O09_02

Experimental validation of a modified Whiplash PCR for profiling temporal and coexistence patterns of nucleic acids

Ken KOMIYA *, Chizuru NODA

Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC)
( * E-mail: komiyak@jamstec.go.jp )

Molecular pattern classification by molecular reaction is of great interest both for biological and medical applications and for basic molecular systems science. Whiplash PCR (WPCR) is a unique molecular reaction system, which implements state machines through repeated DNA extension by DNA polymerase. In WPCR, each state machine executes successive state transitions according to a set of transition rules encoded with a single DNA molecule. Parallel operation of a vast number of state machines, that is MIMD (multiple-instruction multiple-data) computation, can be performed in a single reaction tube [1]. Displacement-WPCR (D-WPCR), in which each transition step is driven by primer binding and extension, was then proposed to overcome the drawbacks of low reaction efficiency and high temperature condition over 80°C [2]. However, as only two rounds of state transitions have been reported so far [3], its feasibility and usefulness has not yet been explored. In this presentation, we will report the experimental optimization of the reaction conditions and propose the design for allowing the use of genetic sequences toward biological applications. We will also discuss the challenges and prospects of D-WPCR.

[1] Komiya, K.; Sakamoto, K.; Kameda, A.; Yamamoto, M.; Ohuchi, A.; Kiga, D.; Yokoyama, S.; Hagiya M. DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing, BioSystems, 2006, 83, 18–25.
[2] Rose, J.A.; Komiya, K.; Yaegashi, S.; Hagiya, M. Displacement Whiplash PCR: Optimized architecture and experimental validation, Lecture Notes in Computer Science, 2006, 4287, 393–403.
[3] Komiya, K.; Yamamura, M.; Rose, J.A. Experimental Validation and Optimization of Signal Dependent Operation in Whiplash PCR, Natural Computing, 2010, 9, 207–218.