SMDesigner: a program to design sequence mutations to assess RNA structure

The structure of RNA is critical to its function. The advancement of structure prediction algorithms and deep sequencing technology has led to the discovery of numerous conserved RNA structures. However, functional analysis of these sequences is lagging behind the rate of novel RNAs' predictions. Traditionally, mutations are designed to alter the structure of RNA and tested individually to assess function. We developed a program for the large-scale characterization of the structure/function relationship in multiple RNAs. Structure Mutation Designer (SMDesigner) automatically selects both disruptive and compensatory mutations according to inputted structural information. As proof of concept, we designed mutations for riboswitches with SMDesigner and experimentally assessed six of these riboswitches and their mutant sequences using an in-line probing assay to verify the effects on their structure and function. The in-line probing results show expected changes in five of six sequence structure patterns, confirming that SMDesigner can be useful to explore RNA structure and subsequent function. SMDesigner can be download at: https://github.com/lilihou/SMDesigner_0.1/tree/main/dist.