# 2′-19F labelling of ribose in RNAs: a tool to analyse RNA/protein interactions by NMR in physiological conditions

## TL;DR

This paper introduces a new NMR method using 19F labeling to study RNA/protein interactions under physiological conditions, enabling insights into binding sites and competition.

## Contribution

A novel NMR-based approach using 2′-19F labeling of ribose in RNA to analyze RNA/protein interactions in nuclear extracts.

## Key findings

- 19F NMR signal intensity changes indicate proximity of the 19F label to the protein binding site.
- Multiple 19F labels reveal concurrent or competitive binding of protein pairs to ssRNA.
- Trifluoromethoxy group improves NMR sensitivity and reduces RNA degradation in cellular extracts.

## Abstract

Protein-RNA interactions are central to numerous cellular processes. In this work, we present an easy and straightforward NMR-based approach to determine the RNA binding site of RNA binding proteins and to evaluate the binding of pairs of proteins to a single-stranded RNA (ssRNA) under physiological conditions, in this case in nuclear extracts. By incorporation of a 19F atom on the ribose of different nucleotides along the ssRNA sequence, we show that, upon addition of an RNA binding protein, the intensity of the 19F NMR signal changes when the 19F atom is located near the protein binding site. Furthermore, we show that the addition of pairs of proteins to a ssRNA containing two 19F atoms at two different locations informs on their concurrent binding or competition. We demonstrate that such studies can be done in a nuclear extract that mimics the physiological environment in which these protein-ssRNA interactions occur. Finally, we demonstrate that a trifluoromethoxy group (-OCF3) incorporated in the 2′ribose position of ssRNA sequences increases the sensitivity of the NMR signal, leading to decreased measurement times, and reduces the issue of RNA degradation in cellular extracts.