Introduction to Synthetic Biology Dannenberg and Purdy 2012 (Tokos edits 2012)

What is Synthetic Biology? AMbDaQhttps:// AMbDaQ

ELECTRICAL engineering solution

water = weight water<weight MECHANICAL engineering solution

BIOLOGICAL engineering solution

PCR Genetic Engineering Sequencing rDNA

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

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 Sequences of DNA encode “parts” Assemblies of parts make up devices Assemblies of devices make a system

“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?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 PCR for watermarks M. mycoides genome transplanted to M. capricolum

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Dan Gibson, +21, Ham Smith and Craig Venter Science ( 2010) 329: 52 New Directions: The Ethics of Synthetic Biology and Emerging Technologies December 2010 Presidential Commission for the Study of Bioethical Issues