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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)
If the ssDNA forms a hairpin,
then it does not satisfy the
problem
tRNA and Frame Shift Mutations
• The genetic code is read in groups of three bases called
codons
• tRNA reads the codon and builds the protein by adding
the corresponding amino acid to the growing protein
chain
• Frame shift: an extra base of DNA is added that alters
the three letter codon
• A frame shift suppressor tRNA will read a four or five
base codon thus stopping the frame shift mutation
Supressor tRNA can Read
Through a Frame Shift Keeping
the Original Protein Sequence
Using SSL to solve 3SAT
• Logical clause example (a or b or –c)
• cag CCCG cc AAAT tt GGGC cag
• If read straight through there is a frame
shift
• Supp. a=CCCG, b=AAAT, and –c=GGGC
• If any one is present then the reading
frame will be preserved thus satisfying the
logical clause
SSL and 3SAT cont.
• At the level of translation of an individual
transcript this logical clause functions as a
XOR b XOR i
• Moving back in the levels of abstraction to
the entire cell, it functions as a OR b OR i
Choosing Inputs
Sa
Sg
Sb
Sh
Sf
Sl
We will use different suppressor tRNAs to act as all of the not values. -a
will be encoded as suppressor g and –b will be encoded as suppressor h
etc. We will use the hin hix system to allow the bacteria to choose its
inputs.
Model of the 3SAT in a Cell
The colonies will then try
to satisfy the problem with
their chosen inputs and
glow green if they do
PROS
CONS
• Addressing the 3SAT
math problem is the
foundation of the project
• Parallels a published
paper using a DNA in
vitro approach
• SSL logic has many
application beyond this
problem
• There are several stages
of completion
• SSL AND 3SAT ARE
COOL!
• Can a cell handle 12
supp. tRNAs?
• Timing of the suppression
events
• 2008 team also used
logic gates
• May not make a big
splash at iGEM