RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises.

Chemical probing of RNA in living cells.

RNAs need to adopt a specific architecture to exert their task in cells. While significant progress has been made in describing RNA folding landscapes in vitro, understanding intracellular RNA structure formation is still in its infancy. This is in part due to the complex nature of the cellular environment but also to the limited availability of suitable methodologies. To assess the intracellular structure of large RNAs, we recently applied a chemical probing technique and a metal-induced cleavage assay in vivo. These methods are based on the fact that small molecules, like dimethyl sulfate (DMS), or metal ions, such as Pb(2+), penetrate and spread throughout the cell very fast. Hence, these chemicals are able to modify accessible RNA residues or to induce cleavage of the RNA strand in the vicinity of a metal ion in living cells. Mapping of these incidents allows inferring information on the intracellular conformation, metal ion binding sites or ligand-induced structural changes of the respective RNA molecule. Importantly, in vivo chemical probing can be easily adapted to study RNAs in different cell types.