RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks

SE Butcher, AM Pyle - Accounts of chemical research, 2011 - ACS Publications
RNA molecules adopt specific three-dimensional structures critical to their function. Many
essential metabolic processes, including protein synthesis and RNA splicing, are carried out …

A structural analysis of the group II intron active site and implications for the spliceosome

KS Keating, N Toor, PS Perlman, AM Pyle - Rna, 2010 - rnajournal.cshlp.org
Group II introns are self-splicing, mobile genetic elements that have fundamentally
influenced the organization of terrestrial genomes. These large ribozymes remain important …

The tertiary structure of group II introns: implications for biological function and evolution

AM Pyle - Critical reviews in biochemistry and molecular biology, 2010 - Taylor & Francis
Group II introns are some of the largest ribozymes in nature, and they are a major source of
information about RNA assembly and tertiary structural organization. These introns are of …

An RNA folding motif: GNRA tetraloop–receptor interactions

JL Fiore, DJ Nesbitt - Quarterly reviews of biophysics, 2013 - cambridge.org
Nearly two decades after Westhof and Michel first proposed that RNA tetraloops may interact
with distal helices, tetraloop–receptor interactions have been recognized as ubiquitous …

Transposable elements in disease-associated cryptic exons

I Vorechovsky - Human genetics, 2010 - Springer
Transposable elements (TEs) make up a half of the human genome, but the extent of their
contribution to cryptic exon activation that results in genetic disease is unknown. Here, a …

Recognition modes of RNA tetraloops and tetraloop‐like motifs by RNA‐binding proteins

R Thapar, AP Denmon… - Wiley Interdisciplinary …, 2014 - Wiley Online Library
RNA hairpins are the most commonly occurring secondary structural elements in RNAs and
serve as nucleation sites for RNA folding, RNA–RNA, and RNA–protein interactions. RNA …

Tertiary architecture of the Oceanobacillus iheyensis group II intron

N Toor, KS Keating, O Fedorova, K Rajashankar… - Rna, 2010 - rnajournal.cshlp.org
Group II introns are large ribozymes that act as self-splicing and retrotransposable RNA
molecules. They are of great interest because of their potential evolutionary relationship to …

[HTML][HTML] RCrane: semi-automated RNA model building

KS Keating, AM Pyle - Acta Crystallographica Section D: Biological …, 2012 - scripts.iucr.org
RNA crystals typically diffract to much lower resolutions than protein crystals. This low-
resolution diffraction results in unclear density maps, which cause considerable difficulties …

Engineering crystal packing in RNA structures I: past and future strategies for engineering RNA packing in crystals

N Pujari, SL Saundh, FA Acquah, BHM Mooers… - Crystals, 2021 - mdpi.com
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic
and regulatory functions of RNA molecules. However, the technique requires the …