Understanding nucleic acid–ion interactions

J Lipfert, S Doniach, R Das… - Annual review of …, 2014 - annualreviews.org
Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the
folding and dynamics of RNA and DNA and their complexes with proteins and with each …

Theory and modeling of RNA structure and interactions with metal ions and small molecules

LZ Sun, D Zhang, SJ Chen - Annual review of biophysics, 2017 - annualreviews.org
In addition to continuous rapid progress in RNA structure determination, probing, and
biophysical studies, the past decade has seen remarkable advances in the development of …

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 …

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

H Zheng, IG Shabalin, KB Handing… - Nucleic acids …, 2015 - academic.oup.com
The ubiquitous presence of magnesium ions in RNA has long been recognized as a key
factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In …

Recognition of small molecule–RNA binding sites using RNA sequence and structure

H Su, Z Peng, J Yang - Bioinformatics, 2021 - academic.oup.com
Motivation RNA molecules become attractive small molecule drug targets to treat disease in
recent years. Computer-aided drug design can be facilitated by detecting the RNA sites that …

LigandRNA: computational predictor of RNA–ligand interactions

A Philips, K Milanowska, G Łach, JM Bujnicki - Rna, 2013 - rnajournal.cshlp.org
RNA molecules have recently become attractive as potential drug targets due to the
increased awareness of their importance in key biological processes. The increase of the …

Augmented base pairing networks encode RNA-small molecule binding preferences

C Oliver, V Mallet, RS Gendron, V Reinharz… - Nucleic acids …, 2020 - academic.oup.com
RNA-small molecule binding is a key regulatory mechanism which can stabilize 3D
structures and activate molecular functions. The discovery of RNA-targeting compounds is …

Gas-phase conformations and energetics of protonated 2′-deoxyadenosine and adenosine: IRMPD action spectroscopy and theoretical studies

RR Wu, B Yang, G Berden, J Oomens… - The Journal of …, 2015 - ACS Publications
The gas-phase conformations of protonated 2′-deoxyadenosine,[dAdo+ H]+, and its RNA
analogue protonated adenosine,[Ado+ H]+, generated upon electrospray ionization are …

Computational methods for modeling aptamers and designing riboswitches

S Gong, Y Wang, Z Wang, W Zhang - International journal of molecular …, 2017 - mdpi.com
Riboswitches, which are located within certain noncoding RNA region perform functions as
genetic “switches”, regulating when and where genes are expressed in response to certain …

Identification of metal ion-binding sites in RNA structures using deep learning method

Y Zhao, J Wang, F Chang, W Gong… - Briefings in …, 2023 - academic.oup.com
Metal ion is an indispensable factor for the proper folding, structural stability and functioning
of RNA molecules. However, it is very difficult for experimental methods to detect them in …