Direct identification of base-paired RNA nucleotides by correlated chemical probing

Andrey Krokhotin, Anthony M. Mustoe, Kevin M. Weeks, Nikolay V. Dokholyan

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

Many RNA molecules fold into complex secondary and tertiary structures that play critical roles in biological function. Among the best-established methods for examining RNA structure are chemical probing experiments, which can report on local nucleotide structure in a concise and extensible manner. While probing data are highly useful for inferring overall RNA secondary structure, these data do not directly measure through-space base-pairing interactions. We recently introduced an approach for singlemolecule correlated chemical probing with dimethyl sulfate (DMS) that measures RNA interaction groups by mutational profiling (RING-MaP). RING-MaP experiments reveal diverse through-space interactions corresponding to both secondary and tertiary structure. Here we develop a framework for using RING-MaP data to directly and robustly identify canonical base pairs in RNA. When applied to three representative RNAs, this framework identified 20%'50% of accepted base pairs with a <10% false discovery rate, allowing detection of 88% of duplexes containing four or more base pairs, including pseudoknotted pairs. We further show that base pairs determined from RING-MaP analysis significantly improve secondary structure modeling. RING-MaP-based correlated chemical probing represents a direct, experimentally concise, and accurate approach for detection of individual base pairs and helices and should greatly facilitate structure modeling for complex RNAs.

Original languageEnglish (US)
Pages (from-to)6-13
Number of pages8
JournalRNA
Volume23
Issue number1
DOIs
StatePublished - Jan 2017

All Science Journal Classification (ASJC) codes

  • Molecular Biology

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