SURF 2013: Synthetic logic circuits using RNA aptamers
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. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment .
Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations , indicating its potential as a tight regulator of power cycling in in vitro circuits.
The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit  would be tested as a platform to operate such circuits.
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1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.
2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.
3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.
4. 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.
5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.