Related Experiment Video
Updated: Aug 11, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers
Published on: August 20, 2014
A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA
1Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
Abstract:
The VS ribozyme is a 154 nucleotide sequence found in certain natural strains of Neurospora. The RNA can be divided into a substrate and a catalytic domain. Here we present the solution structure of the substrate RNA that is cleaved in a trans reaction by the catalytic domain in the presence of Mg2+. The 30 nucleotide substrate RNA forms a compact helix capped by a flexible loop. The cleavage site bulge contains three non-canonical base-pairs, including an A+.C pair with a protonated adenine. This adenine (A622) is a pH controlled conformational switch that opens up the internal loop at higher pH. The possible significance of this switch for substrate recognition and cleavage is discussed.
Related Concept Videos
Types of RNA
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
Riboswitches
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
Ribozymes
Ribozymes can be...
Ribozymes
Ribozymes can be...
Types of RNA
RNA Performs Diverse...
Transcriptional Regulation: Riboswitches

