SURF 2012: Synthetic biology in a cell-free expression system

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2012 SURF project description

  • Mentor: Richard Murray
  • Co-mentor: Jongmin Kim

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. While the design of synthetic circuits in bacteria is still a pervasive activity in the field of synthetic biology, in vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment.

The project will focus on demonstrating cell-free expression systems such as reconstituted expression kit [1] and E. coli cell-extract [2] as a valuable training ground for synthetic biology [3]. In principle, any circuits implemented in cells can also be implemented in cell-free expression systems, given additional circuit components. Students are expected to work on transcriptional regulatory circuits [4, 5] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for heterogeneous regulatory circuit (e.g. transcriptional, post-transcriptional, small molecules).


  1. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755
  2. Jonghyeon Shin and Vincent Noireaux, (2010) Efficient cell-free expression with the endogenous E. coli RNA polymerase and sigma factor 70, Journal of Biological Engineering 4:8
  3. David K. Karig, Sukanya Iyer, Michael L. Simpson and Mitchel J. Doktycz, (2011) Expression optimization and synthetic gene networks in cell-free systems, Nucleic Acids Research (published online doi: 10.1093/nar/gkr1191)
  4. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465
  5. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences 108:E784-793