2. 3-SAT Problem Sakamoto used hairpin formations in single stranded DNA (ssDNA) as a molecular computer. The formation of a hairpin shows that the problem was not satisfied.

3. 3-SAT Problem 6 Inputs- A,B,C,D,E,F 10 Clauses- ex. (A or B or C), (C or D or -E)… – Expressed as (S A or S B or S C ), (S C or S D or S -E )… In DNA sequence. 10 Clause 3-SAT Problem used by Sakamoto et al. (a or c or d) (a or b or –c) (a or –c or –d) (-a or –c or d) (a or –c or e) (a or d or –f) (-a or c or d) (a or c or –d) (-a or c or –d) (-a or –c or –d)

4. A frameshift is a genetic mutation caused by the addition or deletion of nucleotides. Since codons are read in a series of three, the addition or deletion of nucleotides will disrupt the reading frame. This disruption will most likely cause the production of a nonfunctional protein.

5. ATG CCC GAC g Enzyme A The suppressor tRNA allows the 4 letter sequence to be read as a single codon, therefore, keeping the protein on track. A frameshift occurs and, if nothing is done, enzyme A will not be made, meaning the clause will not be satisfied. Start

6. Supressor tRNA can Read Through a Frame Shift Keeping the Original Protein Sequence

7. Suppressor Suppressor Logic Based on Amber (UAG) and Opal (UGA) suppressor tRNAs PoPS inputs A or B control Amber or Opal suppressor production Repressors and/or activators control PoPS output Basic logic circuits produced

8. OR Gate Using SSL UAG Activator UGA Activator PoPS Input APoPS Input BPoPS Output 000 101 011 111 Amber Suppressor tRNA Opal Suppressor tRNA PoPS Input A PoPS Input B PoPS Output OFF to ON

9. NOR Gate Using SSL PoPS Input APoPS Input BPoPS Output 001 100 010 110 Amber Suppressor tRNA Opal Suppressor tRNA PoPS Input A PoPS Input B UAG Repressor UGA Repressor PoPS Output ON to OFF

10. AND Gate Using SSL PoPS Input APoPS Input BPoPS Output 000 100 010 111 Amber Suppressor tRNA Opal Suppressor tRNA PoPS Input A PoPS Input B UAG Activator UGA PoPS Output OFF to ON

11. NAND Gate Using SSL PoPS Input APoPS Input BPoPS Output 001 101 011 110 Amber Suppressor tRNA Opal Suppressor tRNA PoPS Input A PoPS Input B UAG Repressor UGA PoPS Output ON to OFF

12. XOR Gate Using SSL PoPS Input APoPS Input BPoPS Output 000 101 011 110 Amber Suppressor tRNA Opal Suppressor tRNA PoPS Input A PoPS Input B UAG Repressor UGA UAG Activator PoPS Output UGA Activator ON to OFF OFF to ON

13. NXOR Gate Using SSL PoPS Input APoPS Input BPoPS Output 001 100 010 111 Amber Suppressor tRNA Opal Suppressor tRNA PoPS Input A PoPS Input B UAG Repressor UGA UAG Repressor PoPS Output UGA Repressor ON to OFF ON to OFF

14. Choosing Inputs SaSa SgSg SbSb ShSh SfSf SlSl The triangles are hix sites for hin recombination. If the first activator is the correct one then it will activate a repressor that shuts off the hin and, therefore, stops the recombination from happening. Then it will move on to the next activator. Only forward activators are expressed.

15. SSL and 3-SAT This slide shows that if all ten logical clauses are satisfied green fluorescent protein (or any other protein you might want) is made