MIT Molecular Machines (Jacobson) Group

jacobson@media.mit.edu

Building a FAB for Synthetic Biology

http://www.thetech.org/exhibits/online/robotzoo/about/chameleon.html

Synthetic Biology

to Program Cells to BecomeFactories to Make…

Devices, Sensors, Pharmaceuticals, Renewable Chemicals & Fuels and Food

Using Synthetic Genes…

Tape Programming of the Mark I Computer

Ribosome

only 106 times smaller Like this

Cells as Chemical Factories 1,3 Propanediol

http://3rdpartylogistics.blogspot.com/2011/10/genetic-bacteria-genetic-modification.htmlhttp://www.latonkorea.com/Plant.htmlhttp://3rdpartylogistics.blogspot.com/2011/10/genetic-bacteria-genetic-modification.htmlhttp://www.latonkorea.com/Plant.html

MB Elowitz MB and S Leibler (2000) A synthetic oscillatory network of transcriptional regulators.Nature.403 :335 - 338.

http://echinacea.harvard.edu/research/image-gallery/

Cells as Computers and LogicRing Oscillators from Transcriptional-Translational Logic

Jeff Hasty - UCSD

http://elowitz.caltech.edu/

Bacterial Ring Oscillators

tetRP RBS

T T’lacIP R

BS

T T’P R

BS

T T’

luxRP RBS

T T’luxIP R

BS

T T’P R

BS

T T’

ori resbackbone plasmidcfpP RBS

T T’

BBa_C0040 BBa_C0012

BBa_C0061BBa_C0062

BBa_E0022

BBa_R0051 BBa_R0040 BBa_R0010

BBa_R0010BBa_R0051BBa_R0063

BBa_R0040

TRBS

T’BBa_B0030BBa_B0010BBa_B0012

BB suffix BB prefixBBa_B0001

cIBBa_C0051

aiiABBa_C0060

Silicon

http://www.national.com/company/pressroom/gallery/graphics/full_sized/06_rgb.jpg http://commons.wikimedia.org/wiki/File:InternalIntegratedCircuit2.JPG http://en.labs.wikimedia.org/wiki/File:64-bit_lookahead_carry_unit.svg

From Schematic Design To Fab

To Working ChipTo Product

2

34

1

The Tyranny of Numbers

http://www.chipsetc.com/the-transistor.html

http://www.webenweb.co.uk/museum/comps.htm

DNA SynthesisChemical Synthesis

(Open Loop Protection Group)Biological Synthesis

(Error Correcting Polymerase)

Error Rate: 1:102

Throughput: 300 S per Base Additionhttp://www.med.upenn.edu/naf/services/catalog99.pdf

Throughput Error Rate Product Differential: ~108

template dependant 5'-3' primer extension

5'-3' error-correcting exonuclease

3'-5' proofreading exonuclease

Error Rate: 1:106

Throughput: 10 mS per

Base AdditionBeese et al. (1993), Science, 260, 352-355. http://www.biochem.ucl.ac.uk/bsm/xtal/teach/repl/klenow.html

A. Gene pathway sequence. B. Corresponding array of overlapping oligonucleotides C. Error correcting assembly in to low error rate pathways. D. Expression in cells

BioFAB - From Bits to CellsA B

CD

~ 1M Oligos/Chip

Next Generation (Chip Based) DNA Synthesis

Chow, Brian Y., Christopher J. Emig, and Joseph M. Jacobson. "Photoelectrochemical synthesis of DNA microarrays." Proceedings of the National Academy of Sciences 106.36 (2009): 15219-15224.

http://www.technologyreview.com/biomedicine/20035/

http://learn.genetics.utah.edu/content/labs/microarray/analysis

Accurate multiplex gene synthesis from programmable DNA microchipsJingdong Tian, Hui Gong, Nijing Sheng, Xiaochuan Zhou, Erdogan Gulari, Xiaolian Gao and George ChurchNature 432, 1050-1054(23 December 2004)doi:10.1038/nature03151

~1000x Lower Oligonucleotide Cost

J. Jacobson – MIT CBA – 5.1.14

1M

10G1T

100T

Base

Pai

rs

100M

~ 20

0 M

bp

~ 25

0 M

bp

~ 1.

5 G

bp

~ 1.

6 G

bp

~ 3.

2 G

bp

159.

8 G

bp

~ 20

0 G

bp

1000

0000

000

G T

rans

isto

rs

97 M

bp

~1-1

3 M

b

Scale Factors in DNA Synthesis & Applications Next Generation (Chip Based) DNA Synthesis

12.2

Mbp

Bio Parts for Synthetic Biology

parts.igem.org

Digital BiologyCreating a Fab for Biology

Synthetic Biology Apps

The Genetic CodeLife’s Operating System

Genetically Recoded Organisms

The Genetic CodeCurrently Powering 8.7 Million Species on Earth Organisms

Currently Running the

Standard Genetic Code

Organisms Running a Different Genetic Code

hydrophobichydrophilic

Acetohalobium arabaticumCandida albicans

Pterobranchia mitochondrial code

18 October 2013 Conferring New Function

Phage Resistance

Years1 2

Glo

bal

Cu

mu

lati

ve U

nit

Sh

ipm

en

ts

(Mil

lion

s)

Cumulative Units with Android & iOS Installed

Cumulative Units with GRO OS Installed

Hours

Android / iOS Roll Out VS. GRO - OS