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 …

The building blocks and motifs of RNA architecture

NB Leontis, A Lescoute, E Westhof - Current opinion in structural biology, 2006 - Elsevier
RNA motifs can be defined broadly as recurrent structural elements containing multiple
intramolecular RNA–RNA interactions, as observed in atomic-resolution RNA structures …

[HTML][HTML] Embracing proteins: structural themes in aptamer–protein complexes

AD Gelinas, DR Davies, N Janjic - Current opinion in structural biology, 2016 - Elsevier
Highlights•Traditional aptamers fold into structures with established nucleic acid
motifs.•Modified nucleotides expand the repertoire of known nucleic acid structural …

Review of machine learning methods for RNA secondary structure prediction

Q Zhao, Z Zhao, X Fan, Z Yuan, Q Mao… - PLoS computational …, 2021 - journals.plos.org
Secondary structure plays an important role in determining the function of noncoding RNAs.
Hence, identifying RNA secondary structures is of great value to research. Computational …

RNA STRAND: the RNA secondary structure and statistical analysis database

M Andronescu, V Bereg, HH Hoos, A Condon - BMC bioinformatics, 2008 - Springer
Background The ability to access, search and analyse secondary structures of a large set of
known RNA molecules is very important for deriving improved RNA energy models, for …

Analysis of RNA motifs

NB Leontis, E Westhof - Current opinion in structural biology, 2003 - Elsevier
RNA motifs are directed and ordered stacked arrays of non-Watson–Crick base pairs
forming distinctive foldings of the phosphodiester backbones of the interacting RNA strands …

RNA structural motifs: building blocks of a modular biomolecule

DK Hendrix, SE Brenner, SR Holbrook - Quarterly reviews of …, 2005 - cambridge.org
1. Introduction 2222. What is an RNA motif? 2222.1 Sequence vs. structural motifs 2222.2
RNA structural motifs 2232.3 RNA structural elements vs. motifs 2232.4 Specific recognition …

A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites

Q Du, H Thonberg, J Wang, C Wahlestedt… - Nucleic acids …, 2005 - academic.oup.com
The specificity of small interfering RNA (siRNA)-mediated gene silencing is a critical
consideration for the application of RNA interference (RNAi). While the discovery of potential …

[HTML][HTML] RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications

H Li, T Lee, T Dziubla, F Pi, S Guo, J Xu, C Li, F Haque… - Nano today, 2015 - Elsevier
The value of polymers is manifested in their vital use as building blocks in material and life
sciences. Ribonucleic acid (RNA) is a polynucleic acid, but its polymeric nature in materials …

Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines

A Weixlbaumer, FV Murphy IV, A Dziergowska… - Nature structural & …, 2007 - nature.com
One of the most prevalent base modifications involved in decoding is uridine 5-oxyacetic
acid at the wobble position of tRNA. It has been known for several decades that this …