Engineering Strand-specific DNA Nicking Enzymes from the Type IIS Restriction Endonucleases BsaI, BsmBI, and BsmAI

Journal of Molecular Biology

Volumn 337, Issue 3, 2004, Pages 573-583

  Zhu, Zhenyu ^a   Samuelson, James C ^a   Zhou, Jing ^a,b   Dore, Andrew ^a,c   Xu, Shuang Yong ^a  

^a NEW ENGLAND BIOLABS   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Aa, amino acid; Ds, double stranded; Genetic screening; MTase, methyltransferase; Nt.BsaI, top strand BsaI nicking endonuclease (5 GGTCTCN1 3 ); Strand specific endonuclease; Type IIS REase

Indexed keywords

CELL EXTRACT; DNA; DNA TOPOISOMERASE; ENZYME VARIANT; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BIOTECHNOLOGY; CARBOXY TERMINAL SEQUENCE; CELL CULTURE; CONTROLLED STUDY; DNA CLEAVAGE; DNA ISOLATION; DNA MODIFICATION; DNA SEQUENCE; DNA STRAND; ENZYME ACTIVE SITE; GENETIC ENGINEERING; GENETIC SCREENING; MOLECULAR RECOGNITION; MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RANDOMIZATION; RECOMBINANT DNA TECHNOLOGY; RESTRICTION MAPPING; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; STATISTICAL SIGNIFICANCE; WILD TYPE;

EID: 1542268955     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.02.003     Document Type: Article

References (33)

1. Roberts R.J., Vincze T., Posfai J., Macelis D. REBASE: restriction enzymes and methyltransferases. Nucl. Acids Res. 31:2003;418-420.
2. Xia Y., Morgan R., Schildkraut I., Van Etten J.L. A site-specific single strand endonuclease activity induced by NYs-1 virus infection of a Chlorella-like green alga. Nucl. Acids Res. 16:1988;9477-9487.
3. Zhang Y.N.M., Nietfeldt J., Xia Y., Burbank D., Ropp S., Van Etten J.L. Chlorella virus NY-2A encodes at least 12 DNA endonuclease/methyltransferase genes. Virology. 240:1998;366-375.
4. Abdurashitov M.A., Belitchenko O.A., Shevchenko A.V., Degtiarev S. N.BstSE - a site-specific nickase from Bacillus stearothermophilus SE-589. Mol. Biol. (Mosk). 30:1996;1261-1267.
5. Morgan R.D., Calvet C., Demeter M., Agra R., Kong H. Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI. Biol. Chem. 381:2000;1123-1125.
6. Geider K., Meyer T.F., Baumel I., Reimann A. Proteins and nucleotide sequences involved in DNA replication of filamentous bacteriophage. Advan. Expt. Med. Biol. 179:1984;45-54.
7. Xu Y., Lunnen K.D., Kong H. Engineering a nicking endonuclease N.AlwI by domain swapping. Proc. Natl Acad. Sci. USA. 98:2001;12990-12995.
8. Besnier C.E., Kong H. Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state. EMBO Rep. 2:2001;782-786.
9. Wang H., Hays J.B. Preparation of DNA substrates for in vitro mismatch repair. Mol. Biotechnol. 15:2000;97-104.
10. Kuhn H., Protozanova E., Demidov V.V. Monitoring of single nicks in duplex DNA by gel electrophoretic mobility-shift assay. Electrophoresis. 23:2002;2384-2387.
11. Wang H., Hays J.B. Mismatch repair in human nuclear extracts. Quantitative analyses of excision of nicked circular mismatched DNA substrates, constructed by a new technique employing synthetic oligonucleotides. J. Biol. Chem. 277:2002;26136-26142.
12. Stahl F., Wende W., Jeltsch A., Pingoud A. Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein. Proc. Natl Acad. Sci. USA. 93:1996;6175-6180.
13. Heitman J., Model P. Substrate recognition by the EcoRI endonuclease. Proteins: Struct. Funct. Genet. 7:1990;185-197.
14. Heitman J., Ivanenko T., Kiss A. DNA nicks inflicted by restriction endonucleases are repaired by a RecA- and RecB-dependent pathway in Escherichia coli. Mol. Microbiol. 33:1999;1141-1151.
15. Sasnauskas G., Halford S.E., Siksnys V. How the BfiI restriction enzyme uses one active site to cut two DNA strands. Proc. Natl Acad. Sci. USA. 100:2003;6410-6415.
16. Lunnen K.D., Barsomian J.M., Camp R.R., Card C.O., Chen S.Z., Croft R., et al. Cloning Type II restriction and modification genes. Gene. 74:1988;25-32.
17. Kiss A., Posfai G., Keller C.C., Venetianer P., Roberts R.J. Nucleotide sequence of the BsuRI restriction-modification system. Nucl. Acids Res. 13:1985;6403-6420.
18. Heitman J., Model P. SOS induction as an in vivo assay of enzyme-DNA interactions. Gene. 103:1991;1-9.
19. Magnuson V.L., Ally D.S., Nylund S.J., Karanjawala Z.E., Rayman J.B., Knapp J.I., et al. Substrate nucleotide-determined non-templated addition of adenine by Taq DNA polymerase: implications for PCR-based genotyping and cloning. Biotechniques. 21:1996;700-709.
20. Bitinaite J., Maneliene Z., Menkevicius S., Klimasauskas S., Butkus V., Janulaitis A.A. Alw26I, Eco31I and Esp3I - type IIs methyltransferases modifying cytosine and adenine in complementary strands of the target DNA. Nucl. Acids Res. 20:1992;4981-4985.
21. Bitinaite J., Wah D.A., Aggarwal A.K., Schildkraut I. FokI dimerization is required for DNA cleavage. Proc. Natl Acad. Sci. USA. 95:1998;10570-10575.
22. Wah D.A., Bitinaite J., Schildkraut I., Aggarwal A.K. Structure of FokI has implications for DNA cleavage. Proc. Natl Acad. Sci. USA. 95:1998;10564-10569.
23. Vanamee E.S., Santagata S., Aggarwal A.K. FokI requires two specific DNA sites for cleavage. J. Mol. Biol. 309:2001;69-78.
24. Wah D.A., Hirsch J.A., Dorner L.F., Schildkraut I., Aggarwal A.K. Structure of the multimodular endonuclease FokI bound to DNA. Nature. 388:1997;97-100.
25. Bath A.J., Milsom S.E., Gormley N.A., Halford S.E. Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J. Biol. Chem. 277:2002;4024-4033.
26. Stankevicius K., Lubys A., Timinskas A., Vaitkevicius D., Janulaitis A. Cloning and analysis of the four genes coding for Bpu10I restriction- modification enzymes. Nucl. Acids Res. 26:1998;1084-1091.
27. Hsieh P.-C., Xiao J.-P., O'Loane D., Xu S.-Y. Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI. J. Bacteriol. 182:2000;949-955.
28. Van Ness J., Van Ness L.K., Galas D.J. Isothermal reactions for the amplification of oligonucleotides. Proc. Natl Acad. Sci. USA. 100:2003;4504-4509.
29. Ruan H., Lunnen K.D., Scott M.E., Moran L.S., Slatko B.E., Pelletier J.J., et al. Cloning and sequence comparison of AvaI and BsoBI restriction-modification systems. Mol. Gen. Genet. 252:1996;695-699.
30. Ochman H., Gerber A.S., Hartl D.L. Genetic applications of an inverse polymerase chain reaction. Genetics. 120:1988;621-623.
31. Cadwell R., Joyce G. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2:1992;28-33.
32. Sambrook J., Fritsch E.F., Maniatis T. Nolan C. Molecular Cloning: Preparation and Transformation of Competent E. coli. Molecular Cloning: Preparation and Transformation of Competent E. coli. vol. 1.74:1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
33. Samuelson J.C., Xu S.Y. Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity. J. Mol. Biol. 319:2002;673-683.