A Genetic Differential Amplifier: Design, Simulation, Construction and Testing

1
A Genetic Differential Amplifier Design,
Simulation, Construction and Testing

• Seema Nagaraj and Stephen Davies
• University of Toronto
• Edward S. Rogers Sr. Department of Electrical and
  Computer Engineering
• Institute of Biomaterials and Biomedical
  Engineering

2
Engineered Genetic Circuits

• artificial networks of interacting DNA, mRNA and
  proteins
• behavior is analogous to electrical devices

3
Genetic Differential Amplifier

• differential amplifiers are fundamental
  components in many electronic circuits
• a genetic differential amplifier could be a
  building block for more complex genetic circuits

4
Electronic Differential Amplifier
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Amplifier Behaviour
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Gene Expression
gene
DNA
Promoter
7
Gene Expression
RNA Polymerase
gene
DNA
Promoter
8
Gene Expression
RNA Polymerase
gene
DNA
Promoter
mRNA
9
Gene Expression
RNA Polymerase
gene
DNA
Promoter
Ribosome
mRNA
10
Gene Expression
RNA Polymerase
gene
DNA
Promoter
Ribosome
mRNA
Protein
11
Gene Networks
12
Gene Networks
transcription factor (repressor)
13
Gene Networks
transcription factor (activator)
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Genetic Amplifier Topology
() activator
cI
Ptet
gfp
PRM -
(-) repressor
cro
Plac
15
Wild Type Promoter
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Double Mutation
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Implementation
Input
Amplifier
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Stochastic Modeling

• includes inputs and output
• system behaviour is described through reaction
  probabilities
• system behaviour is simulated using the Gillespie
  algorithm

19
Simulation Results(Low Copy Number)
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Simulation Results(High Copy Number)
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Experimental Results

• Construct HIGH and LOW copy number variants of
  the circuit
• Compare performance to simulated results

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Experimental ResultsHigh Copy Number
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Experimental ResultsLow Copy Number
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Conclusions

• Simulation
• low copy number amplifier based on double-mutant
  PRM yields ideal behaviour
• Experimental
• high copy number amplifier displays differential
  amplifier behaviour
• low copy number amplifier displays positive
  results

25
Acknowledgements

• Anja Lowrance
• Members of Davies Lab
• Rogers Scholarship