Adventures in Synthetic Biology (comic by Drew Endy)
http://mit.edu/endy/www/scraps/comic/AiSB.vol1.pdf
How is synthetic biology different
than genetic engineering?
How is synthetic biology different
than genetic engineering?
“The ambition to formalize the process of designing cellular systems,
in the way that traditional engineering disciplines have formalized design
and manufacture, so that complex behaviors can be achieved for
practical ends.” –Arkin and Fletcher 2006
The addition of three foundational technologies:
1. DNA synthesis
2. Abstraction
3. Standards
http://www.youtube.com/watch?v=XIuh7KDRzLk
DNA synthesis
1. Customer enters sequence data on secure,
dedicated website
2. Proprietary algorithm designs the best "build“
3. Oligonucleotide synthesis
4. Patent-pending gene assembly instrument
5. Cloning and sequence verification
blueheronbio.com
Engineering Life: Building a FAB for Biology, Sci. Am. Feb. 2007
Using abstraction (Generic logic gates)
Standards
Canton et al, Nature Biotech 2008, 26:7
BioBrick Device Data Sheet
Canton et al, Nature Biotech 2008, 26:7
iGEM
(International Genetically Engineered Machine Competition)
A competition by teams of undergrads to build genetically engineered machines
using standardized biological parts (BioBricks) or making their own.
Registry of Standard Biological Parts (BioBricks)
http://parts.mit.edu
Provides free access to an open commons of basic biological functions that can be
used to program synthetic biological systems
Anybody may contribute, draw upon, or improve the parts maintained within the
Registry.
BioBricks
BioBrick Part Types
BioBrick Reporters
GFP generator
Ribosome Binding Site (RBS)
GFP
Transcriptional Terminator
lacI-regulated Promoter
RFP generator
RFP
Problems with synthetic circuits…
1. Registry parts may be incorrect
2. Assembly is often time consuming, tedious, and unpredictable
3. Unknown interactions between circuit parts, host strain, media, etc.
4. Evolution
5. Noise
Evolution can break synthetic circuits
Arkin and Fletcher, Genome Biology 2006, 7:114
Noise affects synthetic systems
Arkin and Fletcher, Genome Biology 2006, 7:114