High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states.

ABSTRACT: The three-dimensional conformations of noncoding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput chemical mapping enables rapid RNA structure inference with unusually strong validation. We revisit a 16S rRNA domain for which SHAPE (selective 2'-hydroxyl acylation with primer extension) and limited mutational analysis suggested a conformational change between apo- and holo-ribosome conformations. Computational support estimates, data from alternative chemical probes, and mutate-and-map (M(2)) experiments highlight issues of prior methodology and instead give a near-crystallographic secondary structure. Systematic interrogation of single base pairs via a h

SUBMITTER: Tian S 

PROVIDER: S-EPMC4201832 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature