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1 9:05-9:35 4-Feb-2009 Wyss Institute for Biologically Inspired Engineering Thanks to: Enabling Technology : Biomaterials Evolution Platform.

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Presentation on theme: "1 9:05-9:35 4-Feb-2009 Wyss Institute for Biologically Inspired Engineering Thanks to: Enabling Technology : Biomaterials Evolution Platform."— Presentation transcript:

1 1 9:05-9:35 4-Feb-2009 Wyss Institute for Biologically Inspired Engineering Thanks to: Enabling Technology : Biomaterials Evolution Platform

2 2 Feb 10 8:30-9:00: Jim Collins - Anticipatory Medical Devices 9:05-9:35: George Church - Biomaterial Evolution 9:40-10:10: Joanna Aizenberg - Adaptive Architectures 10:15-10:45: Don Ingber - Programmable Nanomaterials 10:50-11:20: Don Ingber Biomimetic Microsystems

3 3 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

4 4 Sequencing tracked Moore’s law 2X/2 yr until 2005-9 10,000x/4yr 2009 goal of 2% for $200 (coding + regulatory) $/bp 2005 $50M 2009 $5K

5 5 Open-architecture hardware, software, wetware Polonator $150K - 2 billion beads/run e.g. 1981 IBM PC Rich Terry Senior Engineer

6 6 DNA Synthesis, assembly & analysis on chips Nitrobenzyl linkers for selective release of beads or cells Digital micromirror & inkjet

7 7 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

8 8 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 N H J H J  V H *D H *N H *J H *V  *J  N 6 5 46*23*N * 6 * 67* 5 = > 2M combinations, 750 bp, >1E10 cells

9 9 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

10 10 First practical application of DNA nanostructures Residual NMR dipolar couplings for membrane proteins >15kDa Douglas, et al. PNAS 2007

11 11 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 800 Thermal conduction: 6000 W/mK vs Cu 385 Electrical current density of 4000 MA/cm 2, vs Cu 4 C60 fullerite Bulk Modulus: 491 GPa vs diamond 442, steel 160 metalic vs. semiconducting

12 12 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

13 13 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-aminoacids D-nucleotides (current biosphere) D-aminoacids L-nucleotides (Mirror-biopolymers) Duhee Bang

14 14 113 kbp DNA 151 genes Pure translation: Forster & Church MSB ’05 GenomeRes.’06 Shimizu, Ueda ’01 Synthetic Life High speed & accuracy Route to mirror proteins Jewett

15 15 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

16 16 Genome Engineering Multiplex Automation (GEMA) for multi-viral resistance

17 17 Genome Engineering Multiplex Automation (GEMASS) in vivo homologous allele replacement (lagging SS mimics) 3 hr Cycle time. Application: 314 change for multivirus resistance

18 18 Improving process yield, health, safety: What threatens all biological systems? What do all viruses have in common? or lack?

19 19 PEG-pAcPhe-hGH (Ambrx) high serum stability 314 TAG to TAA changes Isaacs Charalel Church Sun Wang Carr Jacobson Kong Sterling New genetic code: viral-resistance, novel amino acids no functional GMO DNA exchange TTT F 30362TCT S 11495TAT Y 21999TGT C 7048 TTC22516TCC11720TAC16601TGC8816 TTA L 18932TCA9783TAA STOP 2703TGA STOP 1256 TTG18602TCG12166TAG314TGGW20683 CTT L 15002CCT P 9559CAT H 17613CGT R 28382 CTC15077CCC7485CAC13227CGC29898 CTA5314CCA11471CAA Q 20888CGA4859 CTG71553CCG31515CAG39188CGG7399 ATT I 41309ACT T 12198AAT N 24159AGT S 11970 ATC34178ACC31796AAC29385AGC21862 ATA 5967ACA9670AAA K 45687AGA R 2896 ATGM37915ACG19624AAG14029AGG1692 GTT V 24858GCT A 20762GAT D 43719GGT G 33622 GTC20753GCC34695GAC25918GGC40285 GTA14822GCA27418GAA E 53641GGA10893 GTG35918GCG45741GAG24254GGG15090 1 2 3 4

20 20 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

21 21 Accelerated evolution for valuable metabolites & biofuels

22 22 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

23 23 Re-programming adult human cells to multiple tissues with combinations of DNAs Hair or skin sample

24 24 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, Utf1 Signals: Activin, BMP4, Estrogen, FGF, HGF, PDGF, Retinoate, Shh, TGF, VEGF. Combinations of regulatory genes Cartilage & bone Respiratory epithelium Immature Brain Skin-derived stem cells

25 25 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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