Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera [PDF]
, 2013 DEAD box helicases catalyze the ATP-dependent destabilization of RNA duplexes. Whereas duplex separation is mediated by the helicase core shared by all members of the family, flanking domains often contribute to binding of the RNA substrate.
Klostermeier, Dagmar +5 more
core +1 more source
RNA structure maps across mammalian cellular compartments
Nature Structural & Molecular Biology, 2019 RNA structure is intimately connected to each step of gene expression. Recent advances have enabled transcriptome-wide maps of RNA secondary structure, called ‘RNA structuromes’.
Lei Sun +9 more
semanticscholar +1 more source
RNA structure prediction: progress and perspective
, 2014 Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures.
Shi, Ya-Zhou +3 more
core +1 more source
Alignments of RNA Structures [PDF]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010 We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit ...
Blin, Guillaume +4 more
openaire +4 more sources
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
Nature, 2013 RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA’s ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental ...
Silvi Rouskin +4 more
semanticscholar +1 more source
RNA Interference by Single- and Double-stranded siRNA With a DNA Extension Containing a 3′ Nuclease-resistant Mini-hairpin Structure [PDF]
, 2013 Selective gene silencing by RNA interference (RNAi) involves double-stranded small interfering RNA (ds siRNA) composed of single-stranded (ss) guide and passenger RNAs.
Ahmed +38 more
core +6 more sources
Combinatorial RNA Design Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models [PDF]
, 2016 We consider the Combinatorial RNA Design problem, a minimal instance of RNA design where one must produce an RNA sequence that adopts a given secondary structure as its minimal free-energy structure.
Haleš, Jozef +4 more
core +5 more sources
EMBO Molecular Medicine, 2017 Matrix metalloproteinase 9 (MMP‐9) has recently emerged as a molecule that contributes to pathological synaptic plasticity in schizophrenia, but explanation of the underlying mechanisms has been missing.
Katarzyna Lepeta +10 more
doaj +1 more source
RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure. [PDF]
PLoS ONE, 2015 Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary ...
Corinna Theis +6 more
doaj +1 more source
RNA secondary structure prediction from multi-aligned sequences [PDF]
, 2013 It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution.
A Balik +71 more
core +1 more source