Résumé de l'article

ppGpp and pppGpp [abbreviated here as (p)ppGpp] are highly conserved
stress signaling molecules in bacteria, chloroplasts, and mitochondria.
When induced in response to stress, (p)ppGpp bind to multiple protein
targets involved in functions as diverse as transcription, translation,
nucleotide metabolism, and other metabolic processes. (p)ppGpp can bind
not only to proteins, but also to RNA aptamers : indeed, a
(p)ppGpp-binding family of aptamers recently was described in
firmicutes.These ligand-binding RNAs are embedded within RNA transcripts
upstream of expression platforms forming riboswitches that regulate gene
expression. Here, we implemented the DRaCALA technique, originally
designed to study protein-ligand interactions, for the study of
RNA-ligand binding, permitting rapid screening of dozens of RNA aptamer
candidates concurrently. Using this method, which we call RNA-DRaCALA,
we screened 30 RNA aptamer candidates for binding to (p)ppGpp and
identified candidates with high specificity for ppGpp or pppGpp or both.
By expanding the number of biochemically verified sites, this method not
only allowed construction of more accurate secondary structure models,
but it also enabled prediction of key features that distinguish a ppGpp
from a pppGpp binding site. We suggest this method could facilitate
identification and understanding of the features needed for ligand
binding to other classes of aptamers.