RNA–ligand molecular docking: Advances and challenges

Y Zhou, Y Jiang, SJ Chen - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
With rapid advances in computer algorithms and hardware, fast and accurate virtual
screening has led to a drastic acceleration in selecting potent small molecules as drug …

Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer

P Vallurupalli, A Sekhar, T Yuwen, LE Kay - Journal of biomolecular NMR, 2017 - Springer
Abstract Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments
have been used to study chemical exchange processes in molecules since the early 1960s …

2′-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states

H Abou Assi, AK Rangadurai, H Shi, B Liu… - Nucleic acids …, 2020 - academic.oup.com
O-Methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays
important biological roles through mechanisms that are not entirely understood. There is …

An excited state underlies gene regulation of a transcriptional riboswitch

B Zhao, SL Guffy, B Williams, Q Zhang - Nature chemical biology, 2017 - nature.com
Riboswitches control gene expression through ligand-dependent structural rearrangements
of the sensing aptamer domain. However, we found that the Bacillus cereus fluoride …

Multi‐Site Conformational Exchange in the Synthetic Neomycin‐Sensing Riboswitch Studied by 19F NMR

JH Overbeck, J Vögele, F Nussbaumer… - Angewandte Chemie …, 2023 - Wiley Online Library
The synthetic neomycin‐sensing riboswitch interacts with its cognate ligand neomycin as
well as with the related antibiotics ribostamycin and paromomycin. Binding of these …

Chemical exchange

AG Palmer III, H Koss - Methods in enzymology, 2019 - Elsevier
The phenomenon of chemical or conformational exchange in NMR spectroscopy has
enabled detailed characterization of time-dependent aspects of biomolecular function …

Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion

A Rangadurai, ES Szymaski, IJ Kimsey, H Shi… - Progress in nuclear …, 2019 - Elsevier
This review describes off-resonance R 1ρ relaxation dispersion NMR methods for
characterizing microsecond-to-millisecond chemical exchange in uniformly 13 C/15 N …

NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing

H Shi, B Liu, F Nussbaumer… - Journal of the …, 2019 - ACS Publications
N 6-Methyladenosine (m6A) is an abundant epitranscriptomic modification that plays
important roles in many aspects of RNA metabolism. While m6A is thought to mainly function …

RNA dynamics by NMR spectroscopy

M Marušič, J Schlagnitweit, K Petzold - ChemBioChem, 2019 - Wiley Online Library
An ever‐increasing number of functional RNAs require a mechanistic understanding. RNA
function relies on changes in its structure, so‐called dynamics. To reveal dynamic processes …

Visualizing a protonated RNA state that modulates microRNA-21 maturation

JT Baisden, JA Boyer, B Zhao, SM Hammond… - Nature chemical …, 2021 - nature.com
MicroRNAs are evolutionarily conserved small, noncoding RNAs that regulate diverse
biological processes. Due to their essential regulatory roles, microRNA biogenesis is tightly …