Quantitative kinetics footprinting of protein-DNA association reactions

Methods in Enzymology

Volumn 274, Issue , 1996, Pages 478-492

  Hsieh, Mark ^a   Brenowitz, Michael ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA FOOTPRINTING; DNA SEQUENCE; ENZYME ACTIVITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA INTERACTION; QUANTITATIVE DIAGNOSIS; SEQUENCE HOMOLOGY;

EID: 0029806242     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(96)74038-7     Document Type: Article

References (39)

1. M. Brenowitz, E. Jamison, A. Majumdar, and S. Adhya, Biochemistry 29, 3374 (1990).
2. D. D. Dalma-Weiszhausz and M. Brenowitz, Biochemistry 31, 6980 (1992).
3. M. Brenowitz, A. Pickar, and E. Jamison, Biochemistry 30, 5986 (1991).
4. M. Brenowitz and E. Jamison, Biochemistry 32, 8693 (1993).
5. A. D. Riggs, S. Bourgeois, and M. Cohn, J. Mol. Biol. 53, 401 (1970).
6. A. D. Riggs, H. Suzuki, and S. Bourgeois, J. Mol. Biol. 48, 67 (1970).
7. A. D. Riggs, R. F. Newby, and S. Bourgeois, J. Mol. Biol. 51, 303 (1970).
8. R. B. O'Gorman, M. Dunaway, and K. S. Matthews, J. Biol. Chem. 255, 10100 (1980).
9. R. B. O'Gorman, J. M. Rosenberg, O. B. Kallai, R. E. Dickerson, I. Keichi, A. D. Riggs, and K. S. Matthews, J. Biol. Chem. 255, 10107 (1980).
10. O. G. Berg, R. B. Winter, and P. H. von Hippel, Biochemistry 20, 6929 (1981).
11. R. B. Winter, O. G. Berg, and P. H. von Hippel, Biochemistry 20, 6961 (1981).
12. M. G. Fried and D. M. Crothers, J. Mol. Biol. 172, 263 (1984).
13. M. D. Barkley, Biochemistry 20, 3833 (1981).
14. J. Ha, R. S. Spolar, and M. T. Record, Jr., J. Mol. Biol. 209, 801 (1989).
15. G. R. Bellomy, M. C. Mossing, and M. T. Record, Jr., Biochemistry 27, 3900 (1988).
16. S. J. Mazur and M. T. Record, Jr., Biopolymers 28, 929 (1989).
17. T. Ruusala and D. M. Crothers, Proc. Natl. Acad. Sci. U.S.A. 89, 4903 (1992).
18. R. Fickert and B. Müller-Hill, J. Mol. Biol. 226, 59 (1992).
19. M. Hsieh and M. Brenowitz, manuscript in preparation.
20. V. Petri, M. Hsieh, and M. Brenowitz, Biochemistry 34, 9977 (1995).
21. G. K. Ackers, A. D. Johnson, and M. A. Shea, Proc. Natl. Acad. Sci. U.S.A. 79, 1129 (1982).
22. G. K. Ackers, M. A. Shea, and F. R. Smith, J. Mol. Biol. 170, 223 (1983).
23. M. Brenowitz, D. F. Senear, M. A. Shea, and G. K. Ackers, Methods Enzymol. 130, 132 (1986).
24. M. Brenowitz, D. F. Senear, M. A. Shea, and G. K. Ackers, Proc. Natl. Acad. Sci. U.S.A. 83, 8462 (1986).
25. K. S. Koblan, D. L. Bain, D. Beckett, M. A. Shea, and G. K. Ackers, Methods Enzymol. 210, 405 (1992).
26. M. Brenowitz, and D. F. Senear, in "Current Protocols in Molecular Biology" (F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl, eds.). Wiley, New York, 1989.
27. M. Brenowitz, D. F. Senear, L. Jamison, and D. D. Dalma-Weiszhausz, in "Footprinting Techniques for Studying Nucleic Acid-Protein Complexes" (A. Revzin, ed.), pp. 1-43. Academic Press, New York, 1993.
28. C. Gaillard and F. Strauss, Nucleic Acids Res. 18, 378 (1990).
29. J. Langowski, C. Urbanke, and E. Schuppe, Anal. Biochem. 142, 91 (1984).
30. K. A. Johnson, Methods Enzymol. 134, 677 (1986).
31. These values are determined using the procedures described by the manufacturer (Kin-Tek, State College, PA).
32. S. Moore, "The Enzymes," Vol. XIV, Chap. 15, pp. 281-296. Academic Press, New York, 1981.
33. M. Laskowski, Sr., "The Enzymes," Vol. IV, Chap. 12, pp. 289-311. Academic Press, New York, 1971.
34. C. A. Dekker and H. K. Schacman, Proc. Natl. Acad. Sci. U.S.A. 40, 894 (1954).
35. 8-19
36. 23-27
37. M. L. Johnson and L. M. Faunt, Meth. Enzymol. 210, 1 (1992).
38. 32P label to the protein binding site(s) limits the resolution of the nuclease reaction products by electrophoresis. However, "indirect end-labeling techniques" may potentially relieve this constraint and allow the quantitative analysis of long restriction fragments and circular molecules.
39. D. D. Dalma-Weiszhausz, Ph.D. thesis, Albert Einstein College of Medicine, New York.