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

Abstract

RNA structure plays a crucial role in its function. With the advancement of deep sequencing technology, numerous new ncRNA sequences have been discovered. However, functional analysis of these sequences is lagging. Traditionally, mutations are designed to affect the RNA structure and prepared one by one for experimental assessment of function. For large scale characterization of structure/function relationship in many RNAs, we developed a program: Structure Mutation Designer (SMDesigner) which makes both disruptive and compensatory mutations according to structure information automatically. To test if the program works well, we designed mutations for riboswitches with SMDesigner and experimentally assessed six riboswitches and their mutant sequences to verify the structure and function change with in-line probing assay. The in-line probing results show that five of six sequence structure patterns changed as we excepted validating that SMDesigner can be useful to explore structured RNA function. SMDesigner can be download at: https://github.com/lilihou/SMDesigner_0.1/tree/main/dist.