Probing DNA bulges with designed helical spirocyclic molecules

Biochemistry

Volumn 46, Issue 2, 2007, Pages 561-567

  Kappen, Lizzy S ^a   Lin, Yiqing ^b   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

AMINOGLUCOSE; BULGE FUNCTION; HELICAL SPIROCYCLIC MOLECULES; NATURAL PRODUCTS;

COMPLEXATION; DRUG PRODUCTS; ENZYME INHIBITION; GLUCOSE; METABOLITES; NUCLEIC ACIDS;

DNA;

AMINOGLYCOSIDE; CARBOHYDRATE DERIVATIVE; DNA; DNA DIRECTED DNA POLYMERASE BETA; DOUBLE STRANDED DNA; N METHYLFUCOSAMINE; NUCLEIC ACID; UNCLASSIFIED DRUG; ZINOSTATIN CHROMOPHORE;

ARTICLE; BASE PAIRING; BINDING AFFINITY; CHROMATOPHORE; COMPLEX FORMATION; CONTROLLED STUDY; COVALENT BOND; DNA BINDING; DNA BULGE; DNA CLEAVAGE; DNA MODIFICATION; DNA PROBE; DNA STRAND BREAKAGE; DNA STRUCTURE; DNA SYNTHESIS; DNA TEMPLATE; ENANTIOMER; ENZYME MECHANISM; METABOLITE; MOLECULAR MIMICRY; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION;

BASE SEQUENCE; DNA; DNA PRIMERS; DRUG DESIGN; MOLECULAR PROBES; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; SPIRO COMPOUNDS;

EID: 33846197503     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi061744d     Document Type: Article

References (25)

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. Wells, R. D. (1996) Molecular basis of genetic instability of triplet repeats, J. Biol. Chem. 271, 2875-2878.
5. Kunkel, T. A. (1993) Slippery DNA and diseases, Nature 365, 207-209.
6. Loeb, L. A. (1998) Cancer cells exhibit a mutator phenotype, in Advances in Cancer Research (Vande Woude, G. F., and Klein, G., Eds.) Vol. 72, pp 25-56, Academic Press: New York.
7. Pearson, C. E., and Sinden, R. R. (1998) Slipped strand DNA, dynamic mutations, and human disease, in Genetic Instabilities and Hereditary Neurological Diseases (Wells, R. D., and Warren, S. T., Eds.), pp 585-626, Academic Press: New York.
8. Kappen, L. S., and Goldberg, I. H. (1993) DNA conformation-induced activation of an enediyne for site-specific cleavage, Science 261, 1319-1321.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. Lin, Y., Jones, G. B., Hwang, G.-S., Kappen, L. S., and Goldberg, I. H. (2005) Convenient synthesis of NCS - chromophore metabolite isosteres: Binding agents for bulged DNA microenvironments, Org. Lett. 7, 71-74.
17. Xiao, Z., Kappen, L. S., and Goldberg, I. H. (2006) Development of new simple molecular probes of DNA bulged structures, Bioorg. Med. Chem. Lett. 16, 2895-2899.
18. Kappen, L. S., and Goldberg, I. H. (2003) Stimulation of DNA strand slippage synthesis by a bulge binding synthetic agent, Biochemistry 42, 2166-2173.
19. Jones, G. B., Lin, Y., Xiao, Z., Kappen, L. S., and Goldberg, I. H. Bioorg. Med. Chem., in press.
20. Maniatis, T., Fritsch, E. F., and Sambrook, J. (1982) In Molecular Cloning: A Laboratory Manual, pp 122-123, Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
21. Myers, A. G., Cohen, S. B., and Kwon, B.-M. (1994) DNA cleavage by neocarzinostatin chromophore. Establishing the intermediacy of chromophore-derived cumulene and biradical species and their role in sequence-specific cleavage, J. Am. Chem. Soc. 116, 1670-1682.
22. 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.
23. Kappen, L. S., and Goldberg, I. H. (1999) Replication block by an enediyne drug - DNA deoxyribose adduct, Biochemistry 38, 235-242.
24. Hwang, G. S., Jones, G. B., and Goldberg, I. H. (2003) Solution structure of a wedge-shaped synthetic molecule at a 2-base bulge site in DNA, Biochemistry 42, 8472-8483.
25. 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, 42, 641-650.