Deciphering the universe of RNA structures and trans RNA-RNA interactions of transcriptomes in vivo: from experimental protocols to computational analyses

The last few years have seen an explosion of experimental and computational methods for investigating RNA structures of entire transcriptomes in vivo. Very recent experimental protocols now also allow trans RNA–RNA interactions to be probed in a transcriptome-wide manner. All of the experimental strategies require comprehensive computational pipelines for analysing the raw data and converting it back into actual RNA structure features or trans RNA–RNA interactions. The overall performance of these methods thus strongly depends on the experimental and the computational protocols employed. In order to get the best out of both worlds, both aspects need to be optimised simultaneously. This review introduced the methods and proposes ideas how they could be further improved

On Low Energy Barrier Folding Pathways for Nucleic Acid Sequences

Abstract. Secondary structure folding pathways correspond to the ex-ecution of DNA programs such as DNA strand displacement systems. It is helpful to understand the full diversity of features that such pathways can have, when designing novel folding pathways. In this work, we show that properties of folding pathways over a 2-base strand (a strand with either A and T, or C and G, but not all four bases) may be quite different than those over a 4-base alphabet. Our main result is that, for a simple energy model in which each base pair contributes −1, 2-base sequences of length n always have a folding pathway of length O(n3) with energy barrier at most 2. We provide an efficient algorithm for constructing such a pathway. In contrast, it is unknown whether minimum energy barrier pathways for 4-base sequences can be found efficiently, and such path-ways can have barrier Θ(n). We also present several results that show how folding pathways with temporary and/or repeated base pairs can have lower energy barrier than pathways without such base pairs.