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Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations

Nucleic Acids Research. 2024-10; 
Yoshita Srivastava , Olayinka Akinyemi , Tiana C Rohe , Elizabeth M Pritchett , Cameron D Baker , Akshara Sharma , Jermaine L Jenkins , David H Mathews , Joseph E Wedekind
Products/Services Used Details Operation
Single-Stranded DNA Synthesis A synthetic DNA comprising the preQ1-III riboswitch from Subdoligranulum variabile (Sva) identified in Rfam v14.10 (https://rfam.org) was placed into the pBR327-Lrh(WT)- GFPuv plasmid (28) upstream of the GFPuv reporter gene (GenScript, Inc.). Get A Quote
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Abstract

Riboswitches are structured RNAs that sense small molecules to control expression. Prequeuosine1 (preQ1)-sensing riboswitches comprise three classes (I, II and III) that adopt distinct folds. Despite this difference, class II and III riboswitches each use 10 identical nucleotides to bind the preQ1 metabolite. Previous class II studies showed high sensitivity to binding-pocket mutations, which reduced preQ1 affinity and impaired function. Here, we introduced four equivalent mutations into a class III riboswitch, which maintained remarkably tight preQ1 binding. Co-crystal structures of each class III mutant showed compensatory interactions that preserve the fold. Chemical modification analysis revealed localized ... More

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