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Why synthsize genes and genomes?

10 3. 10 4. 10 5. 10 6. Why synthsize genes and genomes?. -minimal life -genome rewrite. -genetic circuits -metabolic pathways. DNA length (base pairs). -vaccines -gene therapy. -individual genes -assembly scaffolds. A. C. G. G. T. C. T. G. A. C. T. G. von Neumann (1956).

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Why synthsize genes and genomes?

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  1. 103 104 105 106 Why synthsize genes and genomes? -minimal life -genome rewrite -genetic circuits -metabolic pathways DNA length (base pairs) -vaccines -gene therapy -individual genes -assembly scaffolds

  2. A C G G T C T G A C T G von Neumann (1956) A C T A A circuit containing N (error-free) gates can be simulated with probability of error at most e, using N log(N/e) faulty gates, which fail with probability p, so long as p<pth. Error Correction with Flawed Components DNA “consensus vote” Winograd and Cowan (1967) “Reliable Computation in the Presence of Noise”

  3. N N N N M M M M x x x Complete error correction when no strand is error-free Repair Operation Mismatch Recognition + Nuclease Activity

  4. N M x Complete error correction when no strand is error-free Repair Operation Exchange Repair Copies 1 and 2

  5. N M x Complete error correction when no strand is error-free Repair Operation Exchange Repair Copies 1 and 2

  6. Complete error correction when no strand is error-free Repair Operation Exchange Repair Copies 2 and 3

  7. Complete error correction when no strand is error-free Repair Operation Exchange Repair Copies 2 and 3 Current milestone: 1 error per 20,000 bp Next milestone: 1 error per 100,000 bp

  8. Genome Engineering Nonnatural amino acids Why Synthetic Genomes? • Drug biosynthesis of new proteins • Nonnatural Amino Acids • Optimal codons • Genome stability  Safer Bio-isolation Cellular Chassis Virus-resistant strains E. coli rE.coli

  9. 1. UAG stop > UAA stop Remove RF1 - one codon available for unnatural amino acids - Viral resistance? 2. AGR (R) > CGR (R) 3. AGY (S) > UCX (S) Remove tRNAs, tRNA synthetases - three codons “free” - Viral resistance? tRNAs: AGY (S) > AGY (L) 3. UUR/CUX (L) > AGY (S) tRNAs: UUR (L) > UUR (S) 1. Codons: AGY Ser > UCX Ser 2. tRNAs: AGY Ser > AGY Leu 3. Codons: UUR/CUX Leu > AGY Ser 4. tRNAs: UUR Leu > UUR Ser 5. Codons: UCX Ser > UUR Ser (Leu & Ser now switched) RecodingE.coli: rE.coli E. Coli MG1655 4.6 MB

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