1. SS -1 PAC 8/18/11 Recoding the Genome Peter Carr 18 August 2011 FAB7 Lima, Peru

2. SS -2 PAC 8/18/11 DNA On-Demand 10 3 10 6 10 5 10 4 rewrite genomes minimal life genetic circuits metabolic pathways individual genes assembly scaffolds vaccines gene therapy DNA base pairs

3. SS -3 PAC 8/18/11 Carr & Church (2009) Nature Biotech. 1 10 100 1000 10000 100000 1000000 10000000 19501960197019801990200020102020 year nucleotide bonds organic chemistry biochemistry biology How big can we go?

4. SS -4 PAC 8/18/11 The basic genetic code ACGTACGT 4 letters ACGTACGT X ACGTACGT X AAA AAC AAG AAT ACA ACC ACG ACT... 64 words (codons) =

5. SS -5 PAC 8/18/11 Second Position

6. SS -6 PAC 8/18/11 By engineering new genetic codes we can: produce organisms immune to viruses make universal systems for “plug and play” with new amino acids new room for plug & play block exchange of genes, a “genetic firewall” rearrange to block function Second Position

7. SS -7 PAC 8/18/11 Multiplex Automated Genome Engineering (MAGE) “Find and replace” with the DNA of the genome

8. SS -8 PAC 8/18/11 Key features of MAGE: Multiplexed: can address many sites at once Targeted: modifies specific sequences; changes made can be specific or random Iterated: weak efficiency can be compensated by automating many cycles of modification Tunable: can control the range of diversity generated in a population Clean: no DNA scars, no resistance gene markers, etc.

9. SS -9 PAC 8/18/11 All 314 sites in the genome modified (across 32 strains)

10. SS -10 PAC 8/18/11 Genome Engineering base pairs to megabases

11. SS -11 PAC 8/18/11 Joseph Jacobson Bram Sterling* Chris Emig Sam Hwang George Church (HMS) Farren Isaacs Harris Wang Marc LaJoie Shuguang Zhang (MIT) Funding: NSF Thanks to:

12. SS -12 PAC 8/18/11 Atoms to bits...to atoms to bits receivertransmitter Box 1Box 2 me you it clinical + research data genetic counseling health statistics forensics basic research molecules experiments G AT T ACA

13. SS -13 PAC 8/18/11 Personal Box 1 MY GENES Box 2 How will drugs X, Y, Z affect ME ? MY TREATMENT How will MY BODY metabolize drugs X, Y, Z?

14. SS -14 PAC 8/18/11 Box 1 NEW PATHOGEN Box 2 Analyze the PARTS RAPID RESPONSE Test existing DRUGS at many sites Preliminary VACCINE Community

15. SS -15 PAC 8/18/11 MY IDEA Box 2 new biochemistry MY DESIGN FOR... DNA nanostructures new vaccines novel organisms Creativity