Experimental validation and optimization of signal dependent operation in whiplash PCR

Authors:
Ken Komiya;Masayuki Yamamura;John A. Rose
Affiliations:
Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan;Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan;Institute of Information Communication Technology, Ritsumeikan Asia Pacific University, Beppu, Japan
Venue:
Natural Computing: an international journal
Year:
2010

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Abstract

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驴-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.