Evading the proofreading machinery of a replicative DNA polymerase: Induction of a mutation by an environmental carcinogen

Journal of Molecular Biology

Volumn 309, Issue 2, 2001, Pages 519-536

  Perlow, Rebecca A ^a   Broyde, Suse ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

Benzo a pyrene; DNA polymerase; Environmental carcinogen; Molecular dynamics simulations; Mutagenesis

Indexed keywords

ADENINE; BENZO[A]PYRENE; CARCINOGEN; CIGARETTE SMOKE; DNA; DNA POLYMERASE; GUANINE; HYDROGEN; POLYCYCLIC AROMATIC HYDROCARBON;

ARTICLE; DNA ADDUCT; DNA REPLICATION; DNA TEMPLATE; EXHAUST GAS; GENE MUTATION; HUMAN; HUMAN CELL; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN STABILITY; SIMULATION;

MAMMALIA;

EID: 0035366319     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4674     Document Type: Article

References (123)

1. The mechanism of action of T7 DNA polymerase
2. Structural insights into DNA polymerase β fidelity: Hold it tight if you want it right
3. DNA polymerases: Structural diversity and common mechanisms
4. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
5. Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity
6. Mechanism of DNA replication fidelity for three mutants of DNA polymerase I: Klenow fragment KF(exo+), KF(polA5), and KF(exo-)
7. Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5 Å resolution: Structural basis for thermostability
8. Crystal structure of Thermus aquaticus DNA polymerase
9. Structure of Taq ploymerase with DNA at the polymerase active site
10. Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 Å resolution
11. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
12. Dose-dependent differences in the profile of mutations induced by (+)-7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene in the coding region of the hypoxanthine (guanine) phosphoribosyltransferase gene in Chinese hamster V-79 cells
13. 2-Gua adduct of the (+)-anti-benzo[a]pyrene diol epoxide is capable of inducing G → A and G → C, in addition to G → T, mutations
14. In vitro replication by prokaryotic and eukaryotic polymerases on DNA templates containing site-specific and stereospecific benzo[a]pyrene- 7,8-dihydrodiol-9,10-epoxide adducts
15. 6 at the second position of N-ras codon 61
16. 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
17. NMR solution structures of stereoisomeric covalent polycyclic aromatic carcinogen-DNA adducts: Principles, patterns, and diversity
18. A comparison of mutational specificity of mutations induced by S9-activated B[a]P and benzo[a]pyrene-7,8-diol-9,10-epoxide at the endogenous aprt gene in CHO cells
19. Lesions in DNA: Hurdles for polymerases
20. In vitro replication of primer-templates containing benzo[a]-pyrene adducts by exonuclease-deficient Escherichia coli DNA polymerase I (Klenow fragment): Effect of sequence context on lesion bypass
21. 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
22. Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7
23. Kinetic mechanism of DNA polymerase I (Klenow fragment): Identification of a second conformational change and evaluation of the internal equilibrium constant
24. Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4
25. Kinetic analysis of nucleotide incorporation and misincorporation by Klenow fragment of Escherichia coli DNA polymerase I
26. Crystal structure 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
27. Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation
28. A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase β
29. Crystal structures of human DNA polymerase β complexed with DNA: Implications for catalytic mechanism, processivity, and fidelity
30. Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
31. Kinetic mechanism of DNA polymerase I (Klenow)
32. An induced-fit kinetic mechanism for DNA replication fidelity: Direct measurement by single-turnover kinetics
33. DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase β: Implication for the identity of the rate-limiting conformational change
34. The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme
35. Fidelity mechanisms in DNA replication
36. A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity
37. Replication of non-hydrogen bonded bases by DNA polymerases: A mechanism for steric matching
38. Efficient replication between non-hydrogen-bonded nucleoside shape analogs
39. Tightening the belt on polymerases: Evaluating the physical constraints on enzyme substrate size
40. Interaction and solvation energies of nonpolar DNA base analogues and their role in polymerase insertion fidelity
41. Mimicking the structure and function of DNA: Insights into DNA stability and replication
42. Conformational coupling in DNA polymerase fidelity
43. Minor groove interactions between polymerase and DNA: More essential to replication than Watson-Crick hydrogen bonds
44. A specific partner for abasic damage in DNA
45. Side-chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli
46. A minor groove binding track in reverse transcriptase
47. Vertical-scanning mutagenesis of a critical tryptophan in the minor groove binding track of HIV-1 reverse transcriptase. Molecular nature of polymerase-nucleic acid interactions
48. Vertical-scanning mutagenesis of a critical tryptophan in the "minor groove binding track" of HIV-1 reverse transcriptase. Major groove DNA adducts identify specific protein interactions in the minor groove
49. The role of DNA adducts in chemical carcinogenesis
50. p53 mutation spectrum and load: The generation of hypotheses linking the exposure of endogenous or exogenous carcinogens to human cancer
51. Environmental factors as regulators and effectors of multistep carcinogenesis
52. Human cancer, carcinogenic exposures and mutation spectra
53. Relevance of polycyclic aromatic hydrocarbons as environmental carcinogens
54. 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
55. Polycyclic aromatic hydrocarbons in the diet
56. DNA adduct formation in mammalian cell cultures by polycyclic aromatic hydrocarbons (PAH) and nitro-PAH in coke oven emission extract
57. Comparative in vitro and in vivo benzo[a]pyrene-DNA adduct formation and its relationship to CYP1A activity in two species of ictalurid catfish
58. The ratio of deoxyadenosine to deoxyguanosine adducts formed by (+)- (7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene in purified calf thymus DNA and DNA in V-79 cells is independent of dose
59. 2-Gua, the major adduct of activated benzo[a]pyrene, when studied in an Escherichia coli plasmid using site-directed methods
60. DNA polymerase action on benzo[a]pyrene-DNA adducts
61. 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
62. Use of single-turnover kinetics to study bulky adduct bypass by T7 DNA polymerase
63. Fidelity of translesional synthesis past benzo[a]pyrene diol epoxide-2′-deoxyguanosine DNA adducts: Marked effects of host cell, sequence context, and chirality
64. 2-ethenoguanine and 5,6,7,9-tetrahydro-7-hydroxy-9-oxoimidazo[1,2-a]purine in oligonucleotides by Escherichia coli polymerases I exo- and II exo-, T7 polymerase exo-, human immunodeficiency virus-1 reverse transcriptase, and rat polymerase β
65. 2-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
66. 2-2′-deoxyguanosine adducts in Escherichia coli and simian kidney cells
67. DNA polymerase, RNA polymerase and exonuclease activities on a DNA sequence modified by benzo[a]pyrene diol epoxide
68. Effects of bulky polycyclic aromatic hydrocarbon adducts on DNA replication by exonuclease deficient T7 and T4 DNA polymerases
69. Effect of single benzo[a]pyrene diol epoxide-deoxyguanosine adducts on the action of DNA polymerases in vitro
70. Induction of microsomal enzymes by foreign chemicals and carcinogenesis by polycyclic aromatic hydrocarbons
71. Tumorigenicity of the optical enantiomers of the diastereomeric benzo[a]pyrene 7,8-diol-9,10-epoxides in newborn mice: Exceptional activity of (+)-7β,8α-dihydroxy-9α,10αepoxy-7,8,9,10- tetrahydrobenzo[a]pyrene
72. Marked differences in the skin tumor-initiating activities of the optical enantiomers of the diastereomeric benzo[a]pyrene 7,8-diol-9,10-epoxides
73. Solution conformation of the major adduct between the carcinogen (+)- anti-benzo[a]pyrene diol epoxide and DNA
74. 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
75. Structural characterization of a (+)-trans-anti-benzo[a]pyrene-DNA adduct using NMR, restrained energy minimization, and molecular dynamics
76. Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts positioned at a DNA template-primer junction
77. Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template-primer junction
78. The molecular structure of (+/-)- 7 α, 8 β-dihydroxy-7,8-dihydrobenzo[a]pyrene, an early metabolite of benzo[a]pyrene
79. Molecular structure of (+/-)-7,8,9,10-tetrahydroxy-7, 8,9,10-tetrahydrobenzo(a)pyrene determined by X-ray crystallography
80. Benzo[a]pyrene and its analogues: Structural studies of molecular strain
81. Targeting of lung cancer mutational hotspots by polycyclic aromatic hydrocarbons
82. Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in P53
83. 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
84. Database of p53 gene somatic mutations in human tumors and cell lines: Updated compilation and future prospects
85. A second generation force-field for the simulation of proteins, nucleic acids, and organic molecules
86. A modified version of the Cornell et al. force-field with improved sugar pucker phases and helical repeat
87. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
88. Nucleic acids: Theory and computer simulation, Y2K
89. Molecular dynamics simulation of nucleic acids
90. Simulations of the molecular dynamics of nucleic acids
91. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
92. A-form conformational motifs in ligand-bound DNA structures
93. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
94. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes
95. 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
96. 2 in a duplex dodecamer
97. Interactions between DNA polymerase β and the major covalent adduct of the carcinogen (+)-anti-benzo[a]pyrene diol epoxide with DNA at a primer-template junction
98. 2-dG) causes G → T versus G → A mutations based upon a correlation between mutagenesis and molecular modeling results
99. 2-dG adduct of (+)-anti-B[a]PDE shows a dramatically different mutagenic specificity (predominantly, G → A) in a 5′-CGT-3′ sequence context
100. 2-dG adduct of (+)-anti-B[a]PDE induces G → A mutations in a 5′-AGA-3′ sequence context
101. A plethora of lesion-replicating DNA polymerases
102. Error-free and error-prone lesion bypass by human DNA polymerase κ in vitro
103. All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis
104. The expanding polymerase universe
105. Electrostatic interactions in macromolecules: Theory and applications
106. Accurate calculation of hydration free-energies using macroscopic solvent models
107. Classical electrostatics in biology and chemistry
108. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
109. Free energy analysis of the conformational preferences of A and B-forms of DNA in solution
110. Free energy analysis of protein-DNA binding: The EcoRI endonuclease-DNA complex
111. AMBER, a package of computer programs applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules
112. Particle mesh Ewald-An N*log(N) method for Ewald sums in large systems
113. Conformational analysis of the major DNA adduct derived from the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline
114. Water interaction potentials derived from free energy perturbation simulations
115. The Protein Data Bank
116. Dielectric effects in biopolymers: The theory of ionic saturation revisited
117. Comparison of simple potential functions for simulating liquid water