7]  A. Das,et al.  Free‐energy component analysis of 40 protein–DNA complexes: A consensus view on the thermodynamics of binding at the molecular level , 2002, J. Comput. Chem..

[8]  D. Beveridge,et al.  Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility. , 2001, Journal of molecular biology.

[9]  R. Woodgate,et al.  Crystal Structure of a Y-Family DNA Polymerase in Action A Mechanism for Error-Prone and Lesion-Bypass Replication , 2001, Cell.

[10]  Z. Livneh.  DNA Damage Control by Novel DNA Polymerases: Translesion Replication and Mutagenesis* , 2001, The Journal of Biological Chemistry.

[11]  T. Kunkel,et al.  The Y-family of DNA polymerases. , 2001, Molecular cell.

[12]  S. Broyde,et al.  Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen. , 2001, Journal of molecular biology.

[13]  Thomas A. Steitz,et al.  Structure of the Replicating Complex of a Pol α Family DNA Polymerase , 2001, Cell.

[14]  E. Kool,et al.  Significance of nucleobase shape complementarity and hydrogen bonding in the formation and stability of the closed polymerase-DNA complex. , 2001, Biochemistry.

[15]  L. Dzantiev,et al.  Effects of benzo[a]pyrene DNA adducts on Escherichia coli DNA polymerase I (Klenow fragment) primer-template interactions: evidence for inhibition of the catalytically active ternary complex formation. , 2001, Biochemistry.

[16]  Samuel H. Wilson,et al.  DNA Structure and Aspartate 276 Influence Nucleotide Binding to Human DNA Polymerase β , 2001, The Journal of Biological Chemistry.

[17]  J. Wagner,et al.  All three SOS‐inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis , 2000, The EMBO journal.

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

[19]  R. Fuchs,et al.  The processing of a Benzo(a)pyrene adduct into a frameshift or a base substitution mutation requires a different set of genes in Escherichia coli , 2000, Molecular microbiology.

[20]  L. Beese,et al.  Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7. , 2000, Journal of molecular biology.

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

[22]  D. Beveridge,et al.  Nucleic acids: theory and computer simulation, Y2K. , 2000, Current opinion in structural biology.

[23]  K. Guckian,et al.  Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication. , 2000, Angewandte Chemie.

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

[25]  P A Kollman,et al.  Molecular dynamics simulation of nucleic acids. , 2000, Annual review of physical chemistry.

[26]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[27]  Frieden,et al.  Tightening the Belt on Polymerases: Evaluating the Physical Constraints on Enzyme Substrate Size. , 1999, Angewandte Chemie.

[28]  S. Broyde,et al.  Conformational analysis of the major DNA adduct derived from the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline. , 1999, Chemical research in toxicology.

[29]  R. Woodgate.  A plethora of lesion-replicating DNA polymerases. , 1999, Genes & development.

[30]  D. Phillips,et al.  Polycyclic aromatic hydrocarbons in the diet. , 1999, Mutation research.

[31]  T. Steitz.  DNA Polymerases: Structural Diversity and Common Mechanisms* , 1999, The Journal of Biological Chemistry.

[32]  M. Colvin,et al.  Interaction and solvation energies of nonpolar DNA base analogues and their role in polymerase insertion fidelity. , 1999, Journal of biomolecular structure & dynamics.

[33]  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.

[34]  Gabriel Waksman,et al.  Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation , 1998, The EMBO journal.

[35]  S. Doublié,et al.  The mechanism of action of T7 DNA polymerase. , 1998, Current opinion in structural biology.

[36]  G L Verdine,et al.  Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. , 1998, Science.

[37]  E. Kool,et al.  Efficient replication between non-hydrogen-bonded nucleoside shape analogs , 1998, Nature Structural Biology.

[38]  D. Jerina,et al.  Effect of single benzo[a]pyrene diol epoxide-deoxyguanosine adducts on the action of DNA polymerases in vitro. , 1998, International journal of oncology.

[39]  S. Amin,et al.  Mutagenic potential of stereoisomeric bay region (+)- and (-)-cis-anti-benzo[a]pyrene diol epoxide-N2-2'-deoxyguanosine adducts in Escherichia coli and simian kidney cells. , 1998, Biochemistry.

[40]  B. Day,et al.  Effects of bulky polycyclic aromatic hydrocarbon adducts on DNA replication by exonuclease-deficient T7 and T4 DNA polymerases. , 1998, DNA and cell biology.

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

[42]  M. Tang,et al.  Slow repair of bulky DNA adducts along the nontranscribed strand of the human p53 gene may explain the strand bias of transversion mutations in cancers , 1998, Oncogene.

[43]  T. Steitz,et al.  Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. , 1998, Current opinion in structural biology.

[44]  T. Steitz,et al.  Structural biology: A mechanism for all polymerases , 1998, Nature.

[45]  S. Doublié,et al.  Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution , 1998, Nature.

[46]  James R. Kiefer,et al.  Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal , 1998, Nature.

[47]  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.

[48]  E. Kool.  Replication of non‐hydrogen bonded bases by DNA polymerases: A mechanism for steric matching , 1998, Biopolymers.

[49]  N. Geacintov,et al.  How stereochemistry affects mutagenesis by N2-deoxyguanosine adducts of 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene: configuration of the adduct bond is more important than those of the hydroxyl groups. , 1997, Biochemistry.

[50]  E. Kool,et al.  A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Samuel H. Wilson,et al.  Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. , 1997, Biochemistry.

[52]  Mihaly Mezei,et al.  Optimal position of solute for simulations , 1997, J. Comput. Chem..

[53]  N. Geacintov,et al.  Sequence specific mutagenesis of the major (+)-anti-benzo[a]pyrene diol epoxide-DNA adduct at a mutational hot spot in vitro and in Escherichia coli cells. , 1997, Chemical research in toxicology.

[54]  H. L. Carrell,et al.  Benzo[a]pyrene and its analogues: structural studies of molecular strain. , 1997, Carcinogenesis.

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

[56]  L. Beese,et al.  Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution. , 1997, Structure.

[57]  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.

[58]  G. Grimmer,et al.  Determination of urinary metabolites of polycyclic aromatic hydrocarbons (PAH) for the risk assessment of PAH-exposed workers , 1997, International archives of occupational and environmental health.

[59]  S. Spiegel,et al.  Fidelity of translesional synthesis past benzo[a]pyrene diol epoxide-2'-deoxyguanosine DNA adducts: marked effects of host cell, sequence context, and chirality. , 1996, Biochemistry.

[60]  M. Tang,et al.  Preferential Formation of Benzo[a]pyrene Adducts at Lung Cancer Mutational Hotspots in P53 , 1996, Science.

[61]  J. Kraut,et al.  Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity. , 1996, Biochemistry.

[62]  Thomas A. Steitz,et al.  Structure of Taq polymerase with DNA at the polymerase active site , 1996, Nature.

[63]  D. Patel,et al.  Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts positioned at a DNA template-primer junction. , 1995, Biochemistry.

[64]  M. Nayal,et al.  Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Peter A. Kollman,et al.  AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .

[66]  Dae-Sil Lee,et al.  Crystal structure of Thermus aquaticus DNA polymerase , 1995, Nature.

[67]  C. Richardson,et al.  A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

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

[69]  M. Donlin,et al.  Mutants affecting nucleotide recognition by T7 DNA polymerase. , 1994, Biochemistry.

[70]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[71]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[72]  E. Loechler,et al.  Mutational specificity of the (+)-anti-diol epoxide of benzo[a]pyrene in a supF gene of an Escherichia coli plasmid: DNA sequence context influences hotspots, mutagenic specificity and the extent of SOS enhancement of mutagenesis. , 1993, Carcinogenesis.

[73]  E. Loechler,et al.  Mutagenesis by the (+)-anti-diol epoxide of benzo[a]pyrene: what controls mutagenic specificity? , 1993, Biochemistry.

[74]  P. Liska,et al.  Trace enrichment and HPLC analysis of PAHs in edible oils and fat products, using liquid chromatography on electron acceptor stationary phases in connection with reverse phase and fluorescence detection , 1993 .

[75]  K. Johnson,et al.  Conformational coupling in DNA polymerase fidelity. , 1993, Annual review of biochemistry.

[76]  K. Peltonen,et al.  DNA polymerase action on benzo[a]pyrene-DNA adducts. , 1992, Carcinogenesis.

[77]  M. Benasutti,et al.  Mutagenesis by (+)-anti-B[a]P-N2-Gua, the major adduct of activated benzo[a]pyrene, when studied in an Escherichia coli plasmid using site-directed methods. , 1992, Carcinogenesis.

[78]  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.

[79]  J. Timm,et al.  Relevance of polycyclic aromatic hydrocarbons as environmental carcinogens , 1991 .

[80]  S. Benkovic,et al.  Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant. , 1991, Biochemistry.

[81]  S. Benkovic,et al.  Mechanism of DNA replication fidelity for three mutants of DNA polymerase I: Klenow fragment KF(exo+), KF(polA5), and KF(exo-). , 1991, Biochemistry.

[82]  K. Johnson,et al.  An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. , 1991, Biochemistry.

[83]  H. Echols,et al.  Fidelity mechanisms in DNA replication. , 1991, Annual review of biochemistry.

[84]  J. M. Roman,et al.  DNA adducts from carcinogenic and noncarcinogenic enantiomers of benzo[a]pyrene dihydrodiol epoxide. , 1989, Chemical research in toxicology.

[85]  S. Benkovic,et al.  Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. , 1988, Biochemistry.

[86]  S. Benkovic,et al.  Kinetic mechanism of DNA polymerase I (Klenow). , 1987, Biochemistry.

[87]  R. H. Ritchie,et al.  Dielectric effects in biopolymers: The theory of ionic saturation revisited , 1985 .

[88]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[89]  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.

[90]  S. Neidle,et al.  Molecular structure of (+/-)-7,8,9,10-tetrahydroxy-7,8,9,10-tetrahydrobenzo(a)pyrene determined by x-ray crystallography. , 1982, Cancer research.

[91]  S. Neidle,et al.  The molecular structure of (±)- 7α, 8β-dihydroxy-7,8-dihydrobenzo[a]pyrene, an early metabolite of benzo[a]pyrene , 1981 .

[92]  J. A. Allen,et al.  Identification of the proximate and ultimate forms of the carcinogen 15,16-dihydro-11-methylcyclopenta[a]phenanthren-17-one. , 1979, Cancer research.

[93]  K. Straub,et al.  Double-stranded DNA stereoselectively binds benzo(a)pyrene diol epoxides , 1979, Nature.

[94]  D. Jerina,et al.  Tumorigenicity of the optical enantiomers of the diastereomeric benzo[a]pyrene 7,8-diol-9,10-epoxides in newborn mice: exceptional activity of (+)-7beta,8alpha-dihydroxy-9alpha,10alpha-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[95]  D. Jerina,et al.  Evidence that benzo(a)anthracene 3,4-diol-1,2-epoxide is an ultimate carcinogen on mouse skin. , 1978, Cancer research.

[96]  J. W. Cook,et al.  106. The isolation of a cancer-producing hydrocarbon from coal tar. Parts I, II, and III , 1933 .