Natural Computing

, Volume 9, Issue 1, pp 207–218 | Cite as

Experimental validation and optimization of signal dependent operation in whiplash PCR

  • Ken Komiya
  • Masayuki Yamamura
  • John A. Rose


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. In addition, the effect of the 5′-terminal stopper sequence and the competency of DNA polymerases for the rule-protect operation are evaluated. 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.


DNA computing DNA hairpin formation DNA polymerase Strand displacement Whiplash PCR 



Financial support for this work was generously provided by a Grant-in-Aid for Scientific Research B (18300100), from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  1. 1.Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and EngineeringTokyo Institute of TechnologyYokohamaJapan
  2. 2.Institute of Information Communication TechnologyRitsumeikan Asia Pacific UniversityBeppuJapan

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