Control of RNA function by conformational design

Over the past two decades RNA has become a major focus of research. The discovery of ribozymes, riboswitches and small non-coding RNAs being involved in a large number of processes has led to much interest in the understanding of how RNA structure and conformation are linked to its function and how RNA function can be controlled by conformational design. Accordingly, it has become evident that more complex design targets are not amenable to manual sequence design, but require the use of computer based optimization methods. On the other hand, since even small errors in the energy model can significantly shift the balance between alternative conformations, computational RNA structure prediction is often not accurate enough to yield immediately functional RNA molecules. The computational models are, however, very efficiently able to reduce the search space to a small number of candidates that can be probed experimentally. By combining computer-aided prediction with wet-lab experiments, we aim at developing protocols and software tools for the design of functional RNA molecules. In particular three systems will be evaluated: (i) self-splicing and (ii) self-replicating RNAs derived from the hairpin ribozyme, and (iii) self-induced RNA switches. Design of the respective systems will build up on previous experimental work, and will be strongly guided and/or optimized by computational prediction of RNA folding kinetics, RNA complex formation and conformational distribution as an essential tool to successfully solve more complex design problems. In turn, experimental testing of the theoretical predictions will allow us to identify shortcomings of the computational models. Repeated rounds of modeling and testing will be used to iteratively refine model setup and parameters.

RNAs (Ribonucleic acids) play an essential role in the life cycle of every cell. RNA is not only the intermediate between the genetic blueprint (DNA) and the proteins produced, but also performs a variety of regulatory tasks.Our project focused on the computational design and subsequent modeling of RNAs with novel function. In collaboration with the lab of Prof. Sabine Müller in Greifswald, Germany, we were able to show that RNAs can extend themselves by concatenation with- out assistance from protein enzymes. This is important since the RNA World hypothesis claims that RNA emerged before DNA and proteins. It has, however, been hard to imagine how sufficiently long RNA molecules could exist in the RNA world. Our results suggest how pre-biological RNA genomes could have been built up by concatenation of shorter sequences.We also showed that RNAs can induce re-folding through the interaction of two copies. Such self-switching was so far known only from proteins, where it forms the molecular basis of prion diseases such as Creutzfeldt-Jakob. The artificial RNAs designed in this project could help to better understand the mechanism of such diseases, but might also be useful as molecular sensors and amplifiers in biotechnology.