Template-directed interference footprinting of protein-phosphate contacts in DNA

Organic Letters

Volumn 3, Issue 1, 2001, Pages 71-74

  Nyanguile, Origène ^a,b   Verdine, Gregory L ^b  

^a NOVARTIS PHARMA AG   (Switzerland)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PHOSPHATE; PROTEIN;

ARTICLE; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; DNA FOOTPRINTING; DRUG EFFECT; HUMAN; METHODOLOGY; PEPTIDE MAPPING; POLYACRYLAMIDE GEL ELECTROPHORESIS; STRUCTURE ACTIVITY RELATION;

CATALYSIS; DNA; DNA FOOTPRINTING; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; MOLECULAR STRUCTURE; PEPTIDE MAPPING; PHOSPHATES; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0035843334     PISSN: 15237060     EISSN: None     Source Type: Journal    
DOI: 10.1021/ol006792j     Document Type: Article

References (29)

1. (a) Larson, C. J.; Verdine, G. L. The Chemistry of Protein-DNA Interactions. Invited Chapter in Bioorganic Chemistry: Nucleic Acids; Hecht, S. M., Ed.; Oxford University Press: 1996; pp 324-346.
2. (b) Pabo, C. O.; Sauer, R. T. Annu. Rev. Biochem. 1992, 61, 1053-1095.
3. Record, M. T., Jr.; Lohman, T. M.; deHaseth, P. L. J. Mol. Biol. 1976, 107, 145-158.
4. Mandel-Gutfreund, Y.; Schueler, O.; Margalit, H. J. Mol. Biol. 1995, 253, 370-382.
5. Siebenlist, U.; Gilbert, W. Proc. Natl. Acad. Sci. U.S.A. 1980, 77, 122-126.
6. (a) Hayashibara, K. C.; Vereine, G. L. J. Am. Chem. Soc. 1991, 113, 5104-5106.
7. (b) Hayashibara, K. C.; Verdine, G. L. Biochemistry 1992, 11, 11265-11273.
8. Mascareñas, J. L.; Hayashibara, K. C.; Verdine, G. L. J. Am. Chem. Soc. 1993, 115, 373-374.
9. Min, C. H.; Clashing, T. D.; Verdine, G. L. J. Am. Chem. Soc. 1996, 118, 6116-6120.
10. (a) Higuchi, H.; Endo, T.; Kaji, A. Biochemistry 1990, 29, 8747-8753.
11. (b) Victorova, L. S.; Dyatkina, N. B.; Mozzherin, D.; Atrazhev, A. M.; Krayevsky, A. A.; Kukhanova, M. K. Nucleic Acids Res 1992, 20, 783-789.
12. p diastereomer of αMe-dTTP. The stereochemical specificity of terminal deoxynucleotidyl transferase for analogues having modifications at the α-phosphoras is like that of all DNA polymerases tested thus far (Lesnikowski, Z. J. Bioorg. Chem. 1993, 21, 127-155). Although the stereochemical specificity of HIV reverse transcnptase (RT) for α-modified triphosphate analogues has not been reported, the recently determined X-ray crystal structure of an RT/ primer-template/nucleotide complex (Huang, H.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Science 1998, 282, 1669-1675) shows that the enzyme binds the nucleotide in a way that is nearly identical to that of polymerases that have been analyzed stereochemically.
13. p diastereomer of αMe-dTTP. The stereochemical specificity of terminal deoxynucleotidyl transferase for analogues having modifications at the α-phosphoras is like that of all DNA polymerases tested thus far (Lesnikowski, Z. J. Bioorg. Chem. 1993, 21, 127-155). Although the stereochemical specificity of HIV reverse transcnptase (RT) for α-modified triphosphate analogues has not been reported, the recently determined X-ray crystal structure of an RT/ primer-template/nucleotide complex (Huang, H.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Science 1998, 282, 1669-1675) shows that the enzyme binds the nucleotide in a way that is nearly identical to that of polymerases that have been analyzed stereochemically.
14. (a) Smith, S. A.; McLaughlin, L. W. Biochemistry 1997, 36, 6046-6058.
15. (b) Pritchard, C. E.; Grasby, J. A.; Hamy, F.; Zacharek, A. M.; Singh, M.; Karn, J.; Gait, M. J. Nucleic Acids Res. 1994, 22, 2592-2600.
16. Botfield, M. C.; Weiss, M. A. Biochemistry 1994, 33, 2349-2355.
17. Sinha, N. D.; Grossbruchhaus, V.; Köster, H. Tetrahedron Lett. 1983, 24, 877-880.
18. A scheme depicting the overall procedure for TDI-p footprinting, accompanied by a detailed experimental procedure, is available in the Supporting Information or can be obtained via the Internet at the URL http:// glviris.harvard.edu.
19. (a) Crabtree, G. R.; Clipstone, N. A. Annu. Rev. Biochem. 1994, 63, 1045-1083.
20. (b) Rao, A.; Luo, C.; Hogan, P. G. Annu. Rev. Immunol. 1997, 15, 707-747.
21. Ethylation interference footprints also show mixtures of products resulting from 5′- and 3′-cleavage of the ethylphosphotriester by hydroxide ion. The major cleavage pathway, however, involves cleavage of the ethyl substituent (with liberation of ethanol), a process that regenerates the original phosphodiester. The dominance with which this cleavage pathway operates greatly reduces the sensitivity of ethylation interference footprints by erasing most of the information-bearing adducts.
22. Kuijpers, W. H.; Kuyl-Yeheskiely, E.; van Boom, J. H.; van Boeckel, C. A. Nucleic Acids Res. 1993, 21, 3493-3500.
23. Gish, G.; Eckstein, F. Science 1988, 240, 1520-1522.
24. McCaffrey, P. G.; Luo, C.; Kerppola, T. K.; Jain, J.; Badalian, T. M.; Ho, A. M.; Burgeon, E.; Lane, W. S.; Lambert, J. N.; Curran, T.; Verdine, G. L.; Rao, A.; Hogan, P. G. Science 1993, 262, 750-754.
25. Chen, L.; Harrison, S. C. Nature 1998, 392, 42-48.
26. (a) Zhou, P.; Sun, L. J.; Dotsch, V.; Wagner, G.; Vereine, G. L. Cell 1998, 92, 687-696.
27. 16
28. (a) Dineva, M. A.; Petkov, D. D. Nucleosides Nucleotides 1996, 15 1459-1467.
29. (b) Dineva, M. A.; Ivanoc, I. G.; Petkov, D. D. Nucleosides Nucleotides 1997, 16, 1875-1882.