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Minimum GC-Rich Sequences for Overlap Extension PCR and Primer Annealing

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DNA Cloning and Assembly Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1116))

Abstract

PCR is a common method to produce desired DNA fragments from templates. The oligonucleotide primers used for PCR must contain annealing sequences that are usually 20–30 nucleotides long and identical to a part of template DNA. However, primers often contain additional sequences at their 5′ ends, which are restriction enzyme sites, recombination targeting sequences, or overlap sequences for fusion PCR. When these additional sequences are attached to their annealing sequences, the annealing sequences can be shortened. Here, we describe universal GC-rich annealing sequences useful for overlap extension PCR and simple in-frame addition of desired sequences.

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References

  1. Dieffenbach CW, Lowe TMJ, Dveksler GS (1995) General concepts for PCR primer design. In: Dieffenbach CW, Dveksler GS (eds) PCR primer: a laboratory manual. Cold Spring Harbor Laboratory Press, New York, pp 133–142

    Google Scholar 

  2. Suggs SV, Hirose T, Miyake T et al (1981) Use of synthetic oligodeoxyribonucleotides for the isolation of specific cloned DNA sequences. ICN-UCLA Symp Dev Biol 23:683–693

    CAS  Google Scholar 

  3. Cha-aim K, Fukunaga T, Hoshida H et al (2009) Reliable fusion PCR mediated by GC-rich overlap sequences. Gene 434:43–49

    Article  CAS  PubMed  Google Scholar 

  4. Heckman KL, Pease LR (2007) Gene splicing and mutagenesis by PCR-driven overlap extension. Nat Protoc 2:924–932

    Article  CAS  PubMed  Google Scholar 

  5. Lu Q (2005) Seamless cloning and gene fusion. Trends Biotechnol 23:199–207

    Article  CAS  PubMed  Google Scholar 

  6. Vallejo AN, Pogulis RJ, Pease LR (1994) In vitro synthesis of novel genes: mutagenesis and recombination by PCR. Genome Res 4:s123–s130

    Google Scholar 

  7. Levis R (1995) Strategies for cloning PCR products. In: Dieffenbach CW, Dveksler GS (eds) PCR primer: a laboratory manual. Cold Spring Harbor Laboratory Press, New York, pp 539–554

    Google Scholar 

  8. Baudin A, Ozier-Kalogeropoulos O, Denouel A et al (1993) A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res 21:3329–3330

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Kakihara Y, Matsuura Y, Hoshida H et al (2005) Cost-saving design of PCR primers containing additional sequences. ITE Lett 6:135–139

    CAS  Google Scholar 

  10. Benedikt W, Walter N (2000) Mitochondria-targeted green fluorescent proteins: convenient tools for the study of organelle biogenesis in Saccharomyces cerevisiae. Yeast 16:1421–1427

    Article  Google Scholar 

  11. Keppler-Ross S, Douglas L, Konopka JB et al (2010) Recognition of yeast by murine macrophages requires mannan but not glucan. Eukaryot Cell 9:1776–1787

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Amberg DC, Burke D, Strathern JN (2005) Method in yeast genetics: a Cold Spring Harbor Laboratory course manual. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  13. Nonklang S, Abdel-Banat BM, Cha-aim K et al (2008) High-temperature ethanol fermentation and transformation with linear DNA in the thermotolerant yeast Kluyveromyces marxianus DMKU3-1042. Appl Environ Microbiol 74:7514–7521

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Abdel-Banat BM, Nonklang S, Hoshida H et al (2010) Random and targeted gene integrations through the control of non-homologous end joining in the yeast Kluyveromyces marxianus. Yeast 27:29–39

    CAS  PubMed  Google Scholar 

  15. Zha H, Fisk HA, Yaffe MP et al (1996) Structure-function comparisons of the proapoptotic protein Bax in yeast and mammalian cells. Mol Cell Biol 16:6494–6508

    CAS  PubMed Central  PubMed  Google Scholar 

  16. Monosov EZ, Wenzel TJ, Lüers GH et al (1996) Labeling of peroxisomes with green fluorescent protein in living P. pastoris cells. J Histochem Cytochem 44:581–589

    Article  CAS  PubMed  Google Scholar 

  17. Cha-Aim K, Hoshida H, Fukunaga T et al (2012) Fusion PCR via novel overlap sequences. Methods Mol Biol 852:97–110

    Article  CAS  PubMed  Google Scholar 

  18. Winzeler EA, Shoemaker DD, Astromoff A et al (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901–906

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank Yukie Misumi for her technical assistance. This work was supported in part by the Adaptable and Seamless Technology Transfer Program through Target-Driven R & D and the Advanced Low Carbon Technology Research and Development Program (JST, Japan).

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Nakamura, M., Suzuki, A., Hoshida, H., Akada, R. (2014). Minimum GC-Rich Sequences for Overlap Extension PCR and Primer Annealing. In: Valla, S., Lale, R. (eds) DNA Cloning and Assembly Methods. Methods in Molecular Biology, vol 1116. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-764-8_12

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  • DOI: https://doi.org/10.1007/978-1-62703-764-8_12

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-763-1

  • Online ISBN: 978-1-62703-764-8

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