Reactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides: Identical equilibrium constants for binding to specific and non-specific DNA

Journal of Molecular Biology

Volumn 275, Issue 5, 1998, Pages 759-772

  Erskine, Symon G ^a,b   Halford, Stephen E ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

DNA recognition; DNA protein interaction; Fluorescence depolarization; Fluorescence resonance energy transfer; Restriction modification

Indexed keywords

DANSYL CHLORIDE; EOSIN; MAGNESIUM ION; OLIGODEOXYNUCLEOTIDE; RESTRICTION ENDONUCLEASE; DNA; ENDODEOXYRIBONUCLEASE ECORV; FLUORESCENT DYE; OLIGODEOXYRIBONUCLEOTIDE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; CONTROLLED STUDY; DEPOLARIZATION; DNA CLEAVAGE; EQUILIBRIUM CONSTANT; FLUORESCENCE; PRIORITY JOURNAL; PROTEIN DNA BINDING; ANISOTROPY; BINDING SITE; CHEMISTRY; ENZYME SPECIFICITY; KINETICS; METABOLISM;

NEGIBACTERIA;

ANISOTROPY; BINDING SITES; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; FLUORESCENT DYES; KINETICS; OLIGODEOXYRIBONUCLEOTIDES; SUBSTRATE SPECIFICITY;

EID: 0032488670     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1517     Document Type: Article

References (65)

1. Aggarwal, A. K. (1995). Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5, 11-19.
2. Alves, J., Selent, U. & Wolfes, H. (1995). Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligonucleotide substrates. Biochemistry, 34, 11191-11197.
3. Baldwin, G. S., Vipond, I. B. & Halford, S. E. (1995). Rapid reaction analysis of the catalytic cycle of the EcoRV restriction endonuclease. Biochemistry, 34, 705-714.
4. Bougueleret, L., Schwarzstein, M., Tsugita, A. & Zabeau, M. (1984). Characterization of the genes coding for the EcoRV restriction and modification system of Escherichia coli. Nucl. Acids Res. 12, 3659-3678.
5. Brown, T. A. (1991). Molecular Biology Labfax, Bios Scientific Publishers, Oxford, UK.
6. Burston, S. G., Ransom, N. A. & Clarke, A. R. (1995). The origins and consequences of asymmetry in the chaperonin reaction cycle. J. Mol. Biol. 249, 138-152.
7. Cal, S. & Connolly, B. A. (1996). The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition site GATATC. J. Biol. Chem. 271, 1008-1015.
8. Clarke, A. R., Cortes, A., Halsall, D. J., Hart, K. W. & Holbrook, J. J. (1991). Genetic and spectroscopic characterisation of structural changes in dehydrogenase enzymes and their substrates during enzyme catalysis. Spec. Publ. Roy. Soc. Chem. 94, 223-226.
9. Clegg, R. M., Murchie, A. I. H., Zechel, A. & Lilley, D. M. J. (1993). Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer. Proc. Natl Acad. Sci. USA, 90, 2994-2998.
10. Connolly, B. A. (1987). The synthesis of oligonucleotides containing a primary amino group at the 5′-terminus. Nucl. Acids Res. 15, 3131-3139.
11. D'Arcy, A., Brown, R. S., Zabeau, M., van Resandt, R. W. & Winkler, F. K. (1985). Purification and crystallization of the EcoRV restriction endonuclease. J. Biol. Chem. 260, 1987-1990.
12. Engler, L. E., Welch, K. K. & Jen-Jacobson, L. (1997). Specific binding by EcoRV endonuclease to its DNA recognition site GATATC. J. Mol. Biol. 269, 82-101.
13. Erskine, S. G. & Halford, S. E. (1995). Interactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides. Gene, 157, 153-156.
14. Erskine, S. G., Baldwin, G. S. & Halford, S. E. (1997). Rapid reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease. Biochemistry, 36, 7567-7576.
15. Guest, C. R., Hochstrasser, R. A., Dupuy, C. G., Allen, D. J., Benkovic, S. J. & Millar, D. P. (1991). Interaction of DNA with the Klenow fragment of DNA polymerase I studied by time-resolved fluorescence spectroscopy. Biochemistry, 30, 8759-8770.
16. Gutfreund, H. (1995). Kinetics for the Life Sciences, Cambridge University Press, Cambridge, UK.
17. Halford, S. E. (1975). Stopped-flow fluorescence studies on saccharide binding to lysozyme. Biochem. J. 149, 411-422.
18. Halford, S. E. & Goodall, A. J. (1988). Modes of DNA cleavage by the EcoRV restriction endonuclease. Biochemistry, 27, 1771-1777.
19. Halford, S. E. & Johnson, N. P. (1980). The EcoRI restriction endonuclease with bacteriophage (DNA: equilibrium binding studies. Biochem. J. 191, 593-604.
20. Halford, S. E., Lovelady, B. M. & McCallum, S. A. (1986). Relaxed specificity of the EcoRV restriction endonuclease. Gene, 41, 173-185.
21. Halford, S. E., Taylor, J. D., Vermote, C. L. M. & Vipond, I. B. (1993). Mechanism of action of restriction endonuclease EcoRV. In Nucleic Acids and Molecular Biology (Eckstein, F. & Lilley, D. M. J., eds), vol. 7, pp. 47-69, Springer, Berlin, Germany.
22. Hancox, E. L. & Halford, S. E. (1997). Kinetic analysis of a mutational hot-spot in the EcoRV restriction endonuclease. Biochemistry, 36, 7577-7585.
23. Haugland, R. P. (1996). Handbook of Fluorescent Probes and Research Chemicals, 6th edit., Molecular Probes Inc., Eugene, USA.
24. Heyduk, T. & Lee, J. C. (1990). Application of fluorescence energy transfer and polarization to monitor Escherichia coli cAMP receptor protein and lac promoter interaction. Proc. Natl Acad. Sci. USA, 87, 1744-1748.
25. 2+ binding to a metal binding site distinct from the catalytic center of the enzyme. Biochemistry, 34, 6239-6246.
26. Jeltsch, A., Wenz, C., Stahl, F. & Pingoud, A. (1996). Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme. EMBO J. 15, 5104-5111.
27. Jencks, W. P. (1975). Binding energy, specificity and enzymic catalysis: the Circe effect. Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219-410.
28. Kong, H., Roemer, S. E., Waite-Ress, P. A., Benner, J. S., Wilson, G. G. & Nwanko, D. O. (1994). Characterization of BcgI, a new kind of restriction-modification system. J. Biol. Chem. 269, 683-690.
29. 2+ binding to the active site of the EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry, 34, 683-696.
30. Lagunavicius, A., Grazulis, S., Balciunaite, E., Vainius, D. & Siksnys, V. (1997). DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: involvement of active site carboxylate residues. Biochemistry, 36, 11093-11099.
31. Lakowicz, R. J. (1983). Principles of Fluorescence Spectroscopy, Plenum Press, New York.
32. Luke, P. A., McCallum, S. A. & Halford, S. E. (1987). The EcoRV restriction endonuclease. Gene Amplif. Anal. 5, 183-205.
33. Mayer, A. N. & Barany, F. (1994). Interactions of TaqI endonuclease with the phosphate backbone. J. Biol. Chem. 269, 29067-29076.
34. Newman, P. C., Williams, D. M., Cosstick, R., Seela, F. & Connolly, B. A. (1990). Interaction of the EcoRV restriction endonuclease with the deoxyadenosine and thymidine bases in its recognition hexamer d(GATATC). Biochemistry, 29, 9902-9910.
35. Powell, L. M., Dryden, D. T. F., Willcock, D. F., Pain, R. H. & Murray, N. E. (1993). DNA recognition by the EcoK methyltransferase: the influence of DNA methylation and the cofactor S-adenosyl methionine. J. Mol. Biol. 234, 60-71.
36. Roberts, R. J. & Halford, S. E. (1993). Type II restriction endonucleases. In Nucleases (Linn, S. M., Lloyd, R. S. & Roberts, R. J., eds), pp. 35-88, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
37. Schildkraut, I., Banner, C. D. B., Rhodes, C. S. & Parekh, S. (1984). The recognition sequence for EcoRV is GAT/ATC. Gene, 27, 327-329.
38. Selent, U., Ruter, T., Köhler, E., Liedtke, M., Thielking, V., Alves, J., Oelgeschläger, T., Wolfes, H., Peters, F. & Pingoud, A. (1992). A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV. Biochemistry, 31, 4808-4815.
39. Siksnys, V. & Pleckaityte, M. (1993). Catalytic and binding properties of restriction endonuclease Cfr9I. Eur. J. Biochem. 217, 411-419.
40. Shah, R., Bennett, R. J. & West, S. C. (1994). Genetic recombination in E. coli: RuvC protein cleaves Holliday junctions at resolution hotspots in vitro. Cell, 79, 853-864.
41. Shah, R., Cosstick, R. & West, S. C. (1997). The RuvC dimer resolves Holliday junctions by a dual incision mechanism that involves base-specific contacts. EMBO J. 16, 1464-1472.
42. 2+. J. Biol. Chem. 268, 8645-8650.
43. Stryer, L. (1978). Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47, 819-846.
44. Szczelkun, M. D. & Connolly, B. A. (1995). Sequence-specific binding of DNA by the EcoRV restriction and modification enzymes with nucleic acid and cofactor analogues. Biochemistry, 34, 10724-10733.
45. Szczelkun, M. D. & Halford, S. E. (1996). Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. EMBO J. 15, 1460-1469.
46. Taylor, J. D. & Halford, S. E. (1989). Discrimination between DNA sequences by the EcoRV restriction endonuclease. Biochemistry, 28, 6198-6207.
47. Taylor, J. D. & Halford, S. E. (1992). The activity of the EcoRV restriction endonuclease is influenced by flanking DNA sequences both inside and outside the DNA-protein complex. Biochemistry, 31, 90-97.
48. Taylor, J. D., Badcoe, I. G., Clarke, A. R. & Halford, S. E. (1991). EcoRV restriction endonuclease binds all DNA sequences with equal affinity. Biochemistry, 30, 8743-8753.
49. Terry, B. J., Jack, W. E. & Modrich, P. (1983). Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences. J. Biol. Chem. 258, 9820-9825.
50. Terry, B. J., Jack, W. E. & Modrich, P. (1985). Facilitated diffusion during catalysis by EcoRI endonuclease. J. Biol. Chem. 260, 13130-13137.
51. 2+ confers DNA binding specificity to the EcoRV restriction endonuclease. Biochemistry, 31, 3727-3732.
52. Thorogood, H., Grasby, J. A. & Connolly, B. A. (1996a). Influence of the phosphate backbone on the recognition and hydrolysis of DNA by the EcoRV restriction endonuclease - a study using oligodeoxy-nucleotide phosphorothioates. J. Biol. Chem. 271, 8855-8862.
53. Thorogood, H., Waters, T. R., Parker, A. W., Wharton, C. W. & Connolly, B. A. (1996b). Resonance raman spectroscopy of 4-thiothymidine and oligodeoxy-nucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV. Biochemistry, 35, 8723-8733.
54. Vermote, C. L. M., Vipond, I. B. & Halford, S. E. (1992). EcoRV restriction endonuclease: communication between DNA recognition and catalysis. Biochemistry, 31, 6089-6097.
55. 2+ ions. Biochemistry, 34, 1113-1119.
56. Vipond, I. B., Moon, B-J. & Halford, S. E. (1996). An isoleucine-to-leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese. Biochemistry, 35, 1712-1721.
57. Wah, D. A., Hirsch, J. A., Dorner, L. F., Schildkraut, I. & Aggarwal, A. K. (1997). Structure of the multi-modular endonuclease FokI bound to DNA. Nature, 388, 97-100.
58. Waters, T. R. & Connolly, B. A. (1992). Continuous spectrophotometric assay for endonucleases using synthetic oligodeoxynucleotides and based on the hyperchromic effect. Anal. Biochem. 204, 204-209.
59. Waters, T. R. & Connolly, B. A. (1994). Interaction of restriction endonuclease EcoRV with the deoxyguanosine and deoxycytidine bases in its recognition sequence. Biochemistry, 34, 1812-1819.
60. Wenz, C., Jeltsch, A. & Pingoud, A. (1996). Probing the indirect readout of the restriction endonuclease EcoRV. J. Biol. Chem. 211, 5565-5573.
61. Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K. & Wilson, K. S. (1993). The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12, 1781-17945.
62. Withers, B. E. & Dunbar, J. C. (1995). Sequence-specific DNA recognition by the SmaI endonuclease. J. Biol. Chem. 270, 6496-6504.
63. Xu, S.-Y. & Schildkraut, I. (1991). Isolation of BamHI variants with reduced cleavage activities. J. Biol. Chem. 266, 4425-4429.
64. Zebala, J. F., Choi, J. & Barany, F. (1992a). Characterization of steady-state, single-turnover and binding kinetics of the TaqI restriction endonuclease. J. Biol. Chem. 267, 8097-8105.
65. Zebala, J. F., Choi, J., Trainor, J. & Barany, F. (1992b). DNA recognition of base analogue and chemically modified substrates by the TaqI restriction endonuclease. J. Biol. Chem. 267, 8106-8116.