Transcript Slide 1
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