Saturday, May 20, 2006

DNA Synthesis Panel

J. D. Kittle - Coda genomics
  • CODA (Computationally Optimized DNA Assembly), also incorporates its patented Translation Engineering TM into the design of the gene.
John Danner - Codon Devices
  • Mission: to eliminate construction as a barrier to synthetic biology (Drew's point #4).
  • Key enabling technologies: CAD design environment -> multiplexed oligo synthesis & purification -> assembly...
  • The bottom line is that if you want to go bigger with synthesis, you've got to multiplex. For instance, you can get a large number of variants (for cents/bp) if you design a library well. Instead of doing blind mutagenesis, lets use the knowledge we have! Codon's BioFAB(tm) will make length concerns a non-issue in synthesis.
Hans Buegl - GeneArt
  • The market for customers of synthesis tech. has doubled in the last year, and is split nearly into thirds between Big Pharma, academic/research institutions, and ?
  • Largest synthesis ~21kb. They have software which attempts to select the optimal codon distribution by examaning and scoring each codon in turn in a given sequence.
  • They've optimized the synthesis workflow with lots of automation.
Jeremy Minshull - DNA 2.0 (president)
  • Gene Designer is a free program for optimizing codon usage for different organisims (but requires registration).
What are the current bottlenecks in synthesis? Cost of synthesis, cost of sequencing (consider personal genome project), and perhaps surprisingly time required for synthesis. As Drew pointed out, a "compile time" of at least four to eight weeks is completely impractical, especially for students in a competition. But what market pressures exist to drive down the time required? What will spur innovation here?

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