Unknown

Dataset Information

0

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


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 single-molecule 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.

SUBMITTER: Krokhotin A 

PROVIDER: S-EPMC5159650 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

altmetric image

Publications

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

Krokhotin Andrey A   Mustoe Anthony M AM   Weeks Kevin M KM   Dokholyan Nikolay V NV  

RNA (New York, N.Y.) 20161101 1


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 s  ...[more]

Similar Datasets

| S-EPMC6900531 | biostudies-literature
| S-EPMC4183288 | biostudies-literature
| S-EPMC7917579 | biostudies-literature
| S-EPMC3899427 | biostudies-literature
| S-EPMC10328344 | biostudies-literature
2024-10-23 | GSE278422 | GEO
| S-EPMC7717319 | biostudies-literature
| S-EPMC5393180 | biostudies-literature
| S-EPMC4437859 | biostudies-literature
| S-EPMC2018647 | biostudies-literature