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A nanoscale programmable computing machine with input, output, software and hardware made of biomolecules Nature 414, 430-434 (2001) Kobi Benenson supervisor: Ehud Shapiro, Dept of Computer Science & Applied Math Acknowledgements: Ehud Keinan (Technion), Zvi Livneh (WIS), Tami Paz-Elizur (WIS), Rivka Adar (WIS), Aviv Regev (WIS), Irith Sagi (WIS), Ada Yonath (WIS)
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“Medicine in 2050: Doctor in a Cell” Programmable Computer Molecular Input Molecular Output
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Research goal: Design a simplest non-trivial molecular computing machine (two-state two-symbol finite automaton) that works on engineered inputs
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Finite automaton: an example An even number of b ’ s S0, a S0 S0, b S1 S1, a S1 S1, b S0 S1 S0 b a b a Two-states, two-symbols automaton
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Automaton 1 bab S0, a S0 S0, b S1 S1, a S1 S1, b S0 An even number of b ’ s S0
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Automaton 1 bab S0, a S0 S0, b S1 S1, a S1 S1, b S0 An even number of b ’ s S0 S0, b S1
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Automaton 1 ab S0, a S0 S0, b S1 S1, a S1 S1, b S0 An even number of b ’ s S1
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Automaton 1 ab S0, a S0 S0, b S1 S1, a S1 S1, b S0 An even number of b ’ s S1 S1, a S1
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Automaton 1 b S0, a S0 S0, b S1 S1, a S1 S1, b S0 An even number of b ’ s S1
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Automaton 1 b S0, a S0 S0, b S1 S1, a S1 S1, b S0 An even number of b ’ s S1 S1, b S0
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Automaton 1 S0, a S0 S0, b S1 S1, a S1 S1, b S0 An even number of b ’ s S0 The output
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Rationale for the molecular design
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b CGCAGC GCGTCG a CTGGCT GACCGA Rationale for the molecular design
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b CGCAGC GCGTCG a CTGGCT GACCGA CAGC GGCT S0, a Rationale for the molecular design S0, b
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b CGCAGC GCGTCG a CTGGCT GACCGA CAGC GGCT S0, aS0, b CGCAGC CG CTGGCT GA S1, aS1, b Rationale for the molecular design
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Transitions abt CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG S0, b Rationale for the molecular design
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S0, b S1 Transitions abt CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG S0, b Rationale for the molecular design
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Transitions bt CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG S1, a Rationale for the molecular design S0, b S1
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Transitions bt CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG S1, a Rationale for the molecular design S1, a S1
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Transitions t CGCAGCTGTCGC CGACAGCG S1, b Rationale for the molecular design
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S1, b S0 Transitions t CGCAGCTGTCGC CGACAGCG S1, b Rationale for the molecular design
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S1, b S0 Transitions TCGC S0, t Rationale for the molecular design
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Output: S0 Transitions TCGC S0, t Rationale for the molecular design
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Transition procedure: a concept abt CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG S0, b Rationale for the molecular design
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Transition procedure: a concept abt CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG S0, b GTCG 4 nt 8 nt S0, b -> S1 Rationale for the molecular design
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Transition procedure: a concept bt CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG GTCG 4 nt 8 nt S0, b -> S1 Rationale for the molecular design
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Transition procedure: a concept bt CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG S0, b -> S1 S1, a Rationale for the molecular design
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Transition procedure: a concept bt CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG S1, a -> S1 S1, a Rationale for the molecular design
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Transition procedure: a concept bt CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG S1, a -> S1 S1, a GACC 6 nt 10 nt Rationale for the molecular design
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Transition procedure: a concept t CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG S1, a -> S1 GACC 6 nt 10 nt Rationale for the molecular design
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Transition procedure: a concept t CGCAGCTGTCGC CGACAGCG S1, a -> S1 S1, b Rationale for the molecular design
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Transition procedure: a concept t CGCAGCTGTCGC CGACAGCG S1, b -> S0 S1, b GCGT 8 nt 12 nt Rationale for the molecular design
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Transition procedure: a concept CGCAGCTGTCGC CGACAGCG S1, b -> S0 GCGT 8 nt 12 nt Rationale for the molecular design
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Transition procedure: a concept TCGC Output: S0 S0, t Rationale for the molecular design
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In situ detection TCGC Output: S0 S0, t AGCG Detection molecule for S0 output Rationale for the molecular design
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In situ detection TCGC Output: S0 AGCG Reporter molecule for S0 output Rationale for the molecular design
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Inside the transition molecule S0,b -> S1 GTCG 4 nt 8 nt
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Inside the transition molecule S0,b -> S1 GTCG 4 nt 8 nt GGATGACGAC CCTACTGCTG FokI
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Inside the transition molecule S0,b -> S1 GTCG 4 nt 8 nt GGATGACGAC CCTACTGCTG 9 nt 13 nt FokI
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Inside the transition molecule S0,b -> S1 GTCG GGATGACGAC CCTACTGCTG 9 nt 13 nt FokI
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Inside the transition molecule S1,a -> S1 GACC 6 nt 10 nt
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Inside the transition molecule S1,a -> S1 GACC 6 nt 10 nt GGATGACG CCTACTGC 9 nt 13 nt FokI
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Inside the transition molecule S1,a -> S1 GACC GGATGACG CCTACTGC 9 nt 13 nt FokI
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Inside the transition molecule S1,b -> S0 GCGT 8 nt 12 nt
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Inside the transition molecule S1,b -> S0 GCGT 8 nt 12 nt GGATGG CCTACC 9 nt 13 nt FokI
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Inside the transition molecule S1,b -> S0 GCGT GGATGG CCTACC 9 nt 13 nt FokI
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Inside the transition molecule GACC GGATGACG CCTACTGC GTCG GGATGACGAC CCTACTGCTG GCGT GGATGG CCTACC S0 -> S1 S0 -> S0 S1 -> S1 S1 -> S0
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Transition rules: complete list
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Automata programs used to test the molecular implementation
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Transition molecules: complete list
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Input and detection molecules
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Experimental testing of automaton programs A1 – A6
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Computations over 6-symbol long input molecules
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Parallel computation
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Identification of the essential components
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Close inspection of the reaction intermediates
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An estimation of system fidelity
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Summary 10 12 automata run independently and in parallel on potentially distinct inputs in 120 l at room temperature at combined rate of 10 9 transitions per second with accuracy greater than 99.8% per transition, consuming less than 10 -10 Watt.
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