Construction of a suppressor logic toolkit and its use in a bacterial quasi hash function
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Construction of a Suppressor Logic Toolkit and its use in a Bacterial Quasi-Hash Function. iGEM 2008 Finisher Team Bob Cool, Kin Lau, Xiao Zhu. Goals for 2009 Summer Project. Build tRNA suppressor logic gate tool kit with AND, NAND, OR, and NOR logic gate functions

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Construction of a suppressor logic toolkit and its use in a bacterial quasi hash function

Construction of a Suppressor Logic Toolkit and its use in a Bacterial Quasi-Hash Function

iGEM 2008 Finisher Team

Bob Cool, Kin Lau, Xiao Zhu


Goals for 2009 summer project
Goals for 2009 Summer Project Bacterial Quasi-Hash Function

  • Build tRNA suppressor logic gate tool kit with AND, NAND, OR, and NOR logic gate functions

    • AND gate is same basic design as in Anderson 2007, but with different parts, including 5-base frameshift suppressor instead of termination suppressor

    • NAND, OR, and NOR gates are new designs

  • Use the logic gates to construct two distinct quasi-hash functions using cell-to-cell signaling and time-delayed growth


Suppressor logic toolkit

Suppressor Logic Toolkit Bacterial Quasi-Hash Function

Basic design, no specific inputs or outputs


And gate using ssl
AND Gate Using SSL Bacterial Quasi-Hash Function

PoPS Input A

Frameshift Suppressor tRNA

PoPS Output

AGGA

OFF to ON

PoPS Input B

Activator

Note: This design was used by Anderson et al. (2007) with a termination suppressor tRNA


Nand gate using ssl
NAND Gate Using SSL Bacterial Quasi-Hash Function

PoPS Input A

Frameshift Suppressor tRNA

PoPS Output

AGGA

ON to OFF

PoPS Input B

Repressor


Or gate using ssl
OR Gate Using SSL Bacterial Quasi-Hash Function

GACC gg CGGA

PoPS Input A

Frameshift Suppressor 1

Activator

PoPS Output

OFF to ON

Frameshift Suppressor 2

PoPS Input B


Nor gate using ssl
NOR Gate Using SSL Bacterial Quasi-Hash Function

GACC gg CGGA

PoPS Input A

Frameshift Suppressor !

Repressor

PoPS Output

OFF to ON

Frameshift Suppressor 2

PoPS Input B


Construction of a suppressor logic toolkit and its use in a bacterial quasi hash function

Suppressor Logic Toolkit Bacterial Quasi-Hash Function

Specific inputs and outputs


Construction of a suppressor logic toolkit and its use in a bacterial quasi hash function

AND Gate Using SSL Bacterial Quasi-Hash Function

plac Input A

pluxT

IPTG

5 bp Frameshift Suppressor tRNA

LuxI Output

3OC6

AGCGA

OFF to ON

ptet Input B

aTc

Activator luxO

  • Other Genes Needed

  • LacI

  • TetR


Construction of a suppressor logic toolkit and its use in a bacterial quasi hash function

NAND Gate Using SSL Bacterial Quasi-Hash Function

pluxR Input A

5 bp Frameshift Suppressor tRNA

pcI

3OC6

GFP Output

AGGA

ON to OFF

pPrpB Input B

Repressor cI

Propionate

  • Other Genes Needed

  • LuxR

  • PrpR


Or gate using ssl1
OR Gate Using SSL Bacterial Quasi-Hash Function

GACC gg CGGA

plac Input A

5 bp Frameshift Suppressor 1

pluxT

IPTG

Activator luxO

luxI Output

OFF to ON

5 bp Frameshift Suppressor 2

ptet Input B

aTc

  • Other Genes Needed

  • LacI

  • TetR


Nor gate using ssl1
NOR Gate Using SSL Bacterial Quasi-Hash Function

GACC gg CGGA

pLuxR Input A

Frameshift Suppressor !

pcI

3OC6

Repressor cI

GFP Output

OFF to ON

Frameshift Suppressor 2

PprpB Input B

Propionate

  • Other Genes Needed

  • LuxR

  • PrpR


Construction of a suppressor logic toolkit and its use in a bacterial quasi hash function

Suppressor Logic Toolkit Bacterial Quasi-Hash Function

Experimental design


Construction of a suppressor logic toolkit and its use in a bacterial quasi hash function

Biological Quasi-Hash Function Bacterial Quasi-Hash Function

NAND

colony AmpS

message

Key

AND

colony AmpR

aTc

IPTG

3CO6

Growth

propionate

GFP

RFP

or

Hash Value


Construction of a suppressor logic toolkit and its use in a bacterial quasi hash function

Biological Quasi-Hash Function Bacterial Quasi-Hash Function

NOR

message

Key

OR

colony AmpR

aTc

IPTG

3CO6

Time-

delayed

growth

propionate

colony AmpS

GFP

RFP

or

Hash Value


References
References Bacterial Quasi-Hash Function

  • Anderson et al. 2007. “Environmental signal integration by a modular AND gate” http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1964800&blobtype=pdf

  • luxO luxT http://www.jbc.org/cgi/content/full/281/46/34775

  • PprpB propionate http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16269719