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PCR-Mediated Recombination

A General Method Applied to Construct Chimeric Infectious Molecular Clones

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PCR Cloning Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 192))

Abstract

Molecular cloning has proven to be a powerful tool in biology, and chimeric clones are useful in a variety of fields including microbial pathogenesis and the development of vaccines. Chimeras can be created from DNA by using conventional cloning techniques, specifically restriction cleavage and DNA ligation. Such techniques, however, have limitations; most commonly, limitations result from the lack of restriction sites to provide points of entry for inserts in the desired regions or the multiplicity of restriction sites in other regions of the DNA. Because recombinant DNA molecules may be created during polymerase chain reaction (PCR) when two or more different DNA sequences are brought together (1,2), PCR-mediated recombination has been exploited to join DNA fragments of a few hundred bases (3-8). There are two drawbacks to these methods. First, they often involve multiple steps, and second, sequence errors frequently are introduced by certain thermostable polymerases during the PCR reaction (9,10).

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References

  1. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., et al. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491.

    Article  CAS  PubMed  Google Scholar 

  2. Meyerhans, A., Vartanian, J. P., and Wain-Hobson, S. (1990) DNA recombination during PCR. Nucl. Acids Res. 18, 1687–1691.

    Article  CAS  PubMed  Google Scholar 

  3. Horton, R. M., Hunt, H. D., Ho, S. N., Pullen, J., and Pease, L. R. (1989) Engineering hybrid gene without the use of restriction enzymes: gene splicing by overlap extension. Gene 77, 61–68.

    Article  CAS  PubMed  Google Scholar 

  4. Horton, R. M., Cai, Z. L., Ho, S. N., and Pease, L. R. (1990) Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques 8, 528–535.

    CAS  PubMed  Google Scholar 

  5. Yolov, A. A. and Shabarova, Z. A. (1990) Constructing DNA by polymerase recombination. Nucl. Acids Res. 18, 3483–3486.

    Article  Google Scholar 

  6. Klug, J., Wolf, M., and Beato, M. (1991) Creating chimeric molecules by PCR directed homologous DNA recombination. Nucl. Acids Res. 19, 2793.

    Article  CAS  PubMed  Google Scholar 

  7. Gu, H., Planas, J., Gomez, R., and Wilson, D. J. (1991) Full length mouse glycoghorin gene constructed using recombinant polymerase chain reaction. Biochem. Biophy. Res. Commun. 177, 202–208.

    Article  CAS  Google Scholar 

  8. Sandhu, G. S., Aleff, R. A., and Kline, B. C. (1992) Dual asymmetric PCR: one-step construction of synthetic genes. Biotechniques 12, 14–16.

    CAS  PubMed  Google Scholar 

  9. Eckert, K. A. and Kunkel, T. A. (1991) DNA polymerase fidelity and the polymerase chain reaction. PCR Meth. Appl. 1, 17–24.

    CAS  Google Scholar 

  10. Mattila, P., Korpela, J., Tenkanen, T., and Pitkanen, K. (1991) Fidelity of DNA synthesis by the Thermococcus litoralis DNA polymerase-an extremely heat stable enzyme with proofreading activity. Nucl. Acids Res. 19, 4967–4973.

    Article  CAS  PubMed  Google Scholar 

  11. Coffin, J. M. (1995) HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267, 483–489.

    Article  CAS  PubMed  Google Scholar 

  12. Chun, T. W., Carruth, L., Finzi, D., Shen, X., DiGiuseppe, J. A., Taylor, H., et al. (1997) Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature 387, 183–188.

    Article  CAS  PubMed  Google Scholar 

  13. Myers, G. Korber, B., Foley, B., Jeang, K. T., Mellors, J. W., and Wain-Hobson, S. (1996) Human Retroviruses and AIDS. Los Alamos National Laboratory, Los Alamos, NM.

    Google Scholar 

  14. Fang, G., Weiser, B., Visosky, A., Townsend, L., and Burger, H. (1996) Molecular cloning of full-length HIV-1 genomes directly from plasma viral RNA. J. AIDS 12, 352–357.

    CAS  Google Scholar 

  15. Fang, G., Burger, H., Grimson, R., Tropper, P., Nachman, S., Mayers, D., et al. (1995) Maternal plasma human immunodeficiency virus type 1 RNA level: a determinant and projected threshold for mother-to-child transmission. Proc. Natl. Acad. Sci. USA 92, 12,100–12,104

    Article  CAS  PubMed  Google Scholar 

  16. Salminen, M. O., Koch, C., Sanders-Buell, E., Ehrenberg, P. K., Michael, N. L., Carr, J. K., et al. (1995) Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction. Virology 213, 80–86.

    Article  CAS  PubMed  Google Scholar 

  17. Lundberg, K. S., Shoemaker, D. D., Adams, M. W., Short, J. M., Sorge, J. A., and Mathur, E. J. (1991) High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene 108, 1–6.

    Article  CAS  PubMed  Google Scholar 

  18. Flaman, J. M., Frebourg, T., Moreau, V., Charbonnier, F., Martin, C., Ishioka, C., et al. (1994) A rapid PCR fidelity assay. Nucl. Acids Res. 22, 3259–3260.

    Article  CAS  PubMed  Google Scholar 

  19. Horton, R. M. (1995) SOEing together tailor-made genes. Mol. Biotech. 3, 93–99.

    Article  CAS  Google Scholar 

  20. Fang, G., Weiser, B., Visosky, A., Moran, T., and Burger, H. (1999) PCR-mediated recom-bination: a general method applied to construct chimeric infectious molecular clones of plasma-derived HIV-1 RNA. Nat Med. 5, 239–242.

    Article  CAS  PubMed  Google Scholar 

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© 2002 Humana Press Inc.

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Fang, G., Weiser, B., Visosky, A., Moran, T., Burger, H. (2002). PCR-Mediated Recombination. In: Chen, BY., Janes, H.W. (eds) PCR Cloning Protocols. Methods in Molecular Biology™, vol 192. Humana Press. https://doi.org/10.1385/1-59259-177-9:197

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  • DOI: https://doi.org/10.1385/1-59259-177-9:197

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-969-8

  • Online ISBN: 978-1-59259-177-0

  • eBook Packages: Springer Protocols

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