Overview of post Cohen-Boyer methods for single segment cloning and for multisegment DNA assembly

Current Protocols in Molecular Biology

Volumn 2016, Issue , 2016, Pages

  Sands, Bryan ^a   Brent, Roger ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Biotechnology; DNA cloning; Molecular biology; Multisegment DNA assembly; Plasmid construction

Indexed keywords

DNA FRAGMENT; DNA LIGASE; DOUBLE STRANDED DNA; RESTRICTION ENDONUCLEASE; SINGLE STRANDED DNA;

ARTICLE; BIOTECHNOLOGICAL PROCEDURES; CHEMICAL REACTION; DNA INTEGRATION; DNA RECOMBINATION; DNA REPAIR; DNA SEQUENCE; DNA VECTOR; GENETIC ENGINEERING; HOMOLOGOUS RECOMBINATION; IN VITRO STUDY; INTERMETHOD COMPARISON; LIGASE CYCLING REACTION; MOLECULAR CLONING; MULTISEGMENT DNA ASSEMBLY; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; YEAST;

EID: 85013889018     PISSN: 19343639     EISSN: 19343647     Source Type: Journal    
DOI: 10.1002/0471142727.mb0326s113     Document Type: Article

References (48)

1. Anderson, J.C., Dueber, J.E., Leguia, M., Wu, G.C., Goler, J.A., Arkin, A.P., and Keasling, J.D. BglBricks: A flexible standard for biological part assembly. J. Biol. Eng. 4:1. doi: 10.1186/1754-1611-4-1
2. Annaluru, N., Muller, H., Mitchell, L.A., Ramalingam, S., Stracquadanio, G., Richardson, S.M., Dymond, J.S., Kuang, Z., Scheifele, L.Z., Cooper, E.M., Cai, Y., Zeller, K., Agmon, N., Han, J.S., Hadjithomas, M., Tullman, J., Caravelli, K., Cirelli, K., Guo, Z., London, V., Yeluru, A., Murugan, S., Kandavelou, K., Agier, N., Fischer, G., Yang, K., Martin, J.A., Bilgel, M., Bohutski, P., Boulier, K.M., Capaldo, B.J., Chang, J., Charoen, K., Choi, W.J., Deng, P., DiCarlo, J.E., Doong, J., Dunn, J., Feinberg, J.I., Fernandez, C., Floria, C.E., Gladowski, D., Hadidi, P., Ishizuka, I., Jabbari, J., Lau, C.Y., Lee, P.A., Li, S., Lin, D., Linder, M.E., Ling, J., Liu, J., Liu, J., London, M., Ma, H., Mao, J., McDade, J.E., McMillan, A., Moore, A.M., Oh, W.C., Ouyang, Y., Patel, R., Paul, M., Paulsen, L.C., Qiu, J., Rhee, A., Rubashkin, M.G., Soh, I.Y., Sotuyo, N.E., Srinivas, V., Suarez, A., Wong, A., Wong, R., Xie, W.R., Xu, Y., Yu, A.T., Koszul, R., Bader, J.S., Boeke, J.D., and Chandrasegaran, S. 2014. Total synthesis of a functional designer eukaryotic chromosome. Science 344:55-58. doi: 10.1126/science. 1249252
3. Aslanidis, C. and de Jong, P.J. 1990. Ligationindependent cloning of PCR products (LICPCR). Nucleic Acids Res. 18:6069-6074. doi: 10.1093/nar/18.20.6069
4. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. Current Protocols in Molecular Biology. Greene Publishing Associates and John Wiley & Sons, New York.
5. Barany, F. 1991. Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. U.S.A. 88:189-193. doi: 10.1073/pnas.88.1.189
6. Bernard, P., Gabant, P., Bahassi, E.M., and Couturier, M. 1994. Positive-selection vectors using the F plasmid ccdB killer gene. Gene 148:71-74. doi: 10.1016/0378-1119(94)90235-6
7. Canton, B., Labno, A., and Endy, D. 2008. Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 26:787-793. doi: 10.1038/nbt1413
8. Cohen, S.N., Chang, A.C., Boyer, H.W., and Helling, R.B. 1973. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl. Acad. Sci. U.S.A. 70:3240-3244. doi: 10.1073/pnas.70.11.3240
9. de Kok, S., Stanton, L.H., Slaby, T., Durot, M., Holmes, V.F., Patel, K.G., Platt, D., Shapland, E.B., Serber, Z., Dean, J., Newman, J.D., and Chandran, S.S. 2014. Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synth. Biol. 3:97-106. doi: 10.1021/sb4001992
10. Echols, H. and Guaneros, G. 1983. Control of integration and excision. In Lambda II. Volume (R. Hendrix, J. Roberts, F. Stahl, and R. Weisberg, eds.). pp. 75-92. Cold Spring Harbor Laboratory Press, New York.
11. Elion, E.A., Marina, P., and Yu, L. 2007. Constructing recombinant DNA molecules by PCR. Curr. Protoc. Mol. Biol. 78:3.17.1-3.17.12.
12. Endy, D. 2005. Foundations for engineering biology. Nature 438:449-453. doi: 10.1038/nature04342
13. Engler, C., Kandzia, R., andMarillonnet, S. 2008.A one pot, one step, precision cloning method with high throughput capability. PloS One 3:e3647. doi: 10.1371/journal.pone.0003647
14. Engler, C., Gruetzner, R., Kandzia, R., and Marillonnet, S. 2009. Golden Gate shuffling: A onepot DNA shuffling method based on type IIs restriction enzymes. PloS One 4:e5553. doi: 10.1371/journal.pone.0005553
15. Fu, J., Bian, X., Hu, S., Wang, H., Huang, F., Seibert, P.M., Plaza, A., Xia, L., Muller, R., Stewart, A.F., and Zhang, Y. 2012. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat. Biotechnol. 30:440-446. doi: 10.1038/nbt.2183
16. Gibson, D.G. 2011. Gene and genome construction in yeast. Curr. Protoc. Mol. Biol. 94:3.22.1-3.22.17. doi: 10.1002/0471142727.mb0322s94
17. 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., Merryman, C., Young, L., Noskov, V.N., Glass, J.I., Venter, J.C., Hutchison, C.A., 3rd, and Smith, H.O. 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319:1215-1220. doi: 10.1126/science. 1151721
18. Gibson, D.G., Young, L., Chuang, R.-Y., Venter, J.C., Hutchison, C.A., III, and Smith, H.O. 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6:343-345 doi: doi: 10.1038/nmeth.1318
19. Hill, R.E. and Eaton-Rye, J.J. 2014. Plasmid construction by SLIC or sequence and ligation-independent cloning. Methods Mol. Biol. 1116:25-36. doi: 10.1007/978-1-62703-764-8_2
20. Holton, T.A. and Graham, M.W. 1991. A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors. Nucleic Acids Res. 19:1156. doi: 10.1093/nar/19.5.1156
21. Hughes, R.A., Miklos, A.E., and Ellington, A.D. 2012. Enrichment of error-free synthetic DNA sequences by CEL I nuclease. Curr. Protoc. Mol. Biol. 99:3.24.1-3.24.10. doi: 10.1002/0471142727.mb0324s99
22. Hughes, S.S. 2001. Making dollars out of DNA. The first major patent in biotechnology and the commercialization of molecular biology, 1974-1980 Isis 92:541-575. doi: 10.1086/385281
23. Knight, T. 2003. Idempotent Vector Design for Standard Assembly of Biobricks http://hdl.handle.net/1721.1/21168. Accessed 8-30-2015.
24. Kodumal, S.J., Patel, K.G., Reid, R., Menzella, H.G., Welch, M., and Santi, D.V. 2004. Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. U.S.A. 101:15573-15578 doi: 10.1073/pnas.0406911101
25. Kramer, M.F. and Coen, D.M. 2001. Enzymatic amplification of DNA by PCR: Standard procedures and optimization. Curr. Protoc. Mol. Biol. 56:15.1.1-15.1.14.
26. Landy, A., 1989. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu. Rev. Biochem. 58:913-941. doi: 10.1146/annurev.bi.58.070189.004405
27. Li, M.Z. and Elledge, S.J. 2007. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat. Methods 4:251-256. doi: 10.1038/nmeth1010
28. Lippow, S.M., Aha, P.M., Parker, M.H., Blake, W.J., Baynes, B.M., and Lipovsek, D. 2009. Creation of a type IIS restriction endonuclease with a long recognition sequence. Nucleic Acids Res. 37:3061-3073. doi: 10.1093/nar/gkp182
29. Liu, J.K., Chen, W.H., Ren, S.X., Zhao, G.P., and Wang, J. 2014. iBrick: A new standard for iterative assembly of biological parts with homing endonucleases. PloS One 9:e110852. doi: 10.1371/journal.pone.0110852
30. Lundblad, V. 1992.Yeast cloning vectors and genes. Curr. Protoc. Mol. Biol. 21:3.4.1-3.4.10. doi: 10.1002/0471142727.mb0304s21
31. Ma, H., Kunes, S., Schatz, P.J., and Botstein, D. 1987 Plasmid construction by homologous recombination in yeast. Gene 58:201-216. doi: 10.1016/0378-1119(87)90376-3
32. McReynolds, L.A. and Nichols, N.M. 2011. Exonucleases. Curr. Protoc. Mol. Biol. 96:3.11.1-3.11.7. doi: 10.1002/0471142727.mb0311s96
33. Miklos, A.E., Hughes, R.A., and Ellington, A.D. 2012. Design and assembly of large synthetic DNA constructs. Curr. Protoc. Mol. Biol. 99:V:3.23.1-3.23.18. doi: 10.1002/0471142727.mb0323s99
34. New England Biolabs. 2012. Gibson Assembly Cloning Kit Instruction Manual. Version 1.0, Oct. 2012.
35. Orr-Weaver, T.L., Szostak, J.W., and Rothstein, R.J. 1981. Yeast transformation: A model system for the study of recombination. Proc. Natl. Acad. Sci. U.S.A. 78:6354-6358. doi: 10.1073/pnas.78.10.6354
36. Pachuk, C.J., Samuel, M., Zurawski, J.A., Snyder, L., Phillips, P., and Satishchandran, C. 2000 Chain reaction cloning: A one-step method for directional ligation of multiple DNA fragments. Gene 243:19-25. doi: 10.1016/S0378-1119(99)00508-9
37. Park, J., Throop, A.L., and LaBaer, J. 2015. Sitespecific recombinational cloning using Gateway and in-fusion cloning schemes. Curr. Protoc. Mol. Biol. 110:3.20.1-3.20.23. doi: 10.1002/0471142727.mb0320s110
38. Roth, T.L., Milenkovic, L., and Scott, M.P. 2014 A rapid and simple method for DNA engineering using cycled ligation assembly. PloS One 9:e107329. doi: 10.1371/journal.pone.0107329
39. Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989 Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York.
40. Seidman, C.E., Struhl, K., Sheen, J., and Jessen, T. 1997 Introduction of plasmid DNA into cells. Curr. Protoc. Mol. Biol. 37:1.8.1-1.8.10.
41. Serber, Z., Lowe, R., Ubersax, J.A., and Chandran, S.S. 2012. Compositions and methods for the assembly of polynucleotides. US Patent 8110360B2.
42. Shetty, R., Lizarazo, M., Rettberg, R., and Knight, T.F. 2011. Assembly of BioBrick standard biological parts using three antibiotic assembly. In Methods in Enzymology, Vol. 498 (C. Voigt, ed.) pp. 311-326. Academic Press, San Diego. doi: 10.1016/B978-0-12-385120-8.00013-9
43. Shuman, S. 1994. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J. Biol. Chem. 269:32678-32684.
44. Sikorski, R.S. and Hieter, P. 1989.Asystem of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
45. 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:V:1.16.1-1.16.39. doi: 10.1002/0471142727.mb0116s106
46. Voytas, D., 2000. Agarose gel electrophoresis. Curr. Protoc. Mol. Biol. 51:II:2.5A.1-2.5A.9. doi: 10.1002/0471142727.mb0205as51
47. Werner, S., Engler, C., Weber, E., Gruetzner, R., andMarillonnet, S. 2012. Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. Bioeng. Bugs 3:38-43.
48. Wiedmann, M., Wilson, W.J., Czajka, J., Luo, J., Barany, F., and Batt, C.A. 1994. Ligase chain reaction (LCR)-overview and applications. PCR Methods Appl. 3:S51-S64. doi: 10.1101/gr.3.4.S51