Suppressor Logic Toolkit and Quasi-Hash Function

Suppressor Logic Toolkit and Quasi-Hash Function

The following slides describe the basic toolkit design and a specific experiment that would result in a quasi-hash function

Basic Toolkit Design

The AND gate was designed by Anderson using termination suppressors, while the new design would use frame shift suppressors.

Toolkit with Specific Inputs and Outputs

PprpB/propionate and luxO/pluxT are new communication players that would need to be looked into further to verify their usefulness.

See references at bottom of page.

Experimental Design

Parts Needed

Parts from Registry

Promoters

pR R00512009 Kit Plate 1 6K pSB1A2

pLacIQ1 K091112MWSU

pTetR R00402009 Kit Plate 1 6I pSB1A2

pLuxR R00622009 Kit Plate 1 6O pSB1A2

pMnt R00732009 Kit Plate 1 16B pSB2K3

Genes

RBS+lamba cI+TT P04512009 Kit Plate 2 1N pSB1AK3

pBAD+RBS+LacI+TT S03980MWSU

pBAD+RBS+tetR+TT K091145MWSU

pBAD+RBS+luxR+TT K091179MWSU

RBS(B0030)+GFP E55002007 Parts Kit Plate 1 9J pSB1A2

RBS(B0034)+RFP MWSU

Mnt C00722009 Kit Plate 1 12L pSB2K3

LuxO-P K1310222009 Kit Plate 3 8K pSB1AC3

Parts that need modified

LuxO-P K1310222009 Kit Plate 3 8K pSB1AC3

RBS+lamba cI+TT P04512009 Kit Plate 2 1N pSB1AK3

Parts needed to be built from scratch

prpBp Ecocyc

(prpBp text version)

tgaaattaaa catttaattt tattaaggca attgtggcac accccttgct ttgtctttat caacgcaaat aacaagttga taaca

http://gcat.davidson.edu/GcatWiki/images/2/2f/PrpBp.JPG

prpB 2-methylisocitrate lyase in E.coli MG1655 [1]http://gcat.davidson.edu/GcatWiki/images/6/6c/PrpB.JPG

(prpB text version)

atgTCTCTAC ACTCTCCAGG TAAAGCGTTT CGCGCTGCAC TGACTAAAGA AAATCCATTG CAGATTGTTG GCACCATCAA CGCTAATCAT GCGCTGTTGG CGCAGCGTGC CGGATATCAG GCAATTTATC TTTCTGGCGG TGGCGTGGCG GCAGGTTCGC TGGGGCTGCC CGATCTCGGT ATTTCTACCC TTGATGATGT GCTGACCGAC ATTCGCCGTA TCACCGACGT TTGTTCGCTG CCGCTGCTGG TGGATGCGGA TATCGGTTTT GGTTCTTCGG CCTTTAACGT GGCGCGCACC GTGAAATCGA TGATTAAAGC CGGTGCGGCA GGATTGCATA TTGAAGATCA GGTTGGTGCG AAACGCTGCG GTCATCGTCC GAATAAAGCG ATCGTCTCGA AAGAAGAGAT GGTGGATCGG ATCCGCGCGG CGGTGGATGC GAAAACCGAT CCTGATTTTG TGATCATGGC GCGCACCGAT GCTCTGGCGG TAGAGGGGCT GGATGCGGCG ATCGAGCGTG CGCAGGCCTA TGTTGAAGCG GGTGCCGAGA TGTTGTTCCC GGAGGCGATT ACCGAACTCG CCATGTACCG CCAGTTTGCC GATGCGGTGC AGGTGCCGAT CCTCGCCAAC ATCACCGAAT TTGGTGCCAC GCCGCTGTTT ACCACCGACG AATTACGCAG CGCCCATGTC GCAATGGCGC TGTACCCACT TTCAGCGTTC CGCGCCATGA ACCGCGCCGC TGAACATGTC TACAACGTCC TGCGCCAGGA AGGCACGCAG AAAAGCGTCA TCGACACCAT GCAGACCCGC AACGAGCTGT ACGAAAGCAT CAACTACTAC CAGTACGAAG AGAAGCTCGA CAACCTGTTT GCCCGTAGCC AGGTGAAATA A

pLuxT [2] http://gcat.davidson.edu/GcatWiki/images/e/e3/LuxT_upstream.JPG

(pLuxT no text version yet)

frame shift suppressor 1 CUGUCCUAA

frame shift suppressor 2 UUACUAGAC

prpBp and prpB have no EcoR1, Xba1, Spe1, or Pst1 sites. Source www.neb.com

References

Powerpoint File:Suppressorlogic3.ppt

Anderson et al. 2007. “Environmental signal integration by a modular AND gate” [3]

luxO luxT [4]

PprpB propionate [5]