Kinetic analyses of divalent cation-dependent EcoRV digestions on a DNA-immobilized quartz crystal microbalance

Analytical Biochemistry

Volumn 361, Issue 2, 2007, Pages 210-217

  Takahashi, Shuntaro ^a   Matsuno, Hisao ^a   Furusawa, Hiroyuki ^a   Okahata, Yoshio ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Divalent cations; DNA digestion; EcoRV; Endonuclease; Enzymatic reaction kinetics; Quartz crystal microbalance

Indexed keywords

CRYSTALS; DISSOCIATION; DNA; ENZYMES; KINETIC PARAMETERS; POSITIVE IONS; QUARTZ; RATE CONSTANTS;

DIVALENT CATION; DNA DIGESTION; ECORV; ENDONUCLEASES; ENZYMATIC REACTION;

QUARTZ CRYSTAL MICROBALANCES;

CALCIUM; DIVALENT CATION; DNA; MAGNESIUM; RESTRICTION ENDONUCLEASE; SILICON DIOXIDE;

ARTICLE; BINDING SITE; CATALYSIS; CRYSTAL; DISSOCIATION CONSTANT; DNA CLEAVAGE; ENZYME ACTIVE SITE; ENZYME BINDING; IMMOBILIZED CELL; KINETICS; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; TIME;

EID: 33846552664     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.11.030     Document Type: Article

References (34)

1. Pingoud A., and Jeltsch A. Recognition and cleavage of DNA by type-II restriction endonucleases. Eur. J. Biochem. 246 (1997) 1-22
2. Pingoud A., and Jeltsch A. Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29 (2001) 3705-3727
3. Roberts R.J., Vincze T., Posfai J., and Macelis D. Restriction enzymes and methyltransferases. Nucleic Acids Res. 31 (2003) 418-420
4. Schildkraut I., Banner C.D., S Rhodes C., and Parekh S. The cleavage site for the restriction endonuclease EcoRV is 5′-GAT/ATC-3′. Gene 27 (1984) 327-329
5. D'Arcy A., Brown R.S., Zabeau M., van Resandt R.W., and Winkler F.K. Purification and crystallization of the EcoRV restriction endonuclease. J. Biol. Chem. 260 (1985) 1987-1990
6. Luke P.A., McCallum S.A., and Halford S.E. The EcoRV restriction endonuclease. Gene Amplif. Anal. (1987) 185-207
7. Winkler F.K., Banner D.W., Oefner C., Tsernoglou D., Brown R.S., Heathman S.P., Bryan R.K., Martin P.D., Petratos K., and Wilson K.S. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12 (1993) 1781-1795
8. Waters T.R., and Connolly B.A. Interaction of the restriction endonuclease EcoRV with the deoxyguanosine and deoxycytidine bases in its recognition sequence. Biochemistry 33 (1994) 1812-1819
9. Newman P.C., Williams D.M., Cosstick R., Seela F., and Connolly B.A. Interaction of the EcoRV restriction endonuclease with the deoxyadenosine and thymidine bases in its recognition hexamer d(GATATC). Biochemistry 29 (1990) 9902-9910
10. Taylor J.D., and Halford S.E. The activity of the EcoRV restriction endonuclease is influenced by flanking DNA sequences both inside and outside the DNA-protein complex. Biochemistry 31 (1992) 90-97
11. Taylor J.D., Badcoe I.G., Clarke A.R., and Halford S.E. EcoRV restriction endonuclease binds all DNA sequences with equal affinity. Biochemistry 30 (1991) 8743-8753
12. Vermote C.L., and Halford S.E. EcoRV restriction endonuclease: communication between catalytic metal ions and DNA recognition. Biochemistry 31 (1992) 6082-6089
13. Erskine S.G., and Halford S.E. Reactions of the eco RV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA. J. Mol. Biol. 275 (1998) 759-772
14. Reid S.L., Parry D., Liu H.H., and Connolly B.A. Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization. Biochemistry 40 (2001) 2484-2494
15. Hiller D.A., Fogg J.M., Martin A.M., Beechem J.M., Reich N.O., and Perona J.J. Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence. Biochemistry 42 (2003) 14375-14385
16. Vipond I.B., and Halford S.E. Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions. Biochemistry 34 (1995) 1113-1119
17. Horton N.C., Newberry K.J., and Perona J.J. Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. Proc. Natl. Acad. Sci. USA 95 (1998) 13489-13494
18. Horton N.C., Connolly B.A., and Perona J.J. Inhibition of EcoRV endonuclease by deoxyribo-3′-phosphothiolates: a high-resolution X-ray crystallographic study. J. Am. Chem. Soc. 122 (2000) 3314-3324
19. Parry D., Moon S.A., Liu H.H., Heslop P., and Connolly B.A. DNA recognition by the EcoRV restriction endonuclease probed using base analogues. J. Mol. Biol. 331 (2003) 1005-1016
20. 2+ confers DNA binding specificity to the EcoRV restriction endonuclease. Biochemistry 31 (1992) 3727-3732
21. 2+ binding to a metal ion binding site distinct from the catalytic center of the enzyme. Biochemistry 34 (1995) 6239-6246
22. Martin A.M., Horton N.C., Lusetti S., Reich N.O., and Perona J.J. Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease. Biochemistry 38 (1999) 8430-8439
23. Okahata Y., Niikura K., Sugiura Y., Sawada M., and Morii T. Kinetic studies of sequence-specific binding of GCN4-bZIP peptides to DNA strands immobilized on a 27-MHz quartz-crystal microbalance. Biochemistry 37 (1998) 5666-5672
24. Matsuno H., Niikura K., and Okahata Y. Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A.T base pairs of oligonucleotides immobilized on a 27 MHz quartz crystal microbalance. Biochemistry 40 (2001) 3615-3622
25. Matsuno H., Niikura K., and Okahata Y. Direct monitoring kinetic studies of DNA polymerase reactions on a DNA-immobilized quartz-crystal microbalance. Chem. Eur. J. 7 (2001) 3305-3312
26. Matsuno H., Furusawa H., and Okahata Y. Kinetic studies of DNA cleavage reactions catalyzed by an ATP-dependent deoxyribonuclease on a 27-MHz quartz-crystal microbalance. Biochemistry 44 (2005) 2262-2270
27. Oswald T., Wende W., Pingoud A., and Rinas U. Comparison of N-terminal affinity fusion domains: effect on expression level and product heterogeneity of recombinant restriction endonuclease EcoRV. Appl. Microbiol. Biotechnol. 42 (1994) 73-77
28. Reuter M., Kupper D., Meisel A., Schroeder C., and Krüger D.H. Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J. Biol. Chem. 273 (1998) 8294-8300
29. Sauerbrey G. Use of quartz crystal vibrator for weighing thin films on a microbalance. Z. Physik. 155 (1959) 206-222
30. Engler L.E., Welch K.K., and Jen-Jacobson L. Specific binding by EcoRV endonuclease to its DNA recognition site GATATC. J. Mol. Biol. 269 (1997) 82-101
31. Conlan L.H., and Dupureur C.M. Multiple metal ions drive DNA association by PvuII endonuclease. Biochemistry 41 (2002) 14848-14855
32. Horton N.C., and Perona J.J. DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites. Biochemistry 43 (2004) 6841-6857
33. Conlan L.H., and Dupureur C.M. Dissecting the metal ion dependence of DNA binding by PvuII endonuclease. Biochemistry 41 (2002) 1335-1342
34. Baldwin G.S., Vipond I.B., and Halford S.E. Rapid reaction analysis of the catalytic cycle of the EcoRV restriction endonuclease. Biochemistry 34 (1995) 705-714