Experimental Validation of Signal Dependent Operation in Whiplash PCR

  • Ken Komiya
  • Masayuki Yamamura
  • John A. Rose
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5347)


Whiplash PCR (WPCR), which implements self-directed operation, programmed within a single DNA molecule, is a potential candidate for both mathematical and biological applications. However, WPCR-based methods are known to suffer from a serious efficiency problem called back-hybridization (BH). Previously, we proposed and partially validated a new rule-protect operation to abolish BH. In this work, we experimentally demonstrate the ability of rule-protect to drive multi-step WPCR. Successful implementation of isothermal operation at physiological temperatures is an essential benchmark for biological applications. We also propose the use of rule-protect for external signalling to control computational operation. Consequently, signal-dependent self-directed operation, which is conceptually new to DNA computing, is achieved. The present architecture, provided with sensing ability, allows a composite system design layering computational reactions, and would be suitable for functioning as the central processing unit of this system.


Central Processing Unit Transition Rule Hairpin Structure Strand Displacement Sensory Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Ken Komiya
    • 1
  • Masayuki Yamamura
    • 1
  • John A. Rose
    • 2
  1. 1.Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and EngineeringTokyo Institute of TechnologyJapan
  2. 2.Institute of Information Communication TechnologyRitsumeikan Asia Pacific UniversityJapan

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