A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

Tycho Marinus, Adam B Fessler, Craig A Ogle, Danny Incarnato*

*Bijbehorende auteur voor dit werk

OnderzoeksoutputAcademicpeer review

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Due to the mounting evidence that RNA structure plays a critical role in regulating almost any physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid imidazolide (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 shows moderate improvements with respect to the state-of-the-art selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reagent NAI on naked RNA under in vitro conditions, but it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.

Originele taal-2English
Aantal pagina's12
TijdschriftNucleic Acids Research
StatusE-pub ahead of print - 4-jan-2021

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