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

TABLE 1.

Summary of the experimentally assessed structure and function changes of the riboswitch sequences designed by SMDesigner

Structure change Ligand modulation
Wild-type Mu1: disruption Mu2: rescue Wild-type Mu1: disruption Mu2: rescue
SAM-III NA Yes Yes Yes No Yes
PreQ1-I NA Yes Yes Yes No Yes
PreQ1-III NA Yes Yes Yes No Yes
Guanidine-I_seq1 NA Yes Yes No No No
Guanidine-I_seq2 NA Yes Yes No No No
Guanidine-III NA Yes No No No No

  • “Structure change” shows the structural change when we compare the result of in-line probing assay among wild-type, disruption, and rescue constructions. “Yes” indicates we can clearly see structure pattern change (Figs. 3A and 4A, bottom; Figs. 3B and 4B, circles). For “ligand modulation,” “yes” indicates that we can see band modulation in presence/absence of ligands (Figs. 3B and 4B, squares); “no” indicates that the presence of the riboswitch ligand does not affect bands.

This Article

  1. Published in Advance April 10, 2025, doi: 10.1261/rna.080267.124 RNA 31: 874-884

Current Issue

  1. July 2026, 32 (7)
  1. Current Issue
  1. Alert me to new issues of RNA