Site-specific recombinational cloning using gateway and in-fusion cloning schemes

Current Protocols in Molecular Biology

Volumn 2015, Issue , 2015, Pages 3.20.1-3.20.23

  Park, Jaehong ^a   Throop, Andrea L ^b   LaBaer, Joshua ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

Author keywords

Cre lox; Gateway; High throughput; In fusion; Recombinational cloning

Indexed keywords

CRE RECOMBINASE; PLASMID DNA; RECOMBINANT PROTEIN;

ARTICLE; CELL TRANSFORMATION; CLINICAL PROTOCOL; CLONING VECTOR; CONTROLLED STUDY; DNA SEQUENCE; EXPERIMENTAL STUDY; GENE AMPLIFICATION; GENE EXPRESSION SYSTEM; GENE TARGETING; LABORATORY DEVICE; MOLECULAR CLONING; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; REACTION ANALYSIS; RECOMBINATIONAL CLONING; RECOMBINATIONAL CLONING TECHNOLOGY; GENETIC RECOMBINATION; GENETICS; PROCEDURES;

CLONING, MOLECULAR; RECOMBINANT PROTEINS; RECOMBINATION, GENETIC;

EID: 84949184984     PISSN: 19343639     EISSN: 19343647     Source Type: Journal    
DOI: 10.1002/0471142727.mb0320s110     Document Type: Article

References (30)

1. Bernard, P. and Couturier, M. 1992. Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J. Mol. Biol. 226:735-745.
2. Bird, L.E. 2011. High throughput construction and small scale expression screening of multi-tag vectors in Escherichia coli. Methods 55:29-37.
3. Brizuela, L., Richardson, A., Marsischky, G., and LaBaer, J. 2002. The FLEXGene repository: Exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic era. Arch. Med. Res. 33:318-324.
4. Cantor, E.J. and Chong, S. 2001. Intein-mediated rapid purification of cre recombinase. Protein Expr. Purif. 22:135-140.
5. Ceroni, A., Sibani, S., Baiker, A., Pothineni, V.R., Bailer, S.M., LaBaer, J., Hass, J., and Campbell, C.J. 2010. Systematic analysis of the IgG antibody immune response against varicella zoster virus (VSV) using a self-assembled protein microarray. Mol. BioSyst. 6:1604-1610.
6. Festa, F., Steel, J., Bian, X., and LaBaer, J., 2013. High-throughput cloning and expression library creation for functional proteomics. Proteomics 13:1381-1399.
7. Gibson, D.G. 2011. Gene and genome construction in yeast. Curr. Protoc. Mol. Biol. 94:3.22.01-3.22.17.
8. Gibson, D.G., Young, L., Chuang, R.-R., 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.
9. Hamilton, M.D., Nuara, A.A., Gammon, D.B., Buller, R.M., and Evans, D.H. 2006. Duplex strand joining reactions catalyzed by vaccinia virus DNA polymerase. Nucleic Acids Res. 35:143-151.
10. Hartley, J.L., Temple, G.F., and Brasch, M.A. 2000. DNA cloning using in vitro site-specific recombination. Genome Res. 10:1788-1795.
11. Irwin, C.R., Farmer, A., Willer, D.O., and Evans, D.H. 2012. In-Fusion ® cloning with vaccinia virus DNA polyermase. In Vaccinia Virus and Poxvirology: Methods and Protocols, Vol. 890: Methods in Molecular Biology (S.N. Isaacs, ed.), pp. 23-35. Humana Press, New York.
12. Landy, A. 1989. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu. Rev. Biochem. 58:913-949.
13. Liang, X., Peng, L., Baek C., and Katzen, R. 2013. Single step BP/LR combined Gateway reaction. Biotechniques 5:265-268.
14. Marsischky, G. and LaBaer, J. 2004. Many paths to many clones: A comparative look at highthroughput cloning methods. Genome Res. 14:2020-2028.
15. Murthy, T., Rolfs, A., Hu, Y., Zhenwei, S., Raphael, J., Moreira, D., Kelley, F., McCarron, S., Jepson, D., Taycher, E., Zuo, D., Mohr, S.E., Fernadez, M., Brizuela, L., and LaBaer, J. 2007. A fullgenomic sequence-verified protein-coding collection for Francisella tularensis. PLoS One. 2:e577.
16. Nash, H.A. 1977. Integration and excision of bacteriophage lambda. Curr. Top. Microbiol. Immunol. 78:171-199.
17. Nash, H.A. and Robertson, C.A. 1981. Purification and properties of the Escherichia coli protein factor required for lambda integrative recombination. J. Biol. Chem. 256:9246-9253.
18. Ptashne, M. 1992. A Genetic Switch: Phage (Lamda) and Higher Organisms. Cell Press, Cambridge, MA.
19. Reboul, J., Vaglio, P., Tzellas, N., Thierry-Mieg, N., Moore, T., Jackson, C., Shin-I, T., Kohara, Y., Thierry-Mieg, D., Thierry-Mieg, J., Lee, H., Hitti, J., Doucette-Stamm, L., Hartley, J.L., Temple, G.F., Brasch, M.A., Vandenhaute, J., Lamesch, P.E., Hill, D.E., and Vidal, M. 2001. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat. Genet. 27:332-336.
20. Reboul, J., Vaglio, P., Rual, J.F., Lamesch, P., Martinez, M., Armstrong, C.M., Li, S., Jacotot, L., Bertin, N., Janky, R., Moore, T., Hudson, J.R. Jr, Hartley, J.L., Brasch, M.A., Vandenhaute, J., Boulton, S., Endress, G.A., Jenna, S., Chevet, E., Papasotiropoulos, V., Tolias, P.P., Ptacek, J., Snyder, M., Huang, R., Chance, M.R., Lee, H., Doucette-Stamm, L., Hill, D.E., and Vidal, M. 2003. C. elegans ORFeome version 1.1: Experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34:35-41.
21. Rolfs, A., Montor, W.R., Yoon, S.S., Hu, Y., Bhullar, B., Kelley, F., McCarron, S., Jepson, D.A., Shen, B., Taycher, E., Mohr, S.E., Zuo, D., Williamson, J., Mekalanos, J., and LaBaer, J. 2008. Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio cholerae. Proc. Natl. Acad. Sci. U.S.A. 105:4364-4369.
22. Rolfs, A., Hu, Y., Ebert, L., Hoffman, D., Zuo, D., Ramachandran, N., Raphael, J., Kelley, F., McCarron, S., Jepson, D.A., Shen, B., Baqui, M.M.A., Pearlberg, J., Taycher, E., DeLoughery, C., Hoerlein, A., Korn, B., and LaBaer, J. 2008. A biomedically enriched collection of 7000 human ORF clones. PLoS One. 3:e1528.
23. SantaLucia, J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearestneighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A. 95:1460-1465.
24. Saul, J., Petritis, B., Sau, S., Rauf, F., Gaskin, M., Ober-Reynolds, B., Mineyev, I., Magee, M., Chaput, J., Qiu, J., and LaBaer, J. 2014. Development of full-length human protein production pipeline. Protein Sci. 23:1123-1135.
25. Thanawastien, A., Montor, W.R., LaBaer, J., Mekalanos, J.J., and Yoon, S.S. 2009. Vibrio cholerae proteome-wide screen for immunostimulatory proteins identifies phosphatidylserine decarboxylase as a novel toll-like receptor 4 agonist. PLoS Path. 5:e1000556.
26. Walhout, A.J., Temple, G.F., Brasch, M.A., Hartley, J.L., Lorson, M.A, van den Heuvel, S., and Vidal, M. 2000. GATEWAY recombinational cloning: Application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 328:575-592.
27. Weisberg, R.A. and Landy, A. 1983. Site-specific recombination in phage lamda. In Lamda II (R.A. Weisberg, ed.), pp. 211-250. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
28. Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Wu, H.C., Kim, C., Nguyen, M., Pham, P., Cheuk, R., Karlin-Newmann, G., Liu, S.X., Lam, B., Sakano, H., Wu, T., Yu, G., Miranda, M., Quach, H.L., Tripp, M., Chang, C.H., Lee, J.M., Toriumi, M., Chan, M.M., Tang, C.C., Onodera, C.S., Deng, J.M., Akiyama, K., Ansari, Y., Arakawa, T., Banh, J., Banno, F., Bowser, L., Brooks, S., Carninci, P., Chao, Q., Choy, N., Enju, A., Goldsmith, A.D., Gurjal, M., Hansen, N.F., Hayashizaki, Y., Johnson-Hopson, C., Hsuan, V.W., Iida, K., Karnes, M., Khan, S., Koesema, E., Ishida, J., Jiang, P.X., Jones, T., Kawai, J., Kamiya, A., Meyers, C., Nakajima, M., Narusaka, M., Seki, M., Sakurai, T., Satou, M., Tamse, R., Vaysberg, M., Wallender, E.K., Wong, C., Yamamura, Y., Yuan, S., Shinozaki, K., Davis, R.W., Theologis, A., and Ecker, J.R. 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842-846.
29. Yu, X., Bian, X., Throop, A., Song, L., Del Moral, L., Park, J., Seiler, C., Fiacco, M., Steel, J., Hunter, P., Saul, J., Wang, J., Qiu, J., Pipas, J.M., and LaBaer, J. 2014. Exploration of Panviral proteome: High-throughput cloning and functional implications in virus-host interactions. Theranostics 8:808-822.
30. Zhu, B., Cai, G., Hall, E.O., and Freeman, G.J. 2007. In-Fusion assembly: Seamless engineering of multidomain fusion proteins, modular vectors, and mutations. BioTechniques 43:34-359.