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
  • 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

Basic design, no specific inputs or outputs

and gate using ssl
AND Gate Using SSL

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

PoPS Input A

Frameshift Suppressor tRNA

PoPS Output

AGGA

ON to OFF

PoPS Input B

Repressor

or gate using ssl
OR Gate Using SSL

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

GACC gg CGGA

PoPS Input A

Frameshift Suppressor !

Repressor

PoPS Output

OFF to ON

Frameshift Suppressor 2

PoPS Input B

slide8

Suppressor Logic Toolkit

Specific inputs and outputs

slide9

AND Gate Using SSL

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
slide10

NAND Gate Using SSL

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

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

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
slide13

Suppressor Logic Toolkit

Experimental design

slide14

Biological Quasi-Hash Function

NAND

colony AmpS

message

Key

AND

colony AmpR

aTc

IPTG

3CO6

Growth

propionate

GFP

RFP

or

Hash Value

slide15

Biological 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
  • 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
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