DNA excision by the SfiI restriction endonuclease

Journal of Molecular Biology

Volumn 281, Issue 3, 1998, Pages 419-432

  Nobbs, Timothy J ^a   Szczelkun, Mark D ^a   Wentzell, Lois M ^a   Halford, Stephen E ^a  

^a BS8 1TD ^*  (United Kingdom)

Author keywords

DNA protein interaction; Equilibrium centrifugation; Phosphodiester hydrolysis; Rapid reaction kinetics; Restriction modification

Indexed keywords

DNA; RESTRICTION ENDONUCLEASE; ENDODEOXYRIBONUCLEASE SFII; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; DNA CLEAVAGE; DNA PROTEIN COMPLEX; ENZYME ACTIVE SITE; ENZYME SUBSTRATE COMPLEX; NONHUMAN; PLASMID; PRIORITY JOURNAL; BINDING SITE; CHEMISTRY; COMPUTER SIMULATION; DNA SUPERCOILING; METABOLISM; MOLECULAR WEIGHT; PROTEIN CONFORMATION; TEMPERATURE;

BINDING SITES; COMPUTER SIMULATION; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA, SUPERHELICAL; MOLECULAR WEIGHT; PROTEIN CONFORMATION; TEMPERATURE;

EID: 0032555294     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1966     Document Type: Article

References (47)

1. Adzuma K., Mizuuchi K. Interaction of proteins located at a distance along DNA mechanism of target immunity in the Mu DNA strand-transfer reaction. Cell. 57:1989;41-47
2. Aggarwal A.K. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5:1995;11-19
3. Aldaz H., Schuster E., Baker T.A. The interwoven architecture of the Mu transposase couples DNA synapsis to catalysis. Cell. 85:1996;257-269
4. Arciszewska L.K., Sherratt D.J. Xer site-specific recombination in vitro. EMBO J. 14:1995;2112-2120
5. Baker T.A., Mizuuchi M., Savilahti H., Mizuuchi K. Division of labour among monomers within the MuA transposase tetramer. Cell. 74:1993;723-733
6. Baldwin G.S. Enzymology of prokaryotic DNA methyltransferases. 1992;University of Sheffield, Sheffield, UK. PhD thesis
7. Baxter B.K., Topal M.D. Formation of a cleavasome enhancer DNA stabilizes an active conformation of NaeI dimer. Biochemistry. 32:1993;8291-8298
8. Colloms S.D., McCulloch R., Grant K., Neilson L., Sherratt D.J. Xer-mediated site-specific recombination in vitro. EMBO J. 15:1996;1172-1181
9. Craig N.L. Unity in transposition reactions. Science. 270:1995;253-254
10. 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
11. Erskine S.G., Baldwin G.S., Halford S.E. Rapid reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease. Biochemistry. 36:1997;7567-7576
12. Gabbara S., Bhagwat A.S. Interaction of EcoRII endonuclease with DNA substrates containing single recognition sites. J. Biol. Chem. 267:1992;18623-18630
13. Guo F., Gopaul D.N., Van Duyne G.D. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature. 389:1997;40-46
14. Gutfreund H. Kinetics for the Life Sciences. 1995;Cambridge University Press, Cambridge, UK
15. Heath P.J., Stephens K.M., Monnat R.J. Jr, Stoddard B.L. The structure of I-CreI, a group I intron-encoded homing endonuclease. Nature Struct. Biol. 4:1997;468-479
16. Jayaram M. The cis-trans paradox of integrases. Science. 276:1997;49-51
17. Jeltsch A., Alves J., Wofles H., Maass G., Pingoud A. Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA. Biochemistry. 33:1994;10215-10219
18. King G., Murray N.E. Restriction enzymes in cells, not Eppendorfs. Trends Microbiol. 2:1994;465-469
19. Kornberg A., Baker T.A. DNA Replication. 2nd edit. :1992;W. H. Freeman, New York, NY
20. Krüger D.H., Barcak G.J., Reuter M., Smith H.O. EcoRII can be activated to cleave refractory DNA recognition sites. Nucl. Acids Res. 16:1988;3997-4008
21. Laue T.M., Rhodes D.G. Determination of size, molecular weight and presence of subunits. Methods Enzmol. 182:1990;566-587
22. Marko J., Siggia E. Statistical mechanics of supercoiled DNA. Phys. Rev. ser. E. 52:1995;2912-2938
23. Mizuuchi K. Polynucleotidyl transfer reactions in site-specific DNA recombination. Genes to Cells. 2:1997;1-12
24. Nobbs T.J., Halford S.E. DNA cleavage at two recognition sites by the SfiI restriction endonuclease salt dependence of cis and trans interactions between distant DNA sites. J. Mol. Biol. 252:1995;399-411
25. Nobbs T.J., Williams S.A., Connolly B.A., Halford S.E. Phosphorothioate substrates for the SfiI restriction endonuclease. Biol. Chem. 379:1998;599-604
26. Oram M., Marko J.F., Halford S.E. Communications between distant sites on supercoiled DNA from non-exponential kinetics for DNA synapsis by resolvase. J. Mol. Biol. 270:1997;396-412
27. Qiang B-Q., Schildkraut I. A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus. Nucl. Acids Res. 12:1984;4507-4516
28. Reuter M., Kupper D., Meisel A., Schroeder C., Krüger D.H. Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J. Biol. Chem. 273:1998;8294-8300
29. Roberts R.J., Halford S.E. Type II restriction endonucleases. Linn S.M., Lloyd R.S., Roberts R.J. Nucleases. 2nd edit. :1993;35-88 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
30. Roberts R.J., Macelis D. REBASE restriction enzymes and methylases. Nucl. Acids Res. 25:1998;338-350
31. Sakai J., Kleckner N. The Tn10 synaptic complex can capture a target DNA only after transposon excision. Cell. 89:1997;205-214
32. Shah R., Cosstick R., West S.C. The RuvC dimer resolves Holliday junctions by a dual incision mechanism that involves base-specific contacts. EMBO J. 16:1997;1464-1472
33. Stark W.M., Parker C.N., Halford S.E., Boocock M.R. Stereoselectivity of DNA catenane fusion by resolvase. Nature. 368:1994;. 79-78
34. Szczelkun M.D., Halford S.E. Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. EMBO J. 15:1996;1460-1469
35. Szczelkun M.D., Dillingham M.S., Janscak P., Firman K., Halford S.E. Repercussions of DNA tracking by the type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates. EMBO J. 15:1996;6335-6347
36. Szostak J.W., Orr-Weaver T.L., Rothstein R.J., Stahl F.W. The double-strand break repair model for recombination. Cell. 33:1983;25-35
37. Taylor J.D., Halford S.E. Discrimination between DNA sequences by the EcoRV restriction endonuclease. Biochemistry. 28:1989;6198-6207
38. 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
39. Terry B.J., Jack W.E., Modrich P. Mechanism of specific site location and DNA cleavage by EcoRI endonuclease. Gene Amplif. Anal. 5:1987;103-118
40. Topal M.D., Thresher R.J., Conrad M., Griffith J. NaeI endonuclease binding to pBR322 DNA induces looping. Biochemistry. 30:1991;2006-2010
41. Vancott E.M. Method for cloning and producing the SfiI restriction endonuclease and methylase. Publication 0437100, European Patent Office. Publication 0437100. 1991;European Patent Office, Berlin
42. van Gent D.C., Mizuuchi K., Gellert M. Similarities between initiation of V(D)J recombination and retroviral integration. Science. 271:1996;1592-1594
43. Vipond I.B., Baldwin G.S., Oram M., Erskine S.G., Wentzell L.M., Szczelkun M.D., Nobbs T.J., Halford S.E. A general assay for restriction endonucleases and other DNA-modifying enzymes with plasmid substrates. Mol. Biotech. 4:1995;259-268
44. von Hippel P.H., Berg O.G. Facilitated target location in biological systems. J Biol. Chem. 264:1989;675-678
45. Wentzell L.M., Halford S.E. DNA looping by the SfiI restriction endonuclease. J. Mol. Biol. 281:1998;433-444
46. Wentzell L.M., Nobbs T.J., Halford S.E. The SfiI restriction endonuclease makes a 4-strand DNA break at two copies of its recognition sequence. J. Mol. Biol. 248:1995;581-595
47. 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. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1993;1781-17945