Computational Design of RNA Switches

Danny Barash
Ben-Gurion University

Recent discoveries about various capabilities of small RNAs to affect gene expression have led to some biotechnological advances and medical applications. In this talk, I will start with a brief overview on these discoveries, the diverse roles of RNAs, and their potential use. I will then focus on the phenomenon of RNA conformational switching and how it relates to function, introducing the bioinformatics methods that are involved in RNA folding predictions and the design and search for novel RNA switches. I will concentrate on a matrix representation of the RNA secondary structure, using its properties to identify conformational RNA switching by a single point mutation (RNAMute, available at http://www.cs.bgu.ac.il/~RNAMute) as well as other slight changes in the environment.
Finally, I will describe how computer-aided RNA switch design can potentially be performed in the future from an assembly of small RNA building blocks.