2. S, a rest a’ Basic cycle of automaton Iterative processing of input until the end is reached S, a S ’ Detect the result State-symbol tag S’, a’ rest

3. S0,101

4. S0,101 S0,0 FokI S0,1 FokI S1,0 FokI S1,1 FokI

5. S0,1 FokIS0,101 S0,0 FokI S1,0 FokI S1,1 FokI

6. FokI01

7. FokI1S1,0

8. 1S1,0

9. 1S1,0

10. Molecular realization of FA FA Alphabet: {0 = 5’- CTGGCT, 1 = 5’- CGCAGC } 1 = 5’- CGCAGC } States: {S0,S1} S0, 0  S0 S0, 1  S1 S1, 0  S1 S1, 1  S0 S0 S1 0 0 1 1 Transition Table:

11. The encoding for a, b, and terminator and the sticky ends

12. Transition molecules GGATGCCTAC NNNN Fok I (9/13) recognition site S0, 0  S0 S0, 1  S1 S1, 0  S1 S1, 1  S0 3 bp 5 bp 3 bp 1 bp CCGA GTCG GACC GCGT

13. pGGATGTAC GGTCCTACATGCCGAp 22 Fok I recognition site T1: S0  a S0 T2: S0  a S1 pGGATGACGAC GGTCCTACTGCTGCCGAp 22 T3: S0  b S0 T4: S0  b S1 pGGATGACG GGTCCTACTGCGTCGp 28 pGGATGACGAC GGTCCTACTGCTGGTCGp 15 T5: S1  a S0 T6: S1  a S1 pGGATGA GGTCCTACTGACCp 28 pGGATGACG GGTCCTACTGCGACCp 15 S0T7: S1  b T8: S1  b S1 pGGATGG GGTCCTACCGCGTp 21 pGGATGACG GGT CCTACTGCGCGTp 30 Structure of the transition molecules

18. Structure of an input molecule

19. Structure of the output-detection molecules

20. Animation of experiment

21. T110