Introduction to Synthetic
Biology
Dannenberg and Purdy 2012
(Tokos edits 2012)
What is Synthetic Biology?
• https://www.youtube.com/watch?v=rD5uN
AMbDaQ
ELECTRICAL engineering solution
MECHANICAL engineering solution
water = weight
water<weight
BIOLOGICAL engineering solution
BIOLOGICAL engineering solution
Genetic Engineering
rDNA
Sequencing
PCR
A LIVING HOUSE Terreform’s Fab
Tree Hab
• How is Synthetic Biology Different?
Synthetic biology uses four principles
not typically found in genetics,
genomics, or molecular biology:
abstraction, modularity, standardization,
and design and modeling.
Abstraction:
• Abstraction - you can use
parts/devices/systems without having to
worry about how they work.
• DNA
makes parts.
• Parts
into devices.
• Devices
connected to make
systems.
Modularity:
• parts, devices and systems connected as self-contained units and
combined in any combination you want
Standardization:
• All the “Tab A’s” fit into all the “Slot
B’s.”
• An everyday example - all light bulbs fit
into any socket!
Designing and modeling
• build a model
• test the devices capacity
– improves design
– tests basic biological assumptions that
could be false
Registry of Standard biological
Parts
• http://partsregistry.org/Main_Page
DNA is DNA
• E. Coli is our chassis
– Can use parts from any organism
– Can use parts made by a computer
Abstraction Hierarchy
a human invention designed to assist
people in engineering complex systems
Assemblies of devices
make a system
Assemblies of parts
make up devices
Sequences of DNA
encode “parts”
“Part” – sequence of DNA with human
defined function
AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGT
TATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCA
GGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGT
TTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGC
AGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGG
CTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGA
AGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGT
TTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC
Parts assembled into Devices
AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGT
TATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCA
GGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGT
TTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGC
AGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGG
CTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGA
AGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGT
TTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC
Parts assembled into Devices
AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGT
TATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCA
GGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGT
TTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGC
AGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGG
CTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGA
AGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGT
TTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC
Device to System
Plasmids and Transformation
Now for the Good Part
(2009 Cambridge iGEM Team)
The Problem
• Toxins contaminate the environment
• Detection can be expensive and
complicated
• Can cheap bacteria be used as toxin
indicators that change color in response
to toxin levels?
The Color-Generating Device
• Contain violacein pigment devices
(ORF from Chromobacterium violacein)
Genes re-engineered to produce purple and green in E.
Coli
• If all 5 genes in the ORF are expressed - purple
pigment produced
• If third gene in ORF sequence is removed - green
pigment produced
The Chassis
• To a Synthetic Biologist
=
Escherichia coli
Bacterial transformation of
Escherichia coli
• Two different strains of E. coli (4-1 & 4-2)
• Two different plasmids (pPRL & pGRN)
• Can we expect the devices to behave the same in each
strain, or will the chassis have an effect on the intensity
of color produced?
Creation of a Bacterial Cell Controlled
by a Chemically Synthesized Genome
Dan Gibson, +21, Ham Smith and Craig Venter
Science (2010) 329: 52
M. mycoides
genome
transplanted to
M. capricolum
PCR for watermarks
Creation of a Bacterial Cell Controlled
by a Chemically Synthesized Genome
Dan Gibson, +21, Ham Smith and Craig Venter
Science (2010) 329: 52
Presidential Commission
for the Study of Bioethical Issues
New Directions: The Ethics of Synthetic
Biology and Emerging Technologies
December 2010