Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability

Nucleic Acids Research

Volumn 30, Issue 15, 2002, Pages 3422-3432

  Wu, Min ^a   Yan, Shixiang ^a   Patel, Dinshaw J ^b   Geacintov, Nicholas E ^a   Broyde, Suse ^a  

^a NEW YORK UNIVERSITY   (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1,2,3,4 TETRAHYDRO 3,4 DIHYDROXYBENZO[C]PHENANTHRENE 1,2 OXIDE; ADENINE; BENZO[C]PHENANTHRENE; BENZO[C]PHENANTHRENE DIOL EPOXIDE; CARCINOGEN; CYTOSINE; DNA; PHENANTHRENE DERIVATIVE; POLYCYCLIC AROMATIC HYDROCARBON; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; CARCINOGENICITY; CODON; CONTROLLED STUDY; DNA ADDUCT; DNA DAMAGE; DNA SEQUENCE; DNA STRUCTURE; ENANTIOMER; ENERGY; EXCISION REPAIR; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; MUTATION; ONCOGENE N RAS; PRIORITY JOURNAL; SIMULATION; STEREOISOMERISM; THERMOSTABILITY;

EID: 0036682090     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf427     Document Type: Article

References (56)

1. DNA damage recognition during nucleotide excision repair in mammalian cells
2. DNA excision repair
3. Variability in nucleotide excision repair and cancer risk: A review
4. Chemical characterization of DNA adducts derived from the configurationally isomeric benzo[c]phenanthrene-3,4- diol-1,2-epoxides
5. DNA adduct formation in mammalian cell cultures by polycyclic aromatic hydrocarbons (PAH) and nitro-PAH in coke even emission extract
6. Damage recognition in nucleotide excision repair of DNA
7. A multistep damage recognition mechanism for global genomic nucleotide excision repair
8. Sequential assembly of the nucleotide excision repair factors in vivo
9. 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
10. Bipartite substrate discrimination by human nucleotide excision repair
11. Hierarchy of DNA damage recognition in Escherichia coli nucleotide excision repair
12. Recognition of DNA adducts by human nucleotide excision repair: Evidence for a thermodynamic probing mechanism
13. The structure of overcrowded aromatic compounds. Part VII. Out-of-plane deformation in benzo[c]-phenanthrene and 1,12-dimethyl- benzo[c]phenanthrene
14. Tumorigenicity of optical isomers of the diastereomeric bay-region 3,4-diol-1,2-epoxides of benzo[c]phenanthrene in murine tumor models
15. Comparative dose-response tumorigenicity studies of dibenzo[α,1]pyrene versus 7, 12-dimethylbenz[α]anthracene, benzo[α]pyrene and two dibenzo[α,1]pyrene dihydrodiols in mouse skin and rat mammary gland
16. Oxidative metabolism of polycyclic aromatic hydrocarbons to ultimate carcinogens
17. Optically active benzo[c]phenanthrene diol epoxides bind extensively to adenine in DNA
18. N-ras and Human Cancer
19. Unrepaired fjord region polycyclic aromatic hydrocarbon-DNA adducts in ras codon 61 mutational hot spots
20. Free energy analysis of the conformational preferences of A and B forms of DNA in solution
21. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
22. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
23. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
24. Free-energy component analysis of 40 protein-DNA complexes: A consensus view on the thermodynamics of binding at the molecular level
25. Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
26. 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
27. 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 comparison with the (+)-trans-anti-[BPh]dA opposite dT stereoisomer
28. Stereochemical, structural and thermodynamic origins of stability differences between stereoisomeric benzo[a]pyrene diol epoxide deoxyadenosine adducts in a DNA mutational hot spot sequence
29. 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
30. NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addiction of a deoxyadenosine 8,9,10-tetrahydrobenzo[a]pyrene: An unusual syn glycosidic torsion angle at the modified dA
31. 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) tetrahydrobenzo[a]pyrenyl)]- 2′-deoxyadenosyl adduct from 1H NMR
32. NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10R adduct derived from trans addition of a deoxyadenosine 10-tetrahydrobenzo[a]pyrene
33. 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
34. Cyclohexene ring and fjord region twist inversion in stereoisomeric DNA adducts of enantiomeric benzo[c]phenanthrene diol epoxides
35. Prediction of DNA structure from sequence: A build-up technique
36. A second generation force field for the simulation of proteins and nucleic acids
37. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
38. A smooth particle mesh Ewald method
39. Numerical integration of cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
40. Comparison of simple potential functions for simulating liquid water
41. Molecular dynamics with coupling to an external bath
42. Classical electrostatics in biology and chemistry
43. DelPhi
44. Reduced surface: An efficient way to compute molecular surfaces
45. Principles of Nucleic Acid Structure
46. Definitions and nomenclature of nucleic acid structure parameters
47. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
48. Conformational and helicoidal analysis of 30 ps of molecular dynamics on the d(CGCGAATTCGCG) double helix: "Curves", dials and windows
49. Crystal studies of B-DNA: The answers and the questions
50. 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
51. 6-dA lesions in the N-ras codon 61 and other sequence contexts
52. A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques
53. Resolving the discrepancies among nucleic acid conformational analyses
54. Nucleic acid structure analysis: A users guide to a collection of new analysis programs