Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA

Biochemistry

Volumn 46, Issue 16, 2007, Pages 4793-4803

  Zhang, Na ^a   Lin, Yiqing ^b   Xiao, Ziwei ^a   Jones, Graham B ^b   Goldberg, Irving H ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b NORTHEASTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC NEOCARZINOSTATIN; BULGE RESIDUES (GT); LIGAND BINDING;

ANTIBIOTICS; AROMATIC COMPOUNDS; DNA; LIGANDS; METABOLITES; MOLECULAR STRUCTURE;

BINDING ENERGY;

ANTIBIOTIC AGENT; DIHYDRONAPHTHANONE; METHYL GROUP; NAPHTHACENE DERIVATIVE; OLIGODEOXYNUCLEOTIDE; RNA; UNCLASSIFIED DRUG; ZINOSTATIN;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; COMPLEX FORMATION; DNA BINDING; DNA FLANKING REGION; LIGAND BINDING; MOLECULAR DYNAMICS; NUCLEIC ACID IMMOBILIZATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

DNA; ENEDIYNES; FUCOSE; LIGANDS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; SPIRO COMPOUNDS; ZINOSTATIN;

EID: 34247491130     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi602599d     Document Type: Article

References (28)

1. Turner, D. H. (1992) Bulges in nucleic acids, Curr. Opin. Struct. Biol. 2, 334-337.
2. Lilley, D. M. J. (1995) Kinking of DNA and RNA by base bulges, Proc. Natl Acad. Sci. U.S.A. 92, 7140-7142.
3. Chastain, M., and Tinoco, I. (1991) Structural elements in RNA, in Progress in Nucleic Acid Research and Molecular Biology (Cohn, W. E., and Moldave, K., Eds.) Vol. 41, pp 131-177, Academic Press, New York.
4. Kunkel, T. A. (1993) Slippery DNA and diseases, Nature 365, 207-209.
5. Payet, D., Hillisch, A., Lowe, N., Diekmann, S., and Travers, A. (1999) The recognition of distorted DNA structures by HMG-D: A footprinting and molecular modelling study, J. Mol. Biol. 294, 79-91.
6. Degtyareva, N., Subramanian, D., and Griffith, J. D. (2001) Analysis of the binding of p53 to DNAs containing mismatched and bulged bases, J. Biol. Chem. 276, 8778-8784.
7. Dingwall, C., Ernberg, I., Gait, M. J., Green, S. M., Heaphy, S., Karn, J., Lowe, A. D., Singh, M., Skinner, M. A., and Valerio, R. (1989) HIV-1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro, Proc. Natl. Acad. Sci. U.S.A. 86, 6925-6929.
8. Xi, Z., and Goldberg, I. H. (1999) DNA-Damaging Enediyne Compounds, in Comprehensive Natural Products Chemistry (Barton, D. H. R., Nakanishi, K., and Meth-Cohn, O., Eds.) Vol. 7, pp 553-592, Elsevier Science, Oxford, U.K.
9. Kappen, L. S., and Goldberg, I. H. (1993) DNA conformation-induced activation of an enediyne for site-specific cleavage, Science 261, 1319-1321.
10. Kappen, L. S., and Goldberg, I. H. (1993) Site-specific cleavage at a DNA bulge by neocarzinostatin chromophore via a novel mechanism, Biochemistry 32, 13138-13145.
11. Kappen, L. S., and Goldberg, I. H. (1995) Bulge-specific cleavage in transactivation response region RNA and its DNA analogue by neocarzinostatin chromophore, Biochemistry 34, 5997-6002.
12. Xi, Z., Mao, Q. K., and Goldberg, I. H. (1999) Mechanistic studies on the base-catalyzed transformation of neocarzinostatin chromophore: Roles of bulged DNA, Biochemistry 38, 4342-4354.
13. Hensens, O. D., Chin, D.-H., Stassinopoulos, A., Zink, D. L., Kappen, L. S., and Goldberg, I. H. (1994) Spontaneous generation of a biradical species of neocarzinostatin chromophore: Role in DNA bulge-specific cleavage, Proc. Natl. Acad. Sci. U.S.A. 91, 4534-4538.
14. Yang, C. F., Stassinopoulos, A., and Goldberg, I. H. (1995) Specific binding of the biradical analogue of neocarzinostatin chromophore to bulged DNA: Implications for thiol-independent cleavage, Biochemistry 34, 2267-2275.
15. Stassinopoulos, A., Ji, J., Gao, S., and Goldberg, I. H. (1996) Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analogue, Science 272, 1943-1946.
16. Gao, X., Stassinopolous, A., Ji, J., Kwon, Y., Bare, S., and Goldberg, I. H. (2002) Induced formation of a DNA bulge structure by a molecular wedge ligand-post activated neocarzinostatin chromophore, Biochemistry 41, 5131-5143.
17. Xi, Z., Hwang, G.-S., Goldberg, I. H., Harris, J. L., Pennington, W. T., Fouad, F. S., Qabaja, G., Wright, J. M., and Jones, G. B. (2002) Targeting DNA bulged microenvironments with synthetic agents: Lessons from a natural product, Chem. Biol. 9, 925-931.
18. Lin, Y., Jones, G. B., Hwang, G.-S., Kappen, L., and Goldberg, I. H. (2005) Convenient synthesis of NCS-chromophore metabolite isosteres: Binding agents for bulged DNA microenvironments, Org. Lett. 7, 71-74.
19. Stassinopoulos, A., and Goldberg, I. H. (1995) Probing the structure of long single-stranded DNA fragments with neocarzinostatin chromophore. Extension of the base-catalyzed bulge-specific reaction, Biochemistry 34, 15359-15374.
20. Kappen, L. S., Xi, Z., and Goldberg, I. H. (1997) Effect of ribonucleotide substitution on nucleic acid bulge recognition by neocarzinostatin, Bioorg. Med. Chem. 5, 1221-1227.
21. Hwang, G.-S., Jones, G. B., and Goldberg, I. H. (2003) Solution structure of a wedge-shaped synthetic molecule at a two-base bulge site in DNA, Biochemistry 42, 8472-8483.
22. Hwang, G.-S., Jones, G. B., and Goldberg, I. H. (2004) Stereochemical control of small molecule binding to bulged DNA: Comparison of structures of spirocyclic enantiomer-bulged DNA complexes, Biochemistry 43, 641-650.
23. Jones, G. B., Lin, Y., Xiao, Z., Kappen, L., and Goldberg, I. H. (2007) Molecular probes of DNA bulges: Functional assay and spectroscopic analysis, Bioorg. Med. Chem. 15, 784-790.
24. Kappen, L. S., Lin, Y., Jones, G. B., and Goldberg, I. H. (2007) Probing DNA bulges with designed helical spirocyclic molecules, Biochemistry 46, 561-567.
25. Xiao, Z., Zhang, N., Lin, Y., Jones, G. B., and Goldberg, I. H. (2006) Spirocyclic helical compounds as binding agents for bulged RNA, including HIV-2 TAR, Chem. Commun. 42, 4431-4433.
26. 3] G-tetraplex, Structure 1, 263-282.
27. Zhang, N., Lin, C., Huang, X., Kolbanovskiy, A., Hingerty, B. E., Amin, S., Broyde, S., Geacintov, N. E., and Patel, D. J. (2005) Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[α]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement, J. Mol. Biol. 346, 951-965.
28. Brunger, A. T. (1992) X-PLOR. A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT.