3-SAT Problem Sakamoto used hairpin formations in single stranded DNA (ssDNA) as a molecular...

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• 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.

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)

• 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.

ATG CCC GAC g

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

Supressor tRNA can Read Through a Frame Shift Keeping the Original

Protein Sequence

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

OR Gate Using SSL

UAG

Activator

UGA

Activator

PoPS Input A PoPS Input B PoPS Output

0 0 0

1 0 1

0 1 1

1 1 1

Amber Suppressor tRNA

Opal Suppressor tRNA

PoPS Input A

PoPS Input B

PoPS OutputOFF to

ON

NOR Gate Using SSL

PoPS Input A PoPS Input B PoPS Output

0 0 1

1 0 0

0 1 0

1 1 0

Amber Suppressor tRNA

Opal Suppressor tRNA

PoPS Input A

PoPS Input B

UAG

Repressor

UGA

Repressor

PoPS OutputON to

OFF

AND Gate Using SSL

PoPS Input A PoPS Input B PoPS Output

0 0 0

1 0 0

0 1 0

1 1 1

Amber Suppressor tRNA

Opal Suppressor tRNA

PoPS Input A

PoPS Input B

UAG

Activator

UGA

PoPS OutputOFF to

ON

NAND Gate Using SSL

PoPS Input A PoPS Input B PoPS Output

0 0 1

1 0 1

0 1 1

1 1 0

Amber Suppressor tRNA

Opal Suppressor tRNA

PoPS Input A

PoPS Input B

UAG

Repressor

UGA

PoPS OutputON to

OFF

XOR Gate Using SSL

PoPS Input A PoPS Input B PoPS Output

0 0 0

1 0 1

0 1 1

1 1 0

Amber Suppressor tRNA

Opal Suppressor tRNA

PoPS Input A

PoPS Input B

UAG

Repressor

UGA

UAG

Activator

PoPS Output

UGA

ActivatorON to OFF

OFF to ON

NXOR Gate Using SSL

PoPS Input A PoPS Input B PoPS Output

0 0 1

1 0 0

0 1 0

1 1 1

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

Choosing Inputs

Sa Sg Sb Sh Sf Sl

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.

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