Template-derived interference footprinting of protein-adenine contacts

Journal of the American Chemical Society

Volumn 118, Issue 26, 1996, Pages 6116-6120

  Min, Changhee ^a   Cushing, Timothy D ^a   Verdine, Gregory L ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA FOOTPRINTING; PROTEIN DNA INTERACTION; SEQUENCE ANALYSIS; TECHNIQUE;

EID: 0030062222     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja953658z     Document Type: Article

References (23)

1. (a) For a review see: Steitz, T. A. Q. Rev. Biophys. 1990, 23, 205- 280.
2. (b) Pabo, C. O.; Sauer, R. T. Annu. Rev. Biochem. 1992, 61, 1053- 1095.
3. (c) Larson, C. J.; Verdine, G. L. In Bioorganic Chemistry: Nucleic Acids; Hecht, S. M., Ed.; Oxford University Press: New York, 1996; pp 324-346.
4. (d) Harrison, S. C. Nature 1991, 353, 715-719.
5. Siebenlist, U.; Gilbert, W. Proc. Natl. Acad. Sci. U.S.A. 1980, 77, 122-126.
6. For a more detailed discussion of the TDI footprinting protocol, see refs Ic and 4.
7. Hayashibara, K. C.; Verdine, G. L. J. Am. Chem. Soc. 1991, 113, 5104-5106.
8. Hayashibara, K. C.; Verdine, G. L. Biochemistry 1992, 31, 11265- 11273.
9. Mascaren̄as, J. L.; Hayashibara, K. C.; Verdine, G. L. J. Am. Chem. Soc. 1993, 115, 373-374.
10. Cottam, H. B.; Kazimierrczuk, Z.; Geary, S.; McKernan, P. A.; Revankar, G. R.; Robins, R. K. J. Med. Chem. 1985, 28, 1461-1467.
11. Anderson, J.; Ptashne, M.; Harrison, S. C. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 1307-1311.
12. Watanabe, S.-I; Ueda, T. Nucleosides Nucleotides 1983, 2, 113- 125. Watanabe, S.-I; Ueda, T. Nucleosides Nucleotides 1982, 1, 191-203.
13. Watanabe, S.-I; Ueda, T. Nucleosides Nucleotides 1983, 2, 113- 125. Watanabe, S.-I; Ueda, T. Nucleosides Nucleotides 1982, 1, 191-203.
14. Min, C.; Verdine, G. L. Submitted for publication. A long-standing problem in TDI footprinting, like other methods that require long, single- stranded DNA molecules, has been the inability to produce the template DNA consistently and in sufficient quantities for multiple experiments. This problem has been solved conclusively by the use of the PCR/IMAC procedure.
15. Hayashibara, K. C. Ph.D. Thesis, Harvard University, Cambridge, MA, 1993.
16. H = 6-histaminylpurine.
17. Chodish, L. A. In Current Protocols in Molecular Biology; Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Smith, J. A., Seidman, J. G., Struhl, K., Eds.; John Wiley and Sons: New York, 1989; Vol. 2 pp 12.2.1-12.2.10.
18. 2 protons of 7-deaza-dA.
19. In nucleoside model studies, it was determined that treatment of dA* with 1 M aqueous piperidine for 5 min at 90 °C results in complete loss of the characteristic 364 nm 7-deaza-7-nitroadenine chromophore, consistent with base-catalyzed ring-opening.
20. In a separate series of primer-extension/cleavage assays (not shown), the ratio of dA *TP to dATP used in the enzymatic extension was varied over a wide range. The extended samples were divided into two parts, one of which was treated with 1 M aqueous piperidine. The piperidine-treated and untreated samples were analyzed on a high-resolution DNA sequencing gel (not shown). By comparison of the two samples at each dA *TP/dATP ratio, it was determined that (i) dA*TP is fully capable of supporting enzymatic polymerization, even under conditions in which it completely replaces dATP, and (ii) DNA strand cleavage at dA* positions is almost quantitative in the presence of 1 M aqueous piperidine. The dA*TP:dATP ratio (1:3) that gives rise to roughly one dA* incorporation per extension was determined empirically by inspection of this gel.
21. This series of bands is not present in samples that have been extended under the same conditions but not subjected to piperidine treatment. The bands generated by piperidine cleavage of A*-containing DNA migrate slightly faster than the corresponding bands in the Sanger dideoxy-A sequencing lane, because the former DNA strands possess one fewer nucleoside unit at the 3′-end.
22. Aggarwal, A. K.; Rodgers, D. W.; Drottar, M.; Ptashne, M.; Harrison, S. C. Science 1988, 242, 899-907.
23. 18 In TDI footprints of the complementary strand to that shown in Figure 2, interference is observed only at the one position-A14-which is related by symmetry to Al (C. Min and G. L. Verdine, unpublished results).