Rational Design of RNA Regulators

April 8, 2015

Date: Thursday, 4/9/15
Time: 11:00 AM - 12:15 PM
Place: Mechanical Engineering, Room 218

Peter Stadler
University of Leipzig

Rational Design of RNA Regulators

RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computer efficiently, RNA molecules are amenable not only to \emph{in vitro} and \emph{in vivo} selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations.

Riboswitches are an interesting target for constructing synthetic regulatory systems for gene expression. While riboswitches for translational control have been designed successfully, attempts to construct synthetic elements regulating transcription have failed until recently. Rational design of structured RNAs is based on the ability of efficiently predict secondary structures at sufficient accuracy. We use the Vienna RNA Package for this purpose. As an example, we used the well-characterized theophylline-aptamer as sensor. Recent developments aim constructing more complex logic functions into a single RNA molecule. We will discuss in particular the computational challenges for such design tasks.

Peter Stadler received degrees in Chemistry, Mathematics, Physics, and Astronomy at the University of Vienna, and was a postdoc at the Max Planck Insitute for Biophysical Chemistry, Goettingen, with Manfred Eigen. Since 2002, he has been Professor of Bionformatics at the University of Leipzig. He is also External Faculty Member at the Santa Fe Institute.