| Abstract
| - A biomolecular, programmable 3-symbol-3-state finite automaton is reported. This automatoncomputes autonomously with all of its components, including hardware, software, input, and output beingbiomolecules mixed together in solution. The hardware consisted of two enzymes: an endonuclease, BbvI,and T4 DNA ligase. The software (transition rules represented by transition molecules) and the input weredouble-stranded (ds) DNA oligomers. Computation was carried out by autonomous processing of the inputmolecules via repetitive cycles of restriction, hybridization, and ligation reactions to produce a final-stateoutput in the form of a dsDNA molecule. The 3-symbol-3-state deterministic automaton is an extension ofthe 2-symbol-2-state automaton previously reported, and theoretically it can be further expanded to a 37-symbol-3-state automaton. The applicability of this design was further amplified by employing surface-anchored input molecules, using the surface plasmon resonance technology to monitor the computationsteps in real time. Computation was performed by alternating the feed solutions between endonucleaseand a solution containing the ligase, ATP, and appropriate transition molecules. The output detection involvedfinal ligation with one of three soluble detection molecules. Parallel computation and stepwise detectionwere carried out automatically with a Biacore chip that was loaded with four different inputs.
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