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 …

Riboswitch distribution, structure, and function in bacteria

N Pavlova, D Kaloudas, R Penchovsky - Gene, 2019 - Elsevier
Riboswitches are gene control elements that directly bind to specific ligands to regulate
gene expression without the need for proteins. They are found in all three domains of life …

[HTML][HTML] RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

J Singh, J Hanson, K Paliwal, Y Zhou - Nature communications, 2019 - nature.com
The majority of our human genome transcribes into noncoding RNAs with unknown
structures and functions. Obtaining functional clues for noncoding RNAs requires accurate …

Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix

JA Brown, D Bulkley, J Wang, ML Valenstein… - Nature structural & …, 2014 - nature.com
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a highly abundant
nuclear long noncoding RNA that promotes malignancy. A 3′-stem-loop structure is …

Unraveling the structure and biological functions of RNA triple helices

JA Brown - Wiley Interdisciplinary Reviews: RNA, 2020 - Wiley Online Library
It has been nearly 63 years since the first characterization of an RNA triple helix in vitro by
Gary Felsenfeld, David Davies, and Alexander Rich. An RNA triple helix consists of three …

[HTML][HTML] A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

GM Schroeder, CE Cavender, ME Blau… - Nature …, 2022 - nature.com
Riboswitches are structured non-coding RNAs often located upstream of essential genes in
bacterial messenger RNAs. Such RNAs regulate expression of downstream genes by …

Themes and variations in riboswitch structure and function

A Peselis, A Serganov - Biochimica et Biophysica Acta (BBA)-Gene …, 2014 - Elsevier
The complexity of gene expression control by non-coding RNA has been highlighted by the
recent progress in the field of riboswitches. Discovered a decade ago, riboswitches …

Structural insights into translation regulation by the THF-II riboswitch

L Xu, Y Xiao, J Zhang, X Fang - Nucleic Acids Research, 2023 - academic.oup.com
In bacteria, expression of folate-related genes is controlled by the tetrahydrofolate (THF)
riboswitch in response to specific binding of THF and its derivatives. Recently, a second …

RNA triplexes: from structural principles to biological and biotech applications

G Devi, Y Zhou, Z Zhong, DFK Toh… - Wiley Interdisciplinary …, 2015 - Wiley Online Library
The diverse biological functions of RNA are determined by the complex structures of RNA
stabilized by both secondary and tertiary interactions. An RNA triplex is an important tertiary …

Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations

NM Fischer, MD Polêto, J Steuer… - Nucleic acids …, 2018 - academic.oup.com
The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of,
in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray …