Enabling Technology : Biomaterials Evolution Platform
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Transcript of Enabling Technology : Biomaterials Evolution Platform
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9:05-9:35 4-Feb-2009 Wyss Institute for Biologically Inspired Engineering
Thanks to:
Enabling Technology : Biomaterials Evolution Platform
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Feb 10
8:30-9:00: Jim Collins - Anticipatory Medical Devices9:05-9:35: George Church - Biomaterial Evolution9:40-10:10: Joanna Aizenberg - Adaptive Architectures10:15-10:45: Don Ingber - Programmable Nanomaterials10:50-11:20: Don Ingber Biomimetic Microsystems
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Biomaterials Evolution Platform
•DNA Synthesis, assembly & analysis on chips- VDJ-ome (antibody libraries)
• 3-D DNA structures: inorganic interfaces• In vitro systems: multi-enzyme resistance• Microbial systems: multi-virus resistance
- Metabolic engineering fuels & chemicals• Human cell systems: combinatorial regulation
- Organ self-assembly
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Sequencing tracked Moore’s law 2X/2 yr until 2005-9 10,000x/4yr
2009 goal of 2% for $200 (coding + regulatory)
0.0000001
0.000001
0.00001
0.0001
0.001
0.01
0.1
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1990 1995 2000 2005 2010
$/bp 2005 $50M
2009 $5K
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Open-architecture hardware, software, wetware
Polonator
$150K - 2 billion beads/run
e.g.1981IBM PC
Rich TerrySenior Engineer
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DNA Synthesis, assembly & analysis on chips
Nitrobenzyl linkers for selective release of beads or cells
Digital micromirror & inkjet
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Biomaterials Evolution Platform
•DNA Synthesis, assembly & analysis on chips- VDJ-ome (antibody libraries)
• 3-D DNA structures: inorganic interfaces• In vitro systems: multi-enzyme resistance• Microbial systems: multi-virus resistance
- Metabolic engineering fuels & chemicals• Human cell systems: combinatorial regulation
- Organ self-assembly
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Antibody (& TCR) VDJ regions
Roth DB et al Mol Cell Biol. 1989 9:3049 N (1-13): 14 22 13 15 10 4 5 4 2 2 3 2 1 Lefranc, The Immunoglobulin FactsBook; Janeway, Immunobiology 2001
VH*DH*NNHH*JJHH*V*JJ
46*23*N N * 6 6 * 67* 55 = > 2M combinations , 750 bp, >1E10 cells
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Biomaterials Evolution Platform
•DNA Synthesis, assembly & analysis on chips- VDJ-ome (antibody libraries)
• 3-D DNA structures: inorganic interfaces• In vitro systems: multi-enzyme resistance• Microbial systems: multi-virus resistance
- Metabolic engineering fuels & chemicals• Human cell systems: combinatorial regulation
- Organ self-assembly
1010
First practical application of DNA nanostructures
Residual NMR dipolar couplings for membrane proteins >15kDaDouglas, et al. PNAS 2007
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Selection of DNAs enabling selection of CNT structures
Material properties change at the sub-nm scale (& sensitive to defects) Carbon Nanotubes Tensile strength: 62,000 MPa vs CNT-rope 3600, silk 1000, steel 800Thermal conduction: 6000 W/mK vs Cu 385Electrical current density of 4000 MA/cm2, vs Cu 4
C60 fullerite Bulk Modulus: 491 GPa vs diamond 442, steel 160
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Biomaterials Evolution Platform
•DNA Synthesis, assembly & analysis on chips- VDJ-ome (antibody libraries)
• 3-D DNA structures: inorganic interfaces• In vitro systems: multi-enzyme resistance• Microbial systems: multi-virus resistance
- Metabolic engineering fuels & chemicals• Human cell systems: combinatorial regulation
- Organ self-assembly
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Mirror world : resistant to enzymes, parasites, predators
Approach#1: De novo Chemical synthesis (below)
#2: Redesigned peptidyl transferase + D-AA-tRNAs (next slide)
352 AA Synthetic Dpo4 Sulfolobus DNA polymerase IV
4 peptide bonds left to construct
L-aminoacidsD-nucleotides
(current biosphere)
D-aminoacidsL-nucleotides (Mirror-biopolymers)
Duhee Bang
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113 kbp DNA 151 genes
Pure translation:Forster & Church
MSB ’05 GenomeRes.’06
Shimizu, Ueda ’01
Synthetic LifeHigh speed &
accuracy
Route to mirror proteins
Jewett
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Biomaterials Evolution Platform
•DNA Synthesis, assembly & analysis on chips- VDJ-ome (antibody libraries)
• 3-D DNA structures: inorganic interfaces• In vitro systems: multi-enzyme resistance• Microbial systems: multi-virus resistance
- Metabolic engineering fuels & chemicals• Human cell systems: combinatorial regulation
- Organ self-assembly
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Genome Engineering Multiplex Automation (GEMA)
for multi-viral resistance
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Genome Engineering Multiplex Automation (GEMASS)in vivo homologous allele replacement (lagging SS mimics)
3 hr Cycle time. Application: 314 change for multivirus resistance
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Improving process yield, health, safety:
What threatens all biological systems?
What do all viruses have in common? or lack?
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PEG-pAcPhe-hGH (Ambrx) high serum stability314 TAG to TAA changes
IsaacsCharalelChurchSunWang CarrJacobsonKong Sterling
New genetic code: viral-resistance, novel amino acidsno functional GMO DNA exchange
TTT
F
30362 TCT
S
11495 TAT
Y
21999 TGT
C
7048
TTC 22516 TCC 11720 TAC 16601 TGC 8816
TTA
L
18932 TCA 9783 TAASTOP
STOP
2703 TGA STOP 1256
TTG 18602 TCG 12166 TAG 314 TGG W 20683
CTT
L
15002 CCT
P
9559 CAT
H
17613 CGT
R
28382
CTC 15077 CCC 7485 CAC 13227 CGC 29898
CTA 5314 CCA 11471 CAA
Q
20888 CGA 4859
CTG 71553 CCG 31515 CAG 39188 CGG 7399
ATT
I
41309 ACT
T
12198 AAT
N
24159 AGT
S
11970
ATC 34178 ACC 31796 AAC 29385 AGC 21862
ATA 5967 ACA 9670 AAA
K
45687 AGA
R
2896
ATG M 37915 ACG 19624 AAG 14029 AGG 1692
GTT
V
24858 GCT
A
20762 GAT
D
43719 GGT
G
33622
GTC 20753 GCC 34695 GAC 25918 GGC 40285
GTA 14822 GCA 27418 GAA
E
53641 GGA 10893
GTG 35918 GCG 45741 GAG 24254 GGG 15090
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Biomaterials Evolution Platform
•DNA Synthesis, assembly & analysis on chips- VDJ-ome (antibody libraries)
• 3-D DNA structures: inorganic interfaces• In vitro systems: multi-enzyme resistance• Microbial systems: multi-virus resistance
- Metabolic engineering fuels & chemicals• Human cell systems: combinatorial regulation
- Organ self-assembly
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Accelerated evolution for valuable metabolites & biofuels
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Biomaterials Evolution Platform
•DNA Synthesis, assembly & analysis on chips- VDJ-ome (antibody libraries)
• 3-D DNA structures: inorganic interfaces• In vitro systems: multi-enzyme resistance• Microbial systems: multi-virus resistance
- Metabolic engineering fuels & chemicals• Human cell systems: combinatorial regulation
- Organ self-assembly
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Re-programming adult human cells to multiple tissues with combinations of DNAs
Hair or skin sample
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Viral delivery: β-catenin, Dnmt3l, Dppa2,3,4,5, Ecat1, Eras, Fthl17, Grb21, Ecat8, Fbx15, Gdf3, hTERT, Klf4, Myc, Nanog, Oct4, Rex1, Sall4, Sox2, Sox15, Stat3, Tcl1, Utf1Signals: Activin, BMP4, Estrogen, FGF, HGF, PDGF, Retinoate, Shh, TGF, VEGF.
Combinations of regulatory genes
Cartilage & bone
Respiratory epithelium
Immature Brain
Skin-derived stem cells
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Biomaterials Evolution Platform
•DNA Synthesis, assembly & analysis on chips- VDJ-ome (antibody libraries)
• 3-D DNA structures: inorganic interfaces• In vitro systems: multi-enzyme resistance• Microbial systems: multi-virus resistance
- Metabolic engineering fuels & chemicals• Human cell systems: combinatorial regulation
- Organ self-assembly
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