3D Feasibility of 2D RNA-RNA Interaction Paths by stepwise Folding Simulations

RNA. 2023 Dec 1:rna.079756.123. doi: 10.1261/rna.079756.123. Online ahead of print.ABSTRACTThe structure of an RNA, and even more so the interactions it forms with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA-RNA interaction prediction provide a quick way to identify possible interaction targets and structures. However, these tools ignore the effect of steric hindrance on the tertiary (3D) structure level, and do not consider whether a suitable folding pathway exists to form the interaction. As a consequence, these tools often predict interactions that are unrealistically long and could be formed (in three dimensions) only by going through highly entangled intermediates. Here, we present a computational pipeline to assess whether a proposed secondary (2D) structure interaction is sterically feasible and reachable along a plausible folding pathway. To this end we simulate the folding of a series of 3D structures along a given 2D folding path. To avoid the complexity of large scale atomic resolution simulations, our pipeline uses coarse grained 3D modeling and breaks up the folding path into small steps, each corresponding to the extension of the interaction by one or two base pairs. We apply our pipeline to analyse RNA-RNA interaction formation for three selected RNA-RNA complexes. We find that kissing hairpins, in contrast to interactions in the exterior loop, are difficult to extend and tend to get stuck at an interacti...

Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Irene K Beckmann Maria Waldl Sebastian Will Ivo L Hofacker Source Type: research