Integration of the hammerhead ribozyme into structured RNAs to measure ligand-binding events for riboswitch candidates and aptamers.

ABSTRACT: Some structured RNAs, such as riboswitches and aptamers, can bind to their cognate ligands and have been used in biosensors and gene expression control elements. However, current methods for detecting ligand binding to structured RNAs are either severely limited or inconvenient. In this study, we design a multibase pair bridge to integrate a hammerhead ribozyme into structured RNAs to detect ligand binding events. The experimental results demonstrate that the length of the bridge has a significant effect on the cleavage of the ribozyme; optimal cleavage can be achieved with three to six base pairs in the bridge. The dissociation constant ( K _D) values obtained through this method are in agreement with those determined by in-line probing techniques, and 1 pmol of allosteri

SUBMITTER: Zhang S 

PROVIDER: S-EPMC12747935 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature