Displacement Whiplash PCR: Optimized Architecture and Experimental Validation

  • John A. Rose
  • Ken Komiya
  • Satsuki Yaegashi
  • Masami Hagiya
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4287)


Whiplash PCR-based methods of biomolecular computation (BMC), while highly-versatile in principle, are well-known to suffer from a simple but serious form of self-poisoning known as back-hybridization. In this work, an optimally re-engineered WPCR-based architecture, Displacement Whiplash PCR (DWPCR) is proposed and experimentally validated. DWPCR’s new rule protect biostep, which is based on the primer-targeted strand-displacement of back-hybridized hairpins, renders the most recently implemented rule-block of each strand unavailable, abolishing back-hybridization after each round of extension. In addition to attaining a near-ideal efficiency, DWPCR’s ability to support isothermal operation at physiological temperatures eliminates the need for thermal cycling, and opens the door for potential biological applications. DWPCR should also be capable of supporting programmable exon shuffling, allowing XWPCR, a proposed method for programmable protein evolution, to more closely imitate natural evolving systems. DWPCR is expected to realize a highly-efficient, versatile platform for routine and efficient massively parallel BMC.


Klenow Fragment Strand Displacement Template Strand Polymerization Experiment Prime Strand 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • John A. Rose
    • 1
    • 2
    • 3
  • Ken Komiya
    • 3
    • 4
  • Satsuki Yaegashi
    • 3
  • Masami Hagiya
    • 2
    • 3
  1. 1.Institute of Information Communication TechnologyRitsumeikan Asia Pacific University 
  2. 2.Department of Computer Science and UPBSBThe University of Tokyo 
  3. 3.Japan Science and Technology Agency-CREST 
  4. 4.Dept. of Computational Intelligence and Systems ScienceTokyo Institute of Technology 

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