Difference between revisions of "Suppressor Logic Toolkit and Quasi-Hash Function"
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atgTCTCTAC ACTCTCCAGG TAAAGCGTTT CGCGCTGCAC TGACTAAAGA AAATCCATTG | atgTCTCTAC ACTCTCCAGG TAAAGCGTTT CGCGCTGCAC TGACTAAAGA AAATCCATTG | ||
+ | |||
CAGATTGTTG GCACCATCAA CGCTAATCAT GCGCTGTTGG CGCAGCGTGC CGGATATCAG | CAGATTGTTG GCACCATCAA CGCTAATCAT GCGCTGTTGG CGCAGCGTGC CGGATATCAG | ||
+ | |||
GCAATTTATC TTTCTGGCGG TGGCGTGGCG GCAGGTTCGC TGGGGCTGCC CGATCTCGGT | GCAATTTATC TTTCTGGCGG TGGCGTGGCG GCAGGTTCGC TGGGGCTGCC CGATCTCGGT | ||
+ | |||
ATTTCTACCC TTGATGATGT GCTGACCGAC ATTCGCCGTA TCACCGACGT TTGTTCGCTG | ATTTCTACCC TTGATGATGT GCTGACCGAC ATTCGCCGTA TCACCGACGT TTGTTCGCTG | ||
+ | |||
CCGCTGCTGG TGGATGCGGA TATCGGTTTT GGTTCTTCGG CCTTTAACGT GGCGCGCACC | CCGCTGCTGG TGGATGCGGA TATCGGTTTT GGTTCTTCGG CCTTTAACGT GGCGCGCACC | ||
+ | |||
GTGAAATCGA TGATTAAAGC CGGTGCGGCA GGATTGCATA TTGAAGATCA GGTTGGTGCG | GTGAAATCGA TGATTAAAGC CGGTGCGGCA GGATTGCATA TTGAAGATCA GGTTGGTGCG | ||
+ | |||
AAACGCTGCG GTCATCGTCC GAATAAAGCG ATCGTCTCGA AAGAAGAGAT GGTGGATCGG | AAACGCTGCG GTCATCGTCC GAATAAAGCG ATCGTCTCGA AAGAAGAGAT GGTGGATCGG | ||
+ | |||
ATCCGCGCGG CGGTGGATGC GAAAACCGAT CCTGATTTTG TGATCATGGC GCGCACCGAT | ATCCGCGCGG CGGTGGATGC GAAAACCGAT CCTGATTTTG TGATCATGGC GCGCACCGAT | ||
+ | |||
GCTCTGGCGG TAGAGGGGCT GGATGCGGCG ATCGAGCGTG CGCAGGCCTA TGTTGAAGCG | GCTCTGGCGG TAGAGGGGCT GGATGCGGCG ATCGAGCGTG CGCAGGCCTA TGTTGAAGCG | ||
+ | |||
GGTGCCGAGA TGTTGTTCCC GGAGGCGATT ACCGAACTCG CCATGTACCG CCAGTTTGCC | GGTGCCGAGA TGTTGTTCCC GGAGGCGATT ACCGAACTCG CCATGTACCG CCAGTTTGCC | ||
+ | |||
GATGCGGTGC AGGTGCCGAT CCTCGCCAAC ATCACCGAAT TTGGTGCCAC GCCGCTGTTT | GATGCGGTGC AGGTGCCGAT CCTCGCCAAC ATCACCGAAT TTGGTGCCAC GCCGCTGTTT | ||
+ | |||
ACCACCGACG AATTACGCAG CGCCCATGTC GCAATGGCGC TGTACCCACT TTCAGCGTTC | ACCACCGACG AATTACGCAG CGCCCATGTC GCAATGGCGC TGTACCCACT TTCAGCGTTC | ||
+ | |||
CGCGCCATGA ACCGCGCCGC TGAACATGTC TACAACGTCC TGCGCCAGGA AGGCACGCAG | CGCGCCATGA ACCGCGCCGC TGAACATGTC TACAACGTCC TGCGCCAGGA AGGCACGCAG | ||
+ | |||
AAAAGCGTCA TCGACACCAT GCAGACCCGC AACGAGCTGT ACGAAAGCAT CAACTACTAC | AAAAGCGTCA TCGACACCAT GCAGACCCGC AACGAGCTGT ACGAAAGCAT CAACTACTAC | ||
+ | |||
CAGTACGAAG AGAAGCTCGA CAACCTGTTT GCCCGTAGCC AGGTGAAATA A | CAGTACGAAG AGAAGCTCGA CAACCTGTTT GCCCGTAGCC AGGTGAAATA A | ||
Line 101: | Line 115: | ||
http://gcat.davidson.edu/GcatWiki/images/e/e3/LuxT_upstream.JPG | http://gcat.davidson.edu/GcatWiki/images/e/e3/LuxT_upstream.JPG | ||
− | (pLuxT | + | (pLuxT text version) |
+ | |||
+ | agcgagcagt gagctcagtg gagtcatcag ttaaatctgt agtgttgtat tccacatttt | ||
+ | |||
+ | cgtttactgc tttcgccagc tctagatact tggcaaattc cgcttgtagc aattcttttg | ||
+ | |||
+ | aaccagcgta aatcgtcacg tctgcaacgt catcgccttc tttgatgata aagccaattt | ||
+ | |||
+ | caccagcgca accacacgct tcacatactt gggtttcttc gtgttcaatg ctcataacga | ||
+ | |||
+ | atcctcactt aaaaaaggga ttatactcaa ctcgtttttt tttcaataga aataaatgga | ||
+ | |||
+ | acaacttgga taaaaaaata tcggtatgct atgttgtttg ttgagagggt taagcaagag | ||
+ | |||
+ | ataactttag attttgttaa tggacgatgt gatccgagtc aataatttac cggatttcac | ||
+ | |||
+ | cttttactta cttagttatc acagtgagtg agttgcacct agcaagattt tataagagta | ||
+ | |||
+ | tctcgagata aattattttt acataatcta tcgctatcaa tcggttcaaa atgcagatgt | ||
+ | |||
+ | aaatattaaa ctaatgtcat ttaatggtat taatttagtt gcatattctg aaattttgtt | ||
+ | |||
+ | ttgcttgaag acatgcatct gcaaacctgg tttacagtat ttcgtaataa aaagtaggct | ||
+ | |||
+ | tgtttatttc gaaaaagggt gttttctggc aacctattga gaacgatttt cattctgacc | ||
+ | |||
+ | tcagactttg agttagatgg atttacaaag agaagagcta aaatatgcca aagcgtagta | ||
+ | |||
+ | aagaagatac cgaaatcact atccagaaaa ttatggatgc cgttgttgat cagttgctta | ||
+ | |||
+ | ggctcggtta cgacaaaatg tcgtacacga cgttgagtca acagacaggt gtttcacgta | ||
+ | |||
'''frame shift suppressor 1''' CU'''GUCCU'''AA | '''frame shift suppressor 1''' CU'''GUCCU'''AA |
Revision as of 15:10, 22 May 2009
Contents
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 text version)
agcgagcagt gagctcagtg gagtcatcag ttaaatctgt agtgttgtat tccacatttt
cgtttactgc tttcgccagc tctagatact tggcaaattc cgcttgtagc aattcttttg
aaccagcgta aatcgtcacg tctgcaacgt catcgccttc tttgatgata aagccaattt
caccagcgca accacacgct tcacatactt gggtttcttc gtgttcaatg ctcataacga
atcctcactt aaaaaaggga ttatactcaa ctcgtttttt tttcaataga aataaatgga
acaacttgga taaaaaaata tcggtatgct atgttgtttg ttgagagggt taagcaagag
ataactttag attttgttaa tggacgatgt gatccgagtc aataatttac cggatttcac
cttttactta cttagttatc acagtgagtg agttgcacct agcaagattt tataagagta
tctcgagata aattattttt acataatcta tcgctatcaa tcggttcaaa atgcagatgt
aaatattaaa ctaatgtcat ttaatggtat taatttagtt gcatattctg aaattttgtt
ttgcttgaag acatgcatct gcaaacctgg tttacagtat ttcgtaataa aaagtaggct
tgtttatttc gaaaaagggt gttttctggc aacctattga gaacgatttt cattctgacc
tcagactttg agttagatgg atttacaaag agaagagcta aaatatgcca aagcgtagta
aagaagatac cgaaatcact atccagaaaa ttatggatgc cgttgttgat cagttgctta
ggctcggtta cgacaaaatg tcgtacacga cgttgagtca acagacaggt gtttcacgta
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]