Equilibrium and kinetic quantitative DNase I footprinting

Advances in DNA Sequence-Specific Agents

Volumn 4, Issue C, 2002, Pages 139-151

  Dhavan, Gauri M ^a   Mollah, A K M M ^a   Brenowitz, Michael ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77957080402     PISSN: 1067568X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1067-568X(02)80008-1     Document Type: Article

References (40)

1. Brenowitz M., Senear D.F., Shea M.A., and Ackers G.K. Footprint titrations yield valid thermodynamic isotherms. Proc. Nat. Acad. Sci. 83 (1986) 8462-8466
2. Brenowitz M., Senear D.F., Shea M.A., and Ackers G.K. Quantitative DNase footprint titration: A method for studying protein-DNA interactions. Meth. Enzymol. 130 (1986) 132-181
3. Senear D.F., Brenowitz M., and Ackers G.K. Energetics of cooperative protein-DNA interactions: Comparison between quantitative DNase footprint titration and filterbinding. Biochemistry 25 (1986) 7344-7354
4. Ackers G.K., Shea M.A., and Smith F.R. Free energy coupling within macromolecules. The chemical work of ligand binding at the individual sites in co-operative systems. J. Mol. Biol. 170 (1983) 223-242
5. Di Cera E. Thermodynamic Theory of Site-Specific Binding Processes in Biological Macromolecules (1983), Cambridge University Press, Cambridge
6. Brenowitz M., and Senear D.F. DNase I footprint analysis of protein-DNA binding. In: Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., and Struhl K. (Eds). Current Protocols in Molecular Biology (Unit 12.4) (1989), John Wiley & Sons, New York
7. Brenowitz M., Senear D.F., Jamison L., and Dalma-Weiszhausz D.D. Quantitative DNase I footprinting. In: Revzin A. (Ed). Footprinting Techniques for Studying Nucleic Acid-Protein Complexes (a volume of Separation, Detection, and Characterization of Biological Macromolecules) (1993), Academic Press, New York 1-43
8. Mollah A.K.M.M., and Brenowitz M. In: Travers A., and Buckle M. (Eds). Quantitative DNase I kinetics footprinting. Protein-DNA interactions-a practical approach (2000), IRL Press at Oxford University Press, Oxford 281-290
9. Hsieh M., and Brenowitz M. Quantitative kinetics footprinting of protein-DNA association reactions. Meth. Enzymol. 274 (1996) 478-492
10. adi and the native dimeric gal repressor. J. Biol. Chem. 272 (1997) 22092
11. Petri V., and Brenowitz M. Quantitative nucleic acids footprinting-thermodynamic and kinetic approaches. Current Opinion in Biotechnology 8 (1997) 36-44
12. Pray T.R., Bruz D.S., and Ackers G.K. Cooperative non-specific DNA binding by octamerizing λ cI repressors: A site-specific thermodynamic analysis. J. Mol. Biol. 282 (1998) 947-958
13. Streaker E.D., and Beckett D. Coupling of site-specific DNA binding to protein dimerization in assembly of the biotin repressor-biotin operator complex. Biochemistry 37 (1998) 3210-3219
14. Craig M.L., Tsodikov O.V., McQuade K.L., Schlax Jr. P.E., Capp M.W., Saecker R.M., and Record Jr. T.M. DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: Evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol. 283 (1998) 741-756
15. McKnight S. Transcription revisited: A commentary on the 1995 Cold Spring Harbor Laboratory meeting, "Mechanisms of Eukaryotic Transcription". Genes and Development 10 (1996) 367-381
16. Burley S.K., and Roeder R.G. Biochemistry and structural biology of transcription factor IID (TFIID). Annul. Rev. Biochem. 65 (1996) 760-799
17. Kim Y., Geiger J.H., Hahn S., and Sigler P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature 365 (1993) 512-520
18. Kim J.L., and Burley S.K. 1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAG. Nature Struct. Biol. 1 (1994) 638-653
19. Juo Z.S., Chiu T.K., Leibermann P.M., Baikalov I., Berk A.J., and Dickerson R.E. How proteins recognize the TATA box. J. Mol. Biol. 261 (1996) 239-254
20. Nikolov D.B., Chen H., Halay E.D., Hoffman A., Roeder R.G., and Burley S.K. Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl. Acad. Sci. USA 93 (1996) 4862-4867
21. Patikogluou G.A., Kim J.L., Sun L., Yang S.H., Kodadek T., and Burley S.K. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes and Development 15 13 (1999) 3217-3230
22. Gardner J., and Nash H.A. Role of Escherichia coli IHF protein in lambda site-specific recombination. J. Mol. Biol. 191 (1986) 181-189
23. Zin W., and Feiss M. Function of IHF in λ DNA packaging. I. Identification of the strong binding site of integration host factor and the locus for intrinsic bending in cosB. J. Mol. Biol. 230 (1993) 492-504
24. Hwang D.S., and Kornberg A. Opening of the replication origin of Escherichia coli by DnA protein with protein HU or IHF. J. Biol. Chem. 267 (1992) 23083-23086
25. Winkelman J.W., and Hatfield G.W. Characterization of the integration host factor binding site in the ilvPG1 promoter region of the ilvGMEDA operon of Escherichia coli. J. Biol. Chem. 265 (1990) 10055-10060
26. Craig N., and Nash H.A. The mechanism of phage 1 site-specific recombination: site-specific breakage of DNA by Int Topoisomerase. Cell 35 (1983) 795-803
27. Yang S., and Nash H.A. The interaction of E. coli IHF protein with its specific binding sites. Cell 57 (1989) 869-880
28. Yang S., and Nash H.A. Comparison of protein binding to DNA in vivo and in vitro: Defining an effective intracellular target. EMBO J. 14 (1995) 6292-6300
29. Rice P.A., Yang S., Mizuuchi K., and Nash H.A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87 (1996) 1295-1306
30. Bailly C., Payet D., Travers A.A., and Waring M.J. PCR-based development of DNA substrates containing modified bases: An efficient system for investigating the role of the exocyclic groupls in chemical and structural recognition by minor groove binding drugs and proteins. Proc. Natl. Acad. Sci. USA 93 (1996) 13623-13628
31. Petri V., Hsieh M., and Brenowitz M. Thermodynamic and kinetic characterization of the binding of the TATA binding protein to the adenovirus E4 promoter. Biochemistry 34 (1995) 9977-9984
32. Petri V., Hsieh M., Jamison E., and Brenowitz M. DNA Sequence-specific recognition by the "TATA" binding protein: Promoter dependent differences in the thermodynamics and kinetics. Biochemistry 37 (1998) 15842-15849
33. Senear D.F., and Bolen D.W. Simultaneous analysis for testing of models and parameter estimation. Meth. Enzymol. 210 (1992) 463-481
34. Koblan K.S., Bain D.L., Beckett D., Shea M.A., and Ackers G.K. Analysis of site-specific interaction parameters in protein-DNA complexes. Meth. Enzymol. 210 (1992) 405-425
35. Kurumizaka H., Kanke F., Matsumoto U., and Shindo H. Specific and nonspecific interactions of integration host factor with oligo DNAs and revealed by circular dichroism specitroscopy and filter binding assay. Archives of Biochemistry and Biophysics 295 (1992) 297-301
36. Dhavan G.M. The integration host factor-DNA complex: Base-pair opening dynamics measured by NMR and kinetics of complex formation. Ph. D. thesis (1999), Yale University
37. Ruusala T., and Crothers D.M. Sliding and intermolecular transfer of the lac repressor: Kinetic perturbation of a reaction intermediate by a distant DNA sequence. Proc. Natl. Acad. Sci. USA 89 (1992) 4903-4907
38. Parkhurst K.M., Richards R.M., Brenowitz M., and Parkhurst L.J. Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex. J. Mol. Biol. 289 (1999) 1327-1341
39. Johnson K.A. Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates. Meth. Enzymol. 249 (1995) 38-61
40. Winter R.B., Berg O.G., and von Hippel P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: Kinetic measurements and conclusions. Biochemistry 20 (1981) 6961-6977