Applications of the Restriction Free (RF) cloning procedure for molecular manipulations and protein expression

Journal of Structural Biology

Volumn 172, Issue 1, 2010, Pages 34-44

  Unger, Tamar ^a   Jacobovitch, Yossi ^a   Dantes, Ada ^a   Bernheim, Reut ^a   Peleg, Yoav ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

DNA deletion; DNA insertion; Ligation Independent Cloning (LIC); Multiple site mutagenesis; Parallel cloning; Restriction Free (RF) cloning; Simultaneous cloning

Indexed keywords

DNA FRAGMENT; RECOMBINANT PROTEIN;

ARTICLE; ESCHERICHIA COLI; EXPRESSION VECTOR; GENE DELETION; GENE INSERTION; GENE REPLACEMENT THERAPY; MOLECULAR CLONING; MUTATION; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN EXPRESSION; RESTRICTION FREE CLONING; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; BASE SEQUENCE; CLONING, MOLECULAR; DNA; ESCHERICHIA COLI; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PLASMIDS; POLYMERASE CHAIN REACTION; PROTEINS; RECOMBINANT PROTEINS;

ESCHERICHIA COLI;

EID: 77956184308     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.06.016     Document Type: Article

References (28)

1. Aslanidis C., de Jong P.J., Schmitz G. Minimal length requirement of the single-stranded tails for ligation-independent cloning (LIC) of PCR products. PCR Methods Appl. 1994, 4:172-177.
2. Benoit R.M., Wilhelm R.N., Scherer-Becker D., Ostermeier C. An improved method for fast, robust, and seamless integration of DNA fragments into multiple plasmids. Protein Expr. Purif. 2006, 45:66-71.
3. Berrow N.S., Bussow K., Coutard B., Diprose J., Ekberg M., Folkers G.E., Levy N., Lieu V., Owens R.J., Peleg Y., Pinaglia C., Quevillon-Cheruel S., Salim L., Scheich C., Vincentelli R., Busso D. Recombinant protein expression and solubility screening in Escherichia coli: a comparative study. Acta Crystallogr. D Biol. Crystallogr. 2006, 62:1218-1226.
4. Busso D., Delagoutte-Busso B., Moras D. Construction of a set Gateway-based destination vectors for high-throughput cloning and expression screening in Escherichia coli. Anal. Biochem. 2005, 343:313-321.
5. Chen G.J., Qiu N., Karrer C., Caspers P., Page M.G. Restriction site-free insertion of PCR products directionally into vectors. Biotechniques 2000, 28:498-500. 504-505.
6. Geiser M., Cebe R., Drewello D., Schmitz R. Integration of PCR fragments at any specific site within cloning vectors without the use of restriction enzymes and DNA ligase. Biotechniques 2001, 31:88-90. 92.
7. Gileadi O., Burgess-Brown N.A., Colebrook S.M., Berridge G., Savitsky P., Smee C.E., Loppnau P., Johansson C., Salah E., Pantic N.H. High throughput production of recombinant human proteins for crystallography. Methods Mol. Biol. 2008, 426:221-246.
8. Graslund S., Nordlund P., Weigelt J., Hallberg B.M., Bray J., Gileadi O., Knapp S., Oppermann U., Arrowsmith C., Hui R., Ming J., dhe-Paganon S., Park H.W., Savchenko A., Yee A., Edwards A., Vincentelli R., Cambillau C., Kim R., Kim S.H., Rao Z., Shi Y., Terwilliger T.C., Kim C.Y., Hung L.W., Waldo G.S., Peleg Y., Albeck S., Unger T., Dym O., Prilusky J., Sussman J.L., Stevens R.C., Lesley S.A., Wilson I.A., Joachimiak A., Collart F., Dementieva I., Donnelly M.I., Eschenfeldt W.H., Kim Y., Stols L., Wu R., Zhou M., Burley S.K., Emtage J.S., Sauder J.M., Thompson D., Bain K., Luz J., Gheyi T., Zhang F., Atwell S., Almo S.C., Bonanno J.B., Fiser A., Swaminathan S., Studier F.W., Chance M.R., Sali A., Acton T.B., Xiao R., Zhao L., Ma L.C., Hunt J.F., Tong L., Cunningham K., Inouye M., Anderson S., Janjua H., Shastry R., Ho C.K., Wang D., Wang H., Jiang M., Montelione G.T., Stuart D.I., Owens R.J., Daenke S., Schutz A., Heinemann U., Yokoyama S., Bussow K., Gunsalus K.C. Protein production and purification. Nat. Methods 2008, 5:135-146.
9. Hartley, J.L., 2003. Use of the gateway system for protein expression in multiple hosts. Curr. Protoc. Protein Sci., Chapter 5, Unit 5 17.
10. Hogrefe H.H., Cline J., Youngblood G.L., Allen R.M. Creating randomized amino acid libraries with the QuikChange Multi Site-Directed Mutagenesis Kit. Biotechniques 2002, 33:1158-1160. 1162, 1164-1165.
11. Jawhari A., Uhring M., De Carlo S., Crucifix C., Tocchini-Valentini G., Moras D., Schultz P., Poterszman A. Structure and oligomeric state of human transcription factor TFIIE. EMBO Rep. 2006, 7:500-505.
12. Kahana C. Antizyme and antizyme inhibitor, a regulatory tango. Cell. Mol. Life Sci. 2009, 66:2479-2488.
13. Kirsch R.D., Joly E. An improved PCR-mutagenesis strategy for two-site mutagenesis or sequence swapping between related genes. Nucleic Acids Res. 1998, 26:1848-1850.
14. LaVallie E.R., DiBlasio E.A., Kovacic S., Grant K.L., Schendel P.F., McCoy J.M. A thioredoxin gene fusion expression system that circumvents inclusion body formation in the E. coli cytoplasm. Biotechnology (NY) 1993, 11:187-193.
15. Li M.Z., Elledge S.J. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat. Methods 2007, 4:251-256.
16. Miyazaki K., Takenouchi M. Creating random mutagenesis libraries using megaprimer PCR of whole plasmid. Biotechniques 2002, 33:1033-1034. 1036-1038.
17. Moreland N., Ashton R., Baker H.M., Ivanovic I., Patterson S., Arcus V.L., Baker E.N., Lott J.S. A flexible and economical medium-throughput strategy for protein production and crystallization. Acta Crystallogr. D Biol. Crystallogr. 2005, 61:1378-1385.
18. Neilan B.A., Tillett D. Enzyme-free cloning of PCR products and fusion protein expression. Methods Mol. Biol. 2002, 192:125-132.
19. Peleg Y., Unger T. Application of high-throughput methodologies to the expression of recombinant proteins in E. coli. Methods Mol. Biol. 2008, 426:197-208.
20. Perrakis A., Romier C. Assembly of protein complexes by coexpression in prokaryotic and eukaryotic hosts: an overview. Methods Mol. Biol. 2008, 426:247-256.
21. Romier C., Ben Jelloul M., Albeck S., Buchwald G., Busso D., Celie P.H., Christodoulou E., De Marco V., van Gerwen S., Knipscheer P., Lebbink J.H., Notenboom V., Poterszman A., Rochel N., Cohen S.X., Unger T., Sussman J.L., Moras D., Sixma T.K., Perrakis A. Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies. Acta Crystallogr. D Biol. Crystallogr. 2006, 62:1232-1242.
22. Steffens D.L., Williams J.G. Efficient site-directed saturation mutagenesis using degenerate oligonucleotides. J. Biomol. Tech. 2007, 18:147-149.
23. Tillett D., Neilan B.A. Enzyme-free cloning: a rapid method to clone PCR products independent of vector restriction enzyme sites. Nucleic Acids Res. 1999, 27:e26.
24. Tseng W.C., Lin J.W., Wei T.Y., Fang T.Y. A novel megaprimed and ligase-free, PCR-based, site-directed mutagenesis method. Anal. Biochem. 2008, 375:376-378.
25. Tubb J., Groth A.C., Leong L., Emery D.W. Simultaneous sequence transfer into two independent locations of a reporter vector using MultiSite Gateway technology. Biotechniques 2005, 39:553-557.
26. van den Ent F., Lowe J. RF cloning: a restriction-free method for inserting target genes into plasmids. J. Biochem. Biophys. Methods 2006, 67:67-74.
27. Yanai Y., Sanou O., Kayano T., Ariyasu H., Yamamoto K., Yamauchi H., Ikegami H., Kurimoto M. Analysis of the antiviral activities of natural IFN-alpha preparations and their subtype compositions. J. Interferon Cytokine Res. 2001, 21:835-841.
28. Zeev-Ben-Mordehai T., Paz A., Peleg Y., Toker L., Wolf S.G., Rydberg E.H., Sussman J.L., Silman I. Amalgam, an axon guidance Drosophila adhesion protein belonging to the immunoglobulin superfamily: over-expression, purification and biophysical characterization. Protein Expr. Purif. 2009, 63:147-157.