Summary
Nonviral gene therapy vectors are commonly based on recombinant bacterial plasmids or their derivatives. The plasmids are propagated in bacteria, so, in addition to their therapeutic cargo, they necessarily contain a bacterial replication origin and a selection marker, usually a gene conferring antibiotic resistance. Structural and maintenance plasmid stability in bacteria is required for the plasmid DNA production and can be achieved by carefully choosing a combination of the therapeutic DNA sequences, replication origin, selection marker, and bacterial strain. The use of appropriate promoters, other regulatory elements, and mammalian maintenance devices ensures that the therapeutic gene or genes are adequately expressed in target human cells. Optimal immune response to the plasmid vectors can be modulated via inclusion or exclusion of DNA sequences containing immunostimulatory CpG sequence motifs.
DNA fragments facilitating construction of plasmid vectors should also be considered for inclusion in the design of plasmid vectors. Techniques relying on site-specific or homologous recombination are preferred for construction of large plasmids (>15 kb), while digestion of DNA by restriction enzymes with subsequent ligation of the resulting DNA fragments continues to be the mainstream approach for generation of small- and medium-size plasmids. Rapid selection of a desired recombinant plasmid against a background of other plasmids continues to be a challenge. In this chapter, the emphasis is placed on efficient and flexible versions of DNA cloning protocols using selection of recombinant plasmids by restriction endonucleases directly in the ligation mixture.
Similar content being viewed by others
References
Bolivar, F., Rodriguez, R. L., Betlach, M. C., and Boyer, H. W. (1977) Construction and characterization of new cloning vehicles. I. Ampicillin-resistant derivatives of the plasmid pMB9. Gene. 2, 75–93.
Bolivar, F., Rodriguez, R. L., Greene, P. J., Betlach, M. C., Heyneker, H. L., and Boyer, H. W. (1977) Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 2, 95–113.
Vieira, J., and Messing, J. (1982) The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 19, 259–268.
Chistoserdov, A. Y., and Tsygankov, Y. D. (1986) Broad host range vectors derived from an RSF1010::Tn1 plasmid. Plasmid. 16, 161–167.
Sarovich, D. S., and Pemberton, J. M. (2007) pPSX: a novel vector for the cloning and heterologous expression of antitumor antibiotic gene clusters. Plasmid. 57, 306–313.
Wu, F., Levchenko, I., and Filutowicz, M. (1995) A DNA segment conferring stable maintenance on R6K gamma-origin core replicons. J. Bacteriol. 177, 6338–6345.
Seed, B. (1983) Purification of genomic sequences from bacteriophage libraries by recombination and selection in vivo. Nucleic Acids Res. 11, 2427–2445.
Kingsman, S. M., Mitrophanous, K., and Olsen, J. C. (2005) Potential oncogene activity of the woodchuck hepatitis post-transcriptional regulatory element (WPRE). Gene Ther. 12, 3–4.
Storni, T., Ruedl, C., Schwarz, K., Schwendener, R. A., Renner, W. A., and Bachmann, M. F. (2004) Nonmethylated CG motifs packaged into virus-like particles induce protective cytotoxic T cell responses in the absence of systemic side effects. J. Immunol. 172, 1777–1785.
Yew, N. S., Zhao, H., Przybylska, M., Wu, I. H., Tousignant, J. D., Scheule, R. K., et al. (2002) CpG-depleted plasmid DNA vectors with enhanced safety and long-term gene expression in vivo. Mol. Ther. 5, 731–738.
Bigger, B. W., Tolmachov, O., Collombet, J. M., Fragkos, M., Palaszewski, I., and Coutelle, C. (2001) An araC-controlled bacterial cre expression system to produce DNA minicircle vectors for nuclear and mitochondrial gene therapy. J. Biol. Chem. 276, 23018–23027.
Vaysse, L., Gregory, L. G., Harbottle, R. P., Perouzel, E., Tolmachov, O., and Coutelle, C. (2006) Nuclear-targeted minicircle to enhance gene transfer with non-viral vectors in vitro and in vivo. J. Gene Med. 8, 754–763.
Tolmachov, O., and Coutelle, C. (2007) Covalent attachment of multifunctional chimeric terminal proteins to 5' DNA ends: a potential new strategy for assembly of synthetic therapeutic gene vectors. Med. Hypotheses. 68, 328–331.
Lufino, M. M., Manservigi, R., and Wade-Martins, R. (2007) An S/MAR-based infectious episomal genomic DNA expression vector provides long-term regulated functional complementation of LDLR deficiency. Nucleic Acids Res. 35, e98.
Calos, M. P. (2006) The phiC31 integrase system for gene therapy. Curr. Gene Ther. 6, 633–645.
Tolmachov, O., Palaszewski, I., Bigger, B., and Coutelle, C. (2006) RecET driven chromosomal gene targeting to generate a RecA deficient Escherichia coli strain for Cre mediated production of minicircle DNA. BMC Biotechnol. 6, 17.
Gu, W., Putral, L., Hengst, K., Minto, K., Saunders, N. A., Leggatt, G., et al. (2006) Inhibition of cervical cancer cell growth in vitro and in vivo with lentiviral-vector delivered short hairpin RNA targeting human papillomavirus E6 and E7 oncogenes. Cancer Gene Ther. 13, 1023–1032.
Chaffin, D. O., and Rubens, C. E. (1998) Blue/white screening of recombinant plasmids in Gram-positive bacteria by interruption of alkaline phosphatase gene (phoZ) expression. Gene. 219, 91–99.
Bernard, P. (1996) Positive selection of recombinant DNA by CcdB. Biotechniques. 21, 320–323.
Choi, Y. J., Wang, T. T., and Lee, B. H. (2002) Positive selection vectors. Crit. Rev. Biotechnol. 22, 225–244.
Gabant, P., Van Reeth, T., Dreze, P. L., Faelen, M., Szpirer, C., and Szpirer, J. (2000) New positive selection system based on the parD (kis/kid) system of the R1 plasmid. Biotechniques. 28, 784–788.
Heyman, J. A., Cornthwaite, J., Foncerrada, L., Gilmore, J. R., Gontang, E., Hartman, K. J., et al. (1999) Genome-scale cloning and expression of individual open reading frames using topoisomerase I-mediated ligation. Genome Res. 9, 383–392.
Al-Allaf, F. A., Tolmachov, O., Themis, M., and Coutelle, C. (2005) Coupled analysis of bacterial transformants and ligation mixture by duplex PCR enables detection of fatal instability of a nascent recombinant plasmid. J. Biochem. Biophys. Methods. 64, 142–146.
Fromme, T., and Klingenspor, M. (2007) Rapid single step subcloning procedure by combined action of type II and type IIs endonucleases with ligase. J Biol Eng. 1, 7.
Gupta, S., Arora, K., Sampath, A., Khurana, S., Singh, S. S., Gupta, A., et al. (1999) Simplified gene-fragment phage display system for epitope mapping. Biotechniques. 27, 328–330, 332–324.
Worthington, M. T., Pelo, J., and Lo, R. Q. (2001) Cloning of random oligonucleotides to create single-insert plasmid libraries. Anal. Biochem. 294, 169–175.
Cosloy, S. D., and Oishi, M. (1973) Genetic transformation in Escherichia coli K12. Proc. Natl. Acad. Sci. USA. 70, 84–87.
Sawitzke, J. A., Thomason, L. C., Costantino, N., Bubunenko, M., Datta, S., and Court, D. L. (2007) Recombineering: in vivo genetic engineering in E. coli, S. enterica, and beyond. Methods Enzymol. 421, 171–199.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Tolmachov, O. (2009). Designing Plasmid Vectors. In: Walther, W., Stein, U. (eds) Gene Therapy of Cancer. Methods in Molecular Biology™, vol 542. Humana Press. https://doi.org/10.1007/978-1-59745-561-9_6
Download citation
DOI: https://doi.org/10.1007/978-1-59745-561-9_6
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-934115-85-5
Online ISBN: 978-1-59745-561-9
eBook Packages: Springer Protocols