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)

“Medicine in 2050: Doctor in a Cell”

Programmable Computer

Molecular Input

Molecular Output

Research goal:

Design a simplest non-trivial molecular computing machine (two-state two-symbol finite automaton) that works on engineered inputs

Finite automaton: an example

An even number of b’s

S0, a S0S0, b S1S1, a S1S1, b S0

S1S0

b

a

b

a

Two-states, two-symbols automaton

Automaton 1

b a b

S0, a S0S0, b S1S1, a S1S1, b S0

An even number of b’s

S0

Automaton 1

b a b

S0, a S0S0, b S1S1, a S1S1, b S0

An even number of b’s

S0

S0, b S1

Automaton 1

a b

S0, a S0S0, b S1S1, a S1S1, b S0

An even number of b’s

S1

Automaton 1

a b

S0, a S0S0, b S1S1, a S1S1, b S0

An even number of b’s

S1

S1, a S1

Automaton 1

b

S0, a S0S0, b S1S1, a S1S1, b S0

An even number of b’s

S1

Automaton 1

b

S0, a S0S0, b S1S1, a S1S1, b S0

An even number of b’s

S1

S1, b S0

Automaton 1

S0, a S0S0, b S1S1, a S1S1, b S0

An even number of b’s

S0

The output

Rationale for the molecular design

bCGCAGCGCGTCGaCTGGCT

GACCGA

Rationale for the molecular design

bCGCAGCGCGTCGaCTGGCT

GACCGA

CAGC

GGCT

S0, a

Rationale for the molecular design

S0, b

bCGCAGCGCGTCGaCTGGCT

GACCGA

CAGC

GGCT

S0, a S0, b

CGCAGC CG

CTGGCT GA

S1, a S1, b

Rationale for the molecular design

TransitionsTransitions

a b t

CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG

S0, b

Rationale for the molecular design

S0, b S1

TransitionsTransitions

a b t

CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG

S0, b

Rationale for the molecular design

TransitionsTransitions

b t

CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG

S1, a

Rationale for the molecular design

S0, b S1

TransitionsTransitions

b t

CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG

S1, a

Rationale for the molecular design

S1, a S1

S1, a S1

TransitionsTransitions

t

CGCAGCTGTCGC CGACAGCG

S1, b

Rationale for the molecular design

S1, b S0

TransitionsTransitions

t

CGCAGCTGTCGC CGACAGCG

S1, b

Rationale for the molecular design

S1, b S0

TransitionsTransitions

TCGC

S0, t

Rationale for the molecular design

Output: S0

TransitionsTransitions

TCGC

S0, t

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

a b t

CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG

S0, b

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

a b t

CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG

S0, b

GTCG

4 nt

8 nt

S0, b -> S1

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

b t

CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCGGTCG

4 nt

8 nt

S0, b -> S1

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

b t

CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG

S0, b -> S1

S1, a

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

b t

CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG

S1, a -> S1

S1, a

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

b t

CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG

S1, a -> S1

S1, a

GACC

6 nt

10 nt

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

t

CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG

S1, a -> S1

GACC

6 nt

10 nt

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

t

CGCAGCTGTCGC CGACAGCG

S1, a -> S1

S1, b

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

t

CGCAGCTGTCGC CGACAGCG

S1, b -> S0

S1, b

GCGT

8 nt

12 nt

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

CGCAGCTGTCGC CGACAGCG

S1, b -> S0

GCGT

8 nt

12 nt

Rationale for the molecular design

Transition procedure: a conceptTransition procedure: a concept

TCGC

Output: S0

S0, t

Rationale for the molecular design

In situIn situ detection detection

TCGC

Output: S0

S0, t

AGCG

Detection moleculefor S0 output

Rationale for the molecular design

In situIn situ detection detection

TCGC

Output: S0

AGCGReporter moleculefor S0 output

Rationale for the molecular design

Inside the transition molecule

S0,b -> S1

GTCG

4 nt

8 nt

Inside the transition molecule

S0,b -> S1

GTCG

4 nt

8 nt

GGATGACGACCCTACTGCTG

FokI

Inside the transition molecule

S0,b -> S1

GTCG

4 nt

8 nt

GGATGACGACCCTACTGCTG

9 nt

13 nt

FokI

Inside the transition molecule

S0,b -> S1

GTCGGGATGACGACCCTACTGCTG

9 nt

13 nt

FokI

Inside the transition molecule

S1,a -> S1

GACC

6 nt

10 nt

Inside the transition molecule

S1,a -> S1

GACC

6 nt

10 nt

GGATGACG CCTACTGC

9 nt

13 nt

FokI

Inside the transition molecule

S1,a -> S1

GACC GGATGACG CCTACTGC

9 nt

13 nt

FokI

Inside the transition molecule

S1,b -> S0

GCGT

8 nt

12 nt

Inside the transition molecule

S1,b -> S0

GCGT

8 nt

12 nt

GGATGG CCTACC

9 nt

13 nt

FokI

Inside the transition molecule

S1,b -> S0

GCGT GGATGG CCTACC

9 nt

13 nt

FokI

Inside the transition molecule

GACC GGATGACG CCTACTGC

GTCGGGATGACGACCCTACTGCTG

GCGT GGATGG CCTACC

S0 -> S1

S0 -> S0

S1 -> S1

S1 -> S0

Transition rules: complete list

S0 S1

a a

b

A2: at most one b

b

A6: no a after b

S0 S1

a b

S0 S1

a

b

a

A4: no two consecutive b’s

S0

a

A5: only a’s

S0 S1

a a

b b

A3: at least one b

S0 S1

b a

a b

A7: starts with a and ends with b

Automata programs used to test the molecular implementation

Transition molecules: complete list

Input and detection molecules

Experimental testing of automaton programs A1 – A6

Computations over 6-symbol long input molecules

Parallel computation

Identification of the essential components

Close inspection of the reaction intermediates

An estimation of system fidelity

Summary

• 1012 automata run independently and in parallel

• on potentially distinct inputs

• in 120 l

• at room temperature

• at combined rate of 109 transitions per second

• with accuracy greater than 99.8% per transition,

• consuming less than 10-10 Watt.