# Biochemical Characterization of a Non-G4-Type RNA Aptamer That Lights Up a GFP-like Fluorogenic Ligand

## TL;DR

This paper describes an RNA aptamer that activates a fluorescent molecule, revealing its structure and how it binds to the ligand.

## Contribution

The study introduces a new RNA aptamer structure and validates its tertiary interactions using chemical and computational methods.

## Key findings

- The 17-3 RNA aptamer induces fluorescence by stabilizing the phenolate form of DMHBI.
- The minimal active structure of the aptamer includes three stems and two loops, named Karashi and Jigarashi.
- AlphaFold3 predictions align with experimental data on the RNA's tertiary structure.

## Abstract

The 17-3 RNA aptamer recognizes DMHBI and induces its fluorescence. We showed that the 17-3 RNA aptamer predominantly induced emission of the phenolate form of DMHBI. We also demonstrated that the active structure of the minimal form of the 17-3 aptamer possessed three stem elements and two large loop elements, which we named Karashi and its sequence-optimized variant, Jigarashi, respectively. Chemical modification experiments suggested that the two loop regions formed tertiary interactions and/or non-Watson–Crick base pairs, and no remarkable structural alterations occurred upon DMHBI binding. AlphaFold3 also predicted a tertiary structure of the ligand-free form of Jigarashi RNA, which was consistent with the results of chemical modification experiments.