DNA Tiling Enables Precise Acylation-Based Labeling and Control of mRNA

Methods for the site-selective labeling of long, native RNAs are needed for studying mRNA biology and future therapies. Current approaches involve engineering RNA sequences, which may alter folding, or are limited to specific sequences or bases. Here, we describe a versatile strategy for mRNA conjugation via a novel DNA-tiling approach. The method, TRAIL, exploits a pool of protector oligodeoxynucleotides to hybridize and block the mRNA, combined with an inducer DNA that extrudes a reactive RNA loop for acylation at a predetermined site. Using TRAIL, an azido-acylimidazole reagent was employed for labeling and controlling RNA for multiple applications in vitro and in cells, including analysis of RNA-binding proteins, imaging mRNA in cells, and analysis and control of translation. The TRAIL approach offers an efficient and accessible way to label and manipulate RNAs of virtually any length or origin without altering native sequence.

Automated summary

This study presents a novel TRAIL method for site-selective labeling and manipulation of mRNA through a DNA tiling strategy, which can be applied to various in vitro and in cell studies, including analysis of RNA-binding proteins, mRNA imaging in cells, and analysis and control of translation.