Modern and simple construction of plasmid: Saving time and cost

Journal of Microbiology

Volumn 52, Issue 11, 2014, Pages 891-897

  Nakayama, Hideki ^a   Shimamoto, Nobuo ^a  

^a KYOTO SANGYO UNIVERSITY   (Japan)

Author keywords

Cloning; Fusion PCR; Gibson assembly; PCR cloning; Plasmid; Recombineering; SLiCE

Indexed keywords

ECONOMICS; ESCHERICHIA COLI; GENETIC ENGINEERING; GENETICS; HOMOLOGOUS RECOMBINATION; MOLECULAR CLONING; PLASMID; POLYMERASE CHAIN REACTION; PROCEDURES;

CLONING, MOLECULAR; ESCHERICHIA COLI; GENETIC ENGINEERING; HOMOLOGOUS RECOMBINATION; PLASMIDS; POLYMERASE CHAIN REACTION;

EID: 84919916788     PISSN: 12258873     EISSN: 19763794     Source Type: Journal    
DOI: 10.1007/s12275-014-4501-6     Document Type: Review

References (34)

1. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., Datsenko K.A., Tomita M., Wanner B.L., and Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol.2, 2006.0008.
2. Barrangou R., Fremaux C., Deveau H., Richards M., Boyaval P., Moineau S., Romero D.A., and Horvath P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science315, 1709–1712.
3. Chung C.T., Niemela S.L., and Miller R.H. 1989. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc. Natl. Acad. Sci. USA86, 2172–2175.
4. Datsenko K.A. and Wanner B.L. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA97, 6640–6645.
5. Ellis H.M., Yu D., DiTizio T., and Court D.L. 2001. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl. Acad. Sci. USA98, 6742–6746.
6. Esvelt K.M. and Wang H.H. 2013. Genome-scale engineering for systems and synthetic biology. Mol. Syst. Biol.9, 6–1.
7. Garneau J.E., Dupuis M.È., Villion M., Romero D.A., Barrangou R., Boyaval P., Fremaux C., Horvath P., Magadán A.H., and Moineau S. 2010. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature468, 67–71.
8. Gasiunas G., Barrangou R., Horvath P., and Siksnys V. 2012. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl. Acad. Sci. USA109, E2579–86.
9. Gibson D.G., Benders G.A., Andrews-Pfannkoch C., Denisova E.A., Baden-Tillson H., Zaveri J., Stockwell T.B., Brownley A., Thomas D.W., Algire M.A., andet al. 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science319, 1215–1220.
10. Hockemeyer D., Wang H., Kiani S., Lai C.S., Gao Q., Cassady J.P., Cost G.J., Zhang L., Santiago Y., Miller J.C., andet al. 2011. Genetic engineering of human pluripotent cells using TALE nucleases. Nat. Biotechnol.29, 731–734.
11. Hu S., Fu J., Huang F., Ding X., Stewart A.F., Xia L., and Zhang Y. 2014. Genome engineering of Agrobacterium tumefaciens using the lambda Red recombination system. Appl. Microbiol. Biotechnol.98, 2165–2172.
12. Isaacs F.J., Carr P.A., Wang H.H., Lajoie M.J., Sterling B., Kraal L., Tolonen A.C., Gianoulis T.A., Goodman D.B., Reppas N.B., andet al. 2011. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science333, 348–353.
13. Kulkarni S.K.S. and Stahl F.W.F. 1989. Interaction between the sbcC gene of Escherichia coli and the gam gene of phage lambda. Genetics123, 249–253.
14. Miller J.C., Tan S., Qiao G., Barlow K.A., Wang J., Xia D.F., Meng X., Paschon D.E., Leung E., Hinkley S.J., andet al. 2011. A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol.29, 143–148.
15. Moerschell R.P., Tsunasawa S., and Sherman F. 1988. Transformation of yeast with synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA85, 524–528.
16. Mullis K.B. 1991. The polymerase chain reaction in an anemic mode: how to avoid cold oligodeoxyribonuclear fusion. PCR Methods Appl.1, 1–4.
17. Murphy K.C. 1991. Lambda Gam protein inhibits the helicase and chi-stimulated recombination activities of Escherichia coli RecBCD enzyme. J. Bacteriol.173, 5808–5821.
18. Murphy K.C. 1998. Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli. J. Bacteriol.180, 2063–2071.
19. Muyrers J.P.J., Zhang Y.Y., Testa G.G., and Stewart A.F.A. 1999. Rapid modification of bacterial artificial chromosomes by ETrecombination. Nucleic Acids Res.27, 1555–1557.
20. New England BioLabs Gibson Assembly® Protocol (E5510). https://www.neb.com/protocols/2012/12/11/gibson-assembly-protocol-e5510?device=pdf.
21. Orr-Weaver T.L., Szostak J.W., and Rothstein R.J. 1983. Genetic applications of yeast transformation with linear and gapped plasmids. Methods Enzymol.101, 228–245.
22. Rashtchian A. 1995. Novel methods for cloning and engineering genes using the polymerase chain reaction. Curr. Opin. Biotechnol.6, 30–36.
23. Ryu Y.S., Biswas R.K., Shin K., Parisutham V., Kim S.M., and Lee S.K. 2014. A simple and effective method for construction of Escherichia coli strains proficient for genome engineering. PLoS ONE9, e942–6.
24. Sambrook J. and Russell D.W. 2006. The Inoue method for preparation and transformation of competent E. coli: “ultra-competent” cells. CSH Protoc.2006, 1–6.
25. Seidman C.E., Struhl K., Sheen J., and Jessen T. 2001. Introduction of plasmid DNA into cells. Current Protocols in Molecular Biology, John Wiley & Sons, Inc., Hoboken, NJ, USA.
26. TAKARA Bio. 2007. PrimeStarMax mutagenesis kit 1–3.
27. Thomason L.C., Sawitzke J.A., Li X., Costantino N., and Court D.L. 2014. Recombineering: genetic engineering in bacteria using homologous recombination. Curr. Protoc. Mol. Biol.106, 1.16.1–1.16.39.
28. Ting J.T. and Feng G. 2014. Recombineering strategies for developing next generation BAC transgenic tools for optogenetics and beyond. Front Behav. Neurosci.8, 1–1.
29. Wang H.H., Isaacs F.J., Carr P.A., Sun Z.Z., Xu G., Forest C.R., and Church G.M. 2009. Programming cells by multiplex genome engineering and accelerated evolution. Nature460, 894–898.
30. Yon J. and Fried M. 1989. Precise gene fusion by PCR. Nucleic Acids Res.17, 48–5.
31. Yu D., Ellis H.M., Lee E.C., Jenkins N.A., Copeland N.G., and Court D.L. 2000. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA97, 5978–5983.
32. Zhang Y.Y., Buchholz F.F., Muyrers J.P.J., and Stewart A.F.A. 1998. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet.20, 123–128.
33. Zhang Y., Werling U., and Edelmann W. 2012. SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res.40, e55–e55.
34. Zheng L. 2004. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res.32, e115–e115.