Intensive In Vitro Experiments of Implementing and Executing Finite Automata in Test Tube

  • Junna Kuramochi
  • Yasubumi Sakakibara
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3892)


We report our intensive in vitro experiments in which we have implemented and executed several finite-state automata in test tube. First, we employ the length-encoding technique proposed and presented in [4, 3] to implement finite automata in test tube. In the length-encoding method, the states and state transition functions of a target finite automaton are effectively encoded into DNA sequences, a computation (accepting) process of finite automata is accomplished by self-assembly of encoded complementary DNA strands, and the acceptance of an input string is determined by the detection of a completely hybridized double-strand DNA. Second, we design and develop practical laboratory protocols which combine several in vitro operations such as annealing, ligation, PCR, and streptavidin-biotin bonding to execute in vitro finite automata based on the length-encoding technique. We have carried laboratory experiments on various finite automata of from 2 states to 6 states for several input strings. To our knowledge, this is the first in vitro experiments that have succeeded to execute 6-states automaton in test tube.


Vitro Experiment Finite Automaton Input String State Transition Function Special Coordination Fund 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Junna Kuramochi
    • 1
  • Yasubumi Sakakibara
    • 2
  1. 1.Softbank BB CorporationJapan
  2. 2.Department of Biosciences and InformaticsKeio UniversityYokohamaJapan

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