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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-SAT Problem. 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)

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3-SAT Problem

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  1. 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-SAT Problem

  2. 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) 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 (SA or SB or SC), (SC or SD or S-E)… In DNA sequence.

  3. 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.

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

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

  6. 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

  7. OR Gate Using SSL PoPS Input A Amber Suppressor tRNA PoPS Output UAG UGA OFF to ON Opal Suppressor tRNA PoPS Input B Activator Activator

  8. NOR Gate Using SSL PoPS Input A Amber Suppressor tRNA PoPS Output UAG UGA ON to OFF Opal Suppressor tRNA PoPS Input B Repressor Repressor

  9. AND Gate Using SSL PoPS Input A UAG Amber Suppressor tRNA UGA PoPS Output Activator OFF to ON Opal Suppressor tRNA PoPS Input B

  10. NAND Gate Using SSL UAG PoPS Input A Amber Suppressor tRNA UGA PoPS Output Repressor ON to OFF Opal Suppressor tRNA PoPS Input B

  11. XOR Gate Using SSL OFF to ON PoPS Output UAG PoPS Input A Amber Suppressor tRNA UGA UAG UGA Repressor Opal Suppressor tRNA PoPS Input B Activator Activator ON to OFF

  12. NXOR Gate Using SSL ON to OFF PoPS Output PoPS Input A UAG Amber Suppressor tRNA UGA UAG UGA Repressor Opal Suppressor tRNA PoPS Input B Repressor Repressor ON to OFF

  13. Choosing Inputs Sh Sg Sl Sb Sa Sf 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.

  14. 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

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