Chain Reaction Systems Based on Loop Dissociation of DNA

  • Keiichiro Takahashi
  • Satsuki Yaegashi
  • Atsushi Kameda
  • Masami Hagiya
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3892)


In the field of DNA computing, more and more efforts are made for constructing molecular machines made of DNA that work in vitro or in vivo. States of some of those machines are represented by their conformations, such as hairpin and bulge loops, and state transitions are realized by conformational changes, in which such loops are opened. The ultimate goal of this study is to implement not only independent molecular machines, but also networks of interacting machines, called chain reaction systems, where a conformational change of one machine triggers a conformational change of another machine in a cascaded manner. A chain reaction system would result in a much larger computational power than a single machine in the number of states and in the complexity of computation. As a simple example, we propose a general-purpose molecular system consisting of logical gates and sensors. As a more complex example, we present a new idea of constructing a DNA automaton by a chain reaction system, which can have an arbitrary number of states.


Logical Gate Transition Rule Logical Circuit Molecular Machine Input Symbol 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Keiichiro Takahashi
    • 1
  • Satsuki Yaegashi
    • 2
  • Atsushi Kameda
    • 2
  • Masami Hagiya
    • 2
    • 3
  1. 1.NovusGene Inc.TokyoJapan
  2. 2.Japan Science and Technology Corporation (JST-CREST)Japan
  3. 3.Department of Computer Science, Graduate School of Information Science and, TechnologyUniversity of TokyoTokyoJapan

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