Structure of the 1,N2-etheno-2′-deoxyguanosine adduct in duplex DNA at pH 8.6

Chemical Research in Toxicology

Volumn 20, Issue 11, 2007, Pages 1601-1611

  Shanmugam, Ganesh ^a   Goodenough, Angela K ^a   Kozekov, Ivan D ^a   Guengerich, F Peter ^a   Rizzo, Carmelo J ^a   Stone, Michael P ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DEOXYGUANOSINE DERIVATIVE; DOUBLE STRANDED DNA; NUCLEOTIDE; OLIGODEOXYNUCLEOTIDE; 1,N(6) ETHENODEOXYADENOSINE; 1,N(6)-ETHENODEOXYADENOSINE; DEOXYADENOSINE DERIVATIVE; DEOXYGUANOSINE; DNA; PROTON; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CHEMICAL BOND; CHEMICAL STRUCTURE; MOLECULAR DYNAMICS; PAIRED HELICAL FILAMENT; PH; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PROTON NUCLEAR MAGNETIC RESONANCE; CHEMISTRY; CONFORMATION; DNA ADDUCT; DNA REPAIR; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

DEOXYADENOSINES; DEOXYGUANOSINE; DNA; DNA ADDUCTS; DNA REPAIR; HYDROGEN-ION CONCENTRATION; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID CONFORMATION; PROTONS;

EID: 37249079875     PISSN: 0893228X     EISSN: None     Source Type: Journal    
DOI: 10.1021/tx7001788     Document Type: Article

References (55)

1. Barbin, A. (2000) Etheno-adduct-forming chemicals: From mutagenicity testing to tumor mutation spectra. Mutat. Res. 462, 55-69.
2. Barbin, A., Bresil, H., Croisy, A., Jacquignon, P., Malaveille, C., Montesano, R., and Bartsch, H. (1975) Liver-microsome-mediated formation of alkylating agents from vinyl bromide and vinyl chloride. Biochem. Biophys. Res. Commun. 67, 596-603.
3. Green, T., and Hathway, D. E. (1978) Interactions of vinyl chloride with rat-liver DNA in vivo. Chem.-Biol. Interact. 22, 211-224.
4. 4-etheno-2′-deoxycytidine detected by monoclonal antibodies in lung and liver DNA of rats exposed to vinyl chloride. Carcinogenesis 10, 209-212.
5. 2,3-ethenoguanine in rat tissue DNA. Carcinogenesis 11, 1287-1292.
6. Guengerich, F. P., Mason, P. S., Stott, W. T., Fox, T. R., and Watanabe, P. G. (1981) Roles of 2-haloethylene oxides and 2-haloacetaldehydes derived from vinyl bromide and vinyl chloride in irreversible binding to protein and DNA. Cancer Res. 41, 4391-4398.
7. 6-ethenoadenosine. Chem. Res. Toxicol. 4, 413-421.
8. Guengerich, F. P. (1992) Roles of the vinyl chloride oxidation products 1-chlorooxirane and 2-chloroacetaldehyde in the in vitro formation of etheno adducts of nucleic acid bases [corrected]. Chem. Res. Toxicol. 5, 2-5.
9. Bartsch, H., Barbin, A., Marion, M. J., Nair, J., and Guichard, Y. (1994) Formation, detection, and role in carcinogenesis of ethenobases in DNA. Drug Metab. Rev. 26, 349-371.
10. 32P-postlabeling. Carcinogenesis 16, 613-617.
11. Guichard, Y., el Ghissassi, F., Nair, J., Bartsch, H., and Barbin, A. (1996) Formation and accumulation of DNA ethenobases in adult Sprague-Dawley rats exposed to vinyl chloride. Carcinogenesis 17, 1553-1559.
12. 2,3-ethenoguanine synthesis and comparison of electronic spectral properties of these linear and angular triheterocycles related to Y bases. J. Org. Chem. 42, 3292-3296.
13. 2- ethenodeoxyguanosine: properties and formation in chloroacetaldehyde-treated polynucleotides and DNA. Chem. Res. Toxicol. 5, 634-638.
14. 2-(2-oxoethyl)guanine. Chem. Res. Toxicol. 6, 635-648.
15. 13C-Labeling patterns with 2-bromoacetaldehyde. Chem. Res. Toxicol. 7, 205-208.
16. 2-ethenoguanine with an immunoaffinity/gas chromatography/high-resolution mass spectrometry assay. Chem. Res. Toxicol. 14, 327-334.
17. 2-ethenoguanine, 5,6,7,9-tetrahydro-9-oxoimidazo[1,2-a]purine, and 5,6,7,9-tetrahydro-7-hydroxy- 9-oxoimidazo[1,2-a]purine. Biochemistry 37, 5184-1593.[Published erratum appears in Biochemistry, 1998 Jun 16; 37(24):8816].
18. 2-ethenoguanine in Chinese hamster ovary cell chromosomal DNA. Chem. Res. Toxicol. 12, 501-507.
19. 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 beta. Biochemistry 36, 6069-6079.
20. 2-ethenoguanine. J. Biol. Chem. 280, 29750-29764.
21. 2-ethenoguanine by human DNA polymerases. Chem. Res. Toxicol. 19, 879-886.
22. de los Santos, C., Zaliznyak, T., Bonala, R. R., Johnson, F., Lukin, M. (2006) Structural Characterization of DNA Duplexes Having Exocyclic 2′-Deoxyguanosine Adducts, 232nd National Meeting of the American Chemical Society, Division of Chemical Toxicology, San Francisco, CA,Sept 10-14.
23. 2-etheno-2′-deoxyguanosine. Chem. Res. Toxicol. 18, 1701-1714.
24. Cavaluzzi, M. J., and Borer, P. N. (2004) Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA. Nucleic Acids Res. 32, e13.
25. Piotto, M., Saudek, V., and Sklenar, V. (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2, 661-665.
26. Piantini, U., Sorensen, O. W., and Ernst, R. R. (1982) Multiple quantum filters for elucidating NMR coupling networks. J. Am. Chem. Soc. 104, 6800-6801.
27. 1H NMR spectra of proteins via double quantum filtering. Biochem. Biophys. Res. Commun. 177, 479-485.
28. Borgias, B. A., and James, T. L. (1990) MARDIGRAS: a procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure. J. Magn. Reson. 87, 475-487.
29. Liu, H., Spielmann, H. P., Ulyanov, N. B., Wemmer, D. E., and James, T. L. (1995) Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors. J. Biomol. NMR 6, 390-402.
30. Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., and Woods, R. J. (2005) The AMBER biomolecular simulation programs. J. Comput. Chem. 26, 1668-1688.
31. Arnott, S., and Hukins, D. W. L. (1972) Optimised parameters for A-DNA and B-DNA. Biochem. Biophys. Res. Commun. 47, 1504-1509.
32. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Jr., Stratmann, R. E., Burant, J. C., Dapprich, S., Millam, J. M., Daniels, A. D., Kudin, K. N., Strain, M. C., Farkas, O., Tomas, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P. Y., Cui, Q., Morukuma, K., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Gonsalez, C., Challacombe, M., Gill, P. M. W., Johnson, B. G., Chen, W., Wong, M. W., Andres, J. L., Head-Gordon, M., Replogle, E. S. (1998) Gaussian 98, Gaussian Inc., Pittsburgh, PA.
33. Wang, J., Wang, W., Kollman, P. A., and Case, D. A. (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graphics Modell. 25, 247-260.
34. Band, L., Bertini, I., Savellini, G. G., Romagnoli, A., Turano, P., Cremonini, M. A., Luchinat, C., and Gray, H. B. (1997) Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins. Proteins 29, 68-76.
35. Bashford, D., and Case, D. A. (2000) Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 51, 129-152.
36. Tsui, V., and Case, D. A. (2000) Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 56, 275-291.
37. Keepers, J. W., and James, T. L. (1984) A theoretical-study of distance determinations from NMR: two-dimensional nuclear Overhauser effect spectra. J. Magn. Reson. 57, 404-426.
38. Lavery, R., and Sklenar, H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6, 63-91.
39. Stofer, E., and Lavery, R. (1994) Measuring the geometry of DNA grooves. Biopolymers 34, 337-346.
40. Reid, B. R. (1987) Sequence-specific assignments and their use in NMR studies of DNA structure. Q. Rev. Biophys. 20, 2-28.
41. Patel, D. J., Shapiro, L., and Hare, D. (1987) DNA and RNA: NMR studies of conformations and dynamics in solution. Q. Rev. Biophys. 20, 35-112.
42. 1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy. Application to a lac operator fragment. J. Magn. Reson. 62, 378-386.
43. 4-etheno-2′- deoxycytidine opposite thymidine: Comparison with the duplex containing deoxyadenosine opposite the adduct. Biochemistry 35, 13319-13327.
44. 4-etheno-2′-deoxycytidine opposite 2′- deoxyadenosine, determined by NMR spectroscopy arid restrained molecular dynamics. Biochemistry 35, 13310-13318.
45. 2-ethenoguanine, a mutagenic DNA adduct, is a primary substrate of Escherichia coli mismatch-specific uracil-DNA glycosylase and human alkylpurine-DNA-N- glycosylase. J. Biol. Chem. 277, 26987-26993.
46. 6- ethenoadenine and 3- methyladenine. Proc. Natl. Acad. Sci. U.S.A. 89, 9386-9390.
47. 4-ethenocytosine and the G/T mismatch. Proc. Natl. Acad. Sci. U.S.A. 95, 13561-13566.
48. Huffman, J. L., Sundheim, O., and Tainer, J. A. (2005) DNA base damage recognition and removal: New twists and grooves. Mutat. Res. 577, 55-76.
49. 4-etheno-2′-deoxycytidine in the dodecamer 5′- CGCGAATTεCGCG-3′. J. Mol. Biol. 329, 685-697.
50. 4- ethenocytosine adduct opposite 2′-deoxycytidine: Implications for the recognition of exocyclic lesions by DNA glycosylases. J. Mol. Biol. 296, 851-861.
51. 4-etheno-2′-deoxycytidine. IARC Sci. PuM. 150, 179-189.
52. 4- etheno-2′-deoxycytidine opposite 2′-deoxyguanosine. Biochemistry 36, 11933-11943.
53. 6- ethenodeoxyadenosine adduct (εdA) opposite thymidine in a DNA duplex. Nonplanar alignment of εdA(anti) and dT(anti) at the lesion site. Biochemistry 30, 1820-1828.
54. 6-ethenoadenine base pairs in the crystal structure of d(CGCGAATT(εdA)GCG). Biochemistry 33, 4755-4761.
55. 6-ethenodeoxyadenosine adduct (εdA) opposite deoxyguanosine in a DNA duplex. εdA(syn):dG(anti) pairing at the lesion site. Biochemistry 30, 1828-1835.