Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA

Protein Expression and Purification

Volumn 69, Issue 2, 2010, Pages 226-234

  Zhang, Penghua ^a   Too, Priscilla Hiu Mei ^a   Samuelson, James C ^a   Chan, Siu Hong ^a   Vincze, Tamas ^a   Doucette, Stephanie ^a   Bäckström, Stefan ^b   Potamousis, Konstantinos D ^c   Schramm, Timothy M ^c   Forrest, Dan ^c   Schwartz, David C ^c   Xu, Shuang yong ^a  

^a NEW ENGLAND BIOLABS   (United States)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

^c Laboratory for Molecular and Computational Genomics   (United States)

Author keywords

Alanine scanning; CatHI; DNA labeling; Nicking endonuclease; Optical mapping of DNA

Indexed keywords

RESTRICTION ENDONUCLEASE; SINGLE STRANDED DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE T7; ENZYME ACTIVE SITE; GENETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SINGLE STRANDED DNA BREAK; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; BACTERIOPHAGE T7; BASE SEQUENCE; CATALYTIC DOMAIN; CLONING, MOLECULAR; DNA BREAKS, SINGLE-STRANDED; DNA RESTRICTION ENZYMES; DNA, SINGLE-STRANDED; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

BACTERIA (MICROORGANISMS); CROCEIBACTER ATLANTICUS; ESCHERICHIA COLI;

EID: 70449705894     PISSN: 10465928     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pep.2009.09.003     Document Type: Article

References (49)

1. Roberts R., Vincze T., Posfai J., and Macelis D. REBASE - enzymes and genes for DNA restriction and modification. Nucleic Acids Res. 35 (2007) 269-270
2. Xia Y., Morgan R., Schildkraut I., and Van Etten J.L. A site-specific single strand endonuclease activity induced by NYs-1 virus infection of a Chlorella-like green alga. Nucleic Acids Res. 16 (1988) 9477-9487
3. Zhang Y., Nelson M., Nietfeldt J., Xia Y., Burbank D., Ropp S., and Van Etten J.L. Chlorella virus NY-2A encodes at least 12 DNA endonuclease/methyltransferase genes. Virology 240 (1998) 366-375
4. Morgan R.D., Calvet C., Demeter M., Agra R., and Kong H. Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI. Biol. Chem. 381 (2000) 1123-1125
5. Xu S.-Y., Zhu Z., Zhang P., Chan S.-H., Samuelson J.C., Xiao J., Ingalls D., and Wilson G.G. Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI. Nucleic Acids Res. 35 (2007) 4608-4618
6. Yunusova A., Rogulin E., Artyukh R., Zheleznaya L., and Matvienko N. Nickase and a protein encoded by an open reading frame downstream from the nickase BspD6I gene form a restriction endonuclease complex. Biochemistry (Mosc) 71 (2007) 815-820
7. Golobova N.S., Okhapkina S.S., Abdurashitov M.A., and Degtiarev S. Determination and analysis of the primary structure of NM.BstSEI operone from Bacillus stearothermophilus SE-589 which produces N.BstSEI site-specific nickase. Mol. Biol. (Mosk) 39 (2005) 960-964
8. Heiter D.F., Lunnen K.D., and Wilson G.G. Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI. J. Mol. Biol. 348 (2005) 631-640
9. Xu Y., Lunnen K.D., and Kong H. Engineering a nicking endonuclease N.AlwI by domain swapping. Proc. Natl. Acad. Sci. USA 98 (2001) 12990-12995
10. Besnier C.E., and Kong H. Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state. EMBO Rep. 2 (2001) 782-786
11. Zhu Z., Samuelson J.C., Zhou J., Dore A., and Xu S.-Y. Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAI. J. Mol. Biol. 337 (2004) 573-583
12. Sanders K.L., Catto L.E., Bellamy S.R., and Halford S.E. Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands. Nucleic Acids Res. 37 (2009) 2105-2115
13. Samuelson J.C., Zhu Z., and Xu S.-Y. The isolation of strand-specific nicking endonucleases from a randomized SapI expression library. Nucleic Acids Res. 32 (2004) 3661-3671
14. Niu Y., Tenney K., Li H., and Gimble F.S. Engineering variants of the I-SceI homing endonuclease with strand-specific and site-specific DNA-nicking activity. J. Mol. Biol. 382 (2008) 188-202
15. McConnell Smith A., Takeuchi R., Pellenz S., Davis L., Maizels N., Monnat Jr. R.J., and Stoddard B.L. Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease. Proc. Natl. Acad. Sci. USA 106 (2009) 5099-5104
16. Wang H., and 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
17. Van Ness J., Van Ness L.K., and Galas D.J. Isothermal reactions for the amplification of oligonucleotides. Proc. Natl. Acad. Sci. USA 100 (2003) 4504-4509
18. Tan E., Erwin B., Dames S., Ferguson T., Buechel M., Irvine B., Voelkerding K., and Niemz A. Specific versus nonspecific isothermal DNA amplification through thermophilic polymerase and nicking enzyme activities. Biochemistry 47 (2008) 9987-9999
19. Chan S.-H., Zhu Z., Van Etten J.L., and Xu S.-Y. Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification. Nucleic Acids Res. 32 (2004) 6187-6199
20. Kiesling T., Cox K., Davidson E.A., Dretchen K., Grater G., Hibbard S., Lasken R.S., Leshin J., Skowronski E., and Danielsen M. Sequence specific detection of DNA using nicking endonuclease signal amplification (NESA). Nucleic Acids Res. 35 (2007) e117
21. Jo K., Dhingra D.M., Odijk T., de Pablo J.J., Graham M.D., Runnheim R., Forrest D., and Schwartz D.C. A single-molecule barcoding system using nanoslits for DNA analysis. Proc. Natl. Acad. Sci. USA 104 (2007) 2673-2678
22. Xiao M., Phong A., Ha C., Chan T.F., Cai D., Leung L., Wan E., Kistler A.L., DeRisi J.L., Selvin P.R., and Kwok P.Y. Rapid DNA mapping by fluorescent single molecule detection. Nucleic Acids Res. 35 (2007) e16
23. Xu S.-Y., and Schildkraut I. Isolation of BamHI variants with reduced cleavage activities. J. Biol. Chem. 266 (1991) 4425-4429
24. Rothberg J.M., and Leamon J.H. The development and impact of 454 sequencing. Nat. Biotechnol. 26 (2008) 1117-1124
25. Zhou S., Bechner M.C., Place M., Churas C.P., Pape L., Leong S.A., Runnheim R., Forrest D.K., Goldstein S., Livny M., and Schwartz D.C. Validation of rice genome sequence by optical mapping. BMC Genomics 8 (2007) 278
26. Cho J.C., and Giovannoni S.J. Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae. Syst. Appl. Microbiol. 26 (2003) 76-83
27. Szomolanyi I., Kiss A., and Venetianer P. Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. Gene 10 (1980) 219-225
28. Fomenkov A., Xiao J.-P., Dila D., Raleigh E., and Xu S.-Y. The 'endo-blue method' for direct cloning of restriction endonuclease genes in E. coli. Nucleic Acids Res. 22 (1994) 2399-2403
29. Heitman J., and Model P. SOS induction as an in vivo assay of enzyme-DNA interactions. Gene 103 (1991) 1-9
30. Kenyon C.J., and Walker G.C. DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. Proc. Natl. Acad. Sci. USA 77 (1980) 2819-2823
31. Xu S.-Y., Xiao J.-P., Ettwiller L., Holden M., Aliotta J., Poh C.L., Dalton M., Robinson D.P., Petronzio T.R., Moran L., Ganatra M., Ware J., Slatko B., and Benner J. Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI, and SapI restriction-modification systems in Escherichia coli. Mol. Gen. Genet. 260 (1998) 226-231
32. Sawaya M.R., Zhu Z., Mersha F., Chan S.-H., Dabur R., Xu S.-Y., and Balendiran G.K. Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site. Structure 13 (2005) 1837-1847
33. Brunelle A., and Schleif R.F. Missing contact probing of DNA-protein interactions. Proc. Natl. Acad. Sci. USA 84 (1987) 6673-6676
34. Wright D.J., King K., and Modrich P. The negative charge of Glu-111 is required to activate the cleavage center of EcoRI endonuclease. J. Biol. Chem. 264 (1989) 11816-11821
35. Jeltsch A., Alves J., Maass G., and Pingoud A. On the catalytic mechanism of EcoRI and EcoRV. A detailed proposal based on biochemical results, structural data and molecular modelling. FEBS Lett. 304 (1992) 4-8
36. Aggarwal A.K. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5 (1995) 11-19
37. Vander Woerd M., Pelletier J., Xu S.-Y., and Friedman A. Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Structure 9 (2001) 133-144
38. Dimalanta E.T., Lim A., Runnheim R., Lamers C., Churas C., Forrest D.K., de Pablo J.J., Graham M.D., Coppersmith S.N., Goldstein S., and Schwartz D.C. A microfluidic system for large DNA molecule arrays. Anal. Chem. 76 (2004) 5293-5301
39. Reslewic S., Zhou S., Place M., Zhang Y., Briska A., Goldstein S., Churas C., Runnheim R., Forrest D., Lim A., Lapidus A., Han C.S., Roberts G.P., and Schwartz D.C. Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Appl. Environ. Microbiol. 71 (2005) 5511-5522
40. Shen B.W., Landthaler M., Shub D.A., and Stoddard B.L. DNA binding and cleavage by the HNH homing endonuclease I-HmuI. J. Mol. Biol. 342 (2004) 43-56
41. Giraud-Panis M.J., and Lilley D.M. T4 endonuclease VII. Importance of a histidine-aspartate cluster within the zinc-binding domain. J. Biol. Chem. 271 (1996) 33148-33155
42. Orlowski J., and Bujnicki J.M. Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res. 36 (2008) 3552-3569
43. Saravanan M., Bujnicki J.M., Cymerman I.A., Rao D.N., and Nagaraja V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucleic Acids Res. 32 (2004) 6129-6135
44. Kriukiene E., Lubiene J., Lagunavicius A., and Lubys A. MnlI - the member of H-N-H subtype of Type IIS restriction endonucleases. Biochim. Biophys. Acta 1751 (2005) 194-204
45. Sokolowska M., Czapinska H., and Bochtler M. Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA. Nucleic Acids Res. 37 (2009) 3799-3810
46. Bujnicki J.M., Radlinska M., and Rychlewski L. Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. Trends Biochem. Sci. 26 (2001) 9-11
47. Vanamee E.S., Hsieh P., Zhu Z., Yates D., Garman E., Xu S.-Y., and Aggarwal A.K. Glucocorticoid receptor-like Zn(Cys)4 motifs in BslI restriction endonuclease. J. Mol. Biol. 334 (2003) 595-603
48. 2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease. J. Biol. Chem. 282 (2007) 32320-32326
49. Lambert A.R., Sussman D., Shen B., Maunus R., Nix J., Samuelson J., Xu S.-Y., and Stoddard B.L. Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure 16 (2008) 558-569