3-sat problem sakamoto used hairpin formations in single stranded dna (ssdna) as a molecular...
TRANSCRIPT
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