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Understanding nucleic acid–ion interactions
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 …
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
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 …
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 …
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
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 …
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
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 …
recent years. Computer-aided drug design can be facilitated by detecting the RNA sites that …
LigandRNA: computational predictor of RNA–ligand interactions
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 …
increased awareness of their importance in key biological processes. The increase of the …
Augmented base pairing networks encode RNA-small molecule binding preferences
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 …
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
The gas-phase conformations of protonated 2′-deoxyadenosine,[dAdo+ H]+, and its RNA
analogue protonated adenosine,[Ado+ H]+, generated upon electrospray ionization are …
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 …
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 …
of RNA molecules. However, it is very difficult for experimental methods to detect them in …