Our ACS SynBio Paper on Fast RNA Circuitry is Out!



Melissa and James’ paper on characterizing the fast dynamics of RNA genetic circuitry is out! We have been hypothesizing for a while that RNA-only circuits would be fast compared to protein circuits because RNAs degrade faster than proteins. (To understand why the speed of genetic circuits is determined by the degradation rates of the signal carriers, see this excellent book by Uri Alon “An Introduction to Systems Biology: Design Principles of Biological Circuits“.) But up until now no one has been able to verify this. In this paper, we, our excellent collaborators from Richard Murray’s lab at Caltech, and some of the students from the first Cold Spring Harbor Lab Summer Course in Synthetic Biology, designed an experiment to do just that.

By using cell-free transcription-translation (TX-TL) reactions, we showed that an RNA cascade propagates information at about ~5 minutes per step, which is about the degradation half-life of one of our RNAs in this system. We also used some of the powerful tools of RNA engineering to show how you can tune this signal propagation time. This allowed us to make an RNA Single-Input Module, which is a network motif found in biology that is used to sequentially turn on one gene after another.

Along the way we learned a lot about using TX-TL to rapidly characterize the dynamics of RNA genetic circuitry. In fact, most of these experiments take around 3 hours to perform making the testing cycle extremely fast! There is still more work to be done to link circuit performance in TX-TL to circuit performance inside the cell, but we are already starting to make progress in that direction.

This paper was also a testament to the spirit of the Cold Spring Harbor Synthetic Biology course. In fact the initial experiments were performed by Vipul Singhal, Kevin Spring, Shaima Al-Khabouri and Chris Fall – all students of the course (under the fearless leadership of Melissa) who had never heard of RNA genetic circuits before doing these experiments in just two weeks!

Congratulations everyone for a job well done!

Link to the Paper: http://pubs.acs.org/doi/abs/10.1021/sb400206c

More Info on TX-TL as a molecular ‘breadboarding system’: http://openwetware.org/wiki/Biomolecular_Breadboards

Link to the Cold Spring Harbor Synthetic Biology Course: http://cshlsynbio.wordpress.com/