DNA recognition by the EcoRV restriction endonuclease probed using base analogues

Journal of Molecular Biology

Volumn 331, Issue 5, 2003, Pages 1005-1016

  Parry, Damian ^a   Moon, Sarah A ^a   Liu, Hsaio Hui ^a   Heslop, Pauline ^a   Connolly, Bernard A ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Base analogues; EcoRV restriction endonuclease; Protein DNA interactions; Specific DNA recognition

Indexed keywords

CALCIUM ION; DOUBLE STRANDED DNA; MANGANESE; METAL ION; RESTRICTION ENDONUCLEASE; THYMINE;

ARTICLE; BASE PAIRING; BINDING SITE; CATALYSIS; CATALYST; COMPLEX FORMATION; DISSOCIATION CONSTANT; DNA BINDING; DNA CONFORMATION; DNA DETERMINATION; DNA PROBE; DNA STRAND; HYDROGEN BOND; HYDROLYSIS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION;

EID: 0043123450     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00861-1     Document Type: Article

References (48)

1. Winkler F.K., Banner D.W., Oefner C., Tsernoglu D., Brown R.S., Heathman S.P., et al. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1993;1781-1795.
2. 2+ binding to the active site of the EcoRV endonuclease: a crystallographic study of the complexes with substrate and product DNA at 2 Å resolution. Biochemistry. 34:1995;683-696.
3. Perona J.J., Martin A.M. Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis. J. Mol. Biol. 273:1997;207-225.
4. Horton N.C., Newberry K.J., Perona J.J. Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. Proc. Natl Acad. Sci USA. 95:1998;13489-13494.
5. Horton N.C., Perona J.J. Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts. J. Biol. Chem. 273:1998;21721-21729.
6. Martin A.M., Sam M.D., Reich N.O., Perona J.J. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. Nature Struct. Biol. 6:1999;269-277.
7. Horton N.C., Connolly B.A., Perona J.J. Inhibition of EcoRV endonuclease by deoxyribo-3′-phosphorothiolates: a high resolution X-ray crystallographic study. J. Am. Chem. Soc. 122:2000;3314-3324.
8. Taylor J.D., Halford S.E. Discrimination between DNA sequences by the EcoRV restriction endonuclease. Biochemistry. 28:1989;6198-6207.
9. Taylor J.D., Badcoe I.G., Clarke A.R., Halford S.E. EcoRV restriction endonuclease binds all DNA sequences with equal affinity. Biochemistry. 30:1991;8743-8753.
10. Jen-Jacobson L. Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. Biopolymers. 44:1997;153-180.
11. Thorogood H., Waters T.R., Parker A.W., Wharton C.W., Connolly B.A. Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV. Biochemistry. 35:1996;8723-8733.
12. 2+ confers DNA binding specificity to the EcoRV restriction endonuclease. Biochemistry. 31:1992;3727-3732.
13. Vermote C.L.M., Vipond I.B., Halford S.E. EcoRV restriction endonuclease: communication bet ween DNA recognition and catalysis. Biochemistry. 31:1992;6089-6097.
14. Vipond I.B., Halford S.E. Specific DNA recognition by EcoRV endonuclease induced by calcium ions. Biochemistry. 34:1995;1113-1119.
15. Szczelkun M.D., Connolly B.A. Sequence-specific binding of DNA by the EcoRV restriction and modification enzymes with nucleic acid and cofactor analogues. Biochemistry. 34:1995;10724-10733.
16. Alves J., Selent U., Wolfes H. Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences. Biochemistry. 34:1995;11191-11197.
17. Martin A.M., Horton N.C., Lusetti S., Reich N.O., Perona J.J. Divalent metal dependence of site-specific binding by EcoRV endonuclease. Biochemistry. 38:1999;8430-8439.
18. Erskine S.G., Halford S.E. Reactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA. J. Mol. Biol. 275:1998;759-772.
19. Reid S.L., Parry D., Liu H.-H., Connolly B.A. Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarisation. Biochemistry. 40:2001;2484-2494.
20. Engler L.E., Welch K.K., Jen-Jacobson L. Specific binding by EcoRV endonuclease to its DNA recognition site GATATC. J. Mol. Biol. 269:1997;82-101.
21. Jen-Jacobson L., Engler L.E., Ames J.T., Kurpiewski M.R., Grigorescu A. Thermodynamic parameters of specific and non-specific protein-DNA binding. Supramol. Chem. 12:2000;143-160.
22. Lagunavicius A., Siksnys V. Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity. Biochemistry. 37:1997;11086-11092.
23. Lagunavicius A., Grazulis S., Balciunaite E., Vainius D., Siksnys V. DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: involvement of active site carboxylate residues. Biochemistry. 37:1997;11093-11099.
24. Selent U., Reuter T., Köhler E., Liedtke M., Thielking V., Alves J., et al. A site-directed mutagenesis study to identify amino acids involved in the catalytic function of the restriction endonuclease EcoRV. Biochemistry. 31:1992;4808-4815.
25. 2+ binding to a metal ion binding site distinct from the catalytic centre of the enzyme. Biochemistry. 34:1995;6239-6246.
26. Jen-Jacobson L. Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions. Methods Enzymol. 259:1995;305-344.
27. Connolly B.A. Oligonucleotides containing modified bases. Eckstein F. Oligonucleotide Analogues - A Practical Approach. 1991;155-183 IRL Press, Oxford, UK.
28. Connolly B.A. Synthetic oligodeoxynucleotides containing modified bases. Methods Enzymol. 211:1992;36-53.
29. Newman P.C., Nwosu V.U., Williams D.M., Cosstick R., Seela F., Connolly B.A. Incorporation of a complete set of deoxyadenosine and thymidine analogues suitable for the study of protein nucleic acid interactions into oligonucleotides. Application to the EcoRV restriction endonuclease and modification methylase. Biochemistry. 29:1990;9891-9901.
30. Newman P.C., Williams D.M., Cosstick R., Seela F., Connolly B.A. Interaction of the EcoRV restriction endonuclease with the dA and T bases in its recognition hexamer GATATC. Biochemistry. 29:1990;9902-9910.
31. Waters T.R., Connolly B.A. Interaction of the restriction endonuclease EcoRV with the deoxyguanosine and deoxycytidine bases in its recognition sequence. Biochemistry. 33:1994;1812-1819.
32. Fliess A., Wolfes H., Rosenthal A., Schwellus K., Blöcker H., Frank R., Pingoud A. Role of thymidine residues in DNA recognition by the EcoRI and EcoRV restriction endonuclease. Nucl. Acids Res. 14:1986;3463-3474.
33. Fliess A., Wolfes H., Seela F., Pingoud A. Analysis of the recognition mechanism involved in the EcoRV catalysed cleavage of DNA using modified oligodeoxynucleotides. Nucl. Acids Res. 16:1988;11781-11793.
34. Mazzarelli J., Scholtissek S., McLaughlin L.W. Effects of functional group changes in the EcoRV recognition on the cleavage reaction catalysed by the endonuclease. Biochemistry. 28:1989;4616-4622.
35. Lesser D.R., Kurpiewski M.R., Jen-Jacobson L. The energetic basis of specificity in the EcoRI endonuclease-DNA interaction. Science. 250:1990;776-786.
36. Lesser D.R., Kurpiewski M.R., Waters T., Connolly B.A., Jen-Jacobson L. Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition. Proc. Natl Acad. Sci. USA. 90:1993;7548-7552.
37. Jen-Jacobson L., Lesser D.R., Kurpiewski M.R. DNA Sequence Discrimination by the EcoRI Endonuclease. Eckstein F., Lilley D.M.J. Nucleic Acids and Molecular Biology. vol. 5:1991;141-170 Springer, Berlin.
38. Vermote C.L.M., Halford S.E. EcoRV restriction endonuclease: communication between catalytic metal ions and DNA recognition. Biochemistry. 31:1992;6082-6089.
39. Vipond I.B., Baldwin G.S., Halford S.E. Divalent metal ions at the active site of the EcoRV and EcoRI endonucleases. Biochemistry. 34:1995;697-704.
40. 2+-dependent catalysis by restriction enzymes: pre-steady-state analysis of EcoRV endonuclease reveals burst kinetics and the origin of reduced activity. J. Am. Chem. Soc. 121:1999;1444-1447.
41. Baldwin G.S., Sessions R.B., Erskine S.G., Halford S.E. DNA cleavage by the EcoRV restriction endonuclease: roles of divalent metal ions in specificity and catalysis. J. Mol. Biol. 288:1999;87-103.
42. Terry B.J., Jack W.E., Rubin R.A., Modrich P. Thermodynamic parameters governing the interaction of EcoRI endonuclease with specific and non-specific DNA sequences. J. Biol. Chem. 258:1983;9820-9825.
43. Fersht A.R. The hydrogen bond in molecular recognition. Trends Biochem. Sci. 12:1987;301-304.
44. Pingoud A., Jeltsch A. Structure and function of type II restriction endonucleases. Nucl. Acids Res. 29:2001;3705-3727.
45. Mordasini T., Curioni A., Andreoni W. Why do divalent metal ions either promote or inhibit enzymatic reactions? J. Biol. Chem. 278:2003;4831-4832.
46. Newman M., Strzelecka T., Dorner L.F., Schildkraut I., Aggarwal A. Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science. 269:1995;656-663.
47. Engler L., Sapienza P., Dorner L.F., Kucera R., Schildkraut I., Jen-Jacobson J. The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC. J. Mol. Biol. 307:2001;619-636.
48. D'Arcy A., Brown R.S., Zabeau M., Van Resandt R.W., Winkler F.K. Purification and characterisation of the EcoRV restriction endonuclease. J. Biol. Chem. 260:1985;1987-1990.