Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

JR Bothe, EN Nikolova, CD Eichhorn, J Chugh… - Nature …, 2011 - nature.com
Many recently discovered noncoding RNAs do not fold into a single native conformation but
sample many different conformations along their free-energy landscape to carry out their …

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey

H Zhou, BJ Hintze, IJ Kimsey… - Nucleic acids …, 2015 - academic.oup.com
Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson–Crick
(WC) bps and can play unique functional roles in duplex DNA. Here, we use structural …

Visualizing spatially correlated dynamics that directs RNA conformational transitions

Q Zhang, AC Stelzer, CK Fisher, HM Al-Hashimi - Nature, 2007 - nature.com
RNAs fold into three-dimensional (3D) structures that subsequently undergo large,
functionally important, conformational transitions in response to a variety of cellular signals …

Topology links RNA secondary structure with global conformation, dynamics, and adaptation

MH Bailor, X Sun, HM Al-Hashimi - Science, 2010 - science.org
Thermodynamic rules that link RNA sequences to secondary structure are well established,
but the link between secondary structure and three-dimensional global conformation …

Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

H Shi, A Rangadurai, H Abou Assi, R Roy… - Nature …, 2020 - nature.com
Biomolecules form dynamic ensembles of many inter-converting conformations which are
key for understanding how they fold and function. However, determining ensembles is …

Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides

MM Islam, SR Chowdhury… - The Journal of Physical …, 2009 - ACS Publications
The interaction of two natural protoberberine plant alkaloids berberine and palmatine and a
synthetic derivative coralyne to three double stranded ribonucleic acids, poly (A). poly (U) …

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

AT Frank, AC Stelzer, HM Al-Hashimi… - Nucleic acids …, 2009 - academic.oup.com
We describe a strategy for constructing atomic resolution dynamical ensembles of RNA
molecules, spanning up to millisecond timescales, that combines molecular dynamics (MD) …

Advances in the determination of nucleic acid conformational ensembles

L Salmon, S Yang, HM Al-Hashimi - Annual review of physical …, 2014 - annualreviews.org
Conformational changes in nucleic acids play a key role in the way genetic information is
stored, transferred, and processed in living cells. Here, we describe new approaches that …

Review NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings

M Getz, X Sun, A Casiano‐Negroni… - Biopolymers …, 2007 - Wiley Online Library
An increasing number of RNAs are being discovered that perform their functions by
undergoing large changes in conformation in response to a variety of cellular signals …

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges

AM Mustoe, HM Al-Hashimi… - The Journal of Physical …, 2014 - ACS Publications
Recent studies have shown that simple stereochemical constraints encoded at the RNA
secondary structure level significantly restrict the orientation of RNA helices across two-way …