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 SaSa SgSg SbSb ShSh SfSf SlSl 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 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! CONS 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