Gene Synthesis pp 215-223 | Cite as

Using DNAWorks in Designing Oligonucleotides for PCR-Based Gene Synthesis

Part of the Methods in Molecular Biology book series (MIMB, volume 852)


The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than where they have been identified originally. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard for the parent genome. Yet design and construction of synthetic genes, especially those coding for large proteins, can be a slow, difficult, and confusing process. DNAWorks automates the design of oligonucleotides for gene synthesis by PCR-based methods.

Key words

Gene synthesis Codon optimization Polymerase chain reaction Cloning Gene expression Oligonucleotide design Simulated annealing 


  1. 1.
    Carr PA, Church GM (2009) Genome engineering. Nature Biotech 27:1151–1162.CrossRefGoogle Scholar
  2. 2.
    Prodromou C, Pearl LH (1992) Recursive PCR: a novel technique for total gene synthesis. Protein Eng 5:827–829.PubMedCrossRefGoogle Scholar
  3. 3.
    Dillon PJ, Rosen CA (1990) A rapid method for the construction of synthetic genes using the polymerase chain reaction. Biotechniques 9:298–300.PubMedGoogle Scholar
  4. 4.
    Gao X, Yo P et al. (2003) Thermodynamically balanced inside-out (TBIO) PCR-based gene synthesis: a novel method of primer design for high-fidelity assembly of longer gene sequences. Nucleic Acids Res 31:e143.PubMedCrossRefGoogle Scholar
  5. 5.
    Czar MJ, Anderson JC et al. (2009) Gene synthesis demystified. Trends Biotechnol 27:63–72.PubMedCrossRefGoogle Scholar
  6. 6.
    Xiong AS, Peng R et al. (2008) Chemical gene synthesis: strategies, softwares, error corrections, and applications. FEMS Microbiol Rev 32:522–540.PubMedCrossRefGoogle Scholar
  7. 7.
    Hoover DM, Lubkowski J (2002) DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res 30:e43.PubMedCrossRefGoogle Scholar
  8. 8.
    Nakamura Y et al. (2000) Nucleic Acids Res 28:292.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Sceince+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Scientific Computing Branch, Center for Information TechnologyNational Institutes of HealthBethesdaUSA

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