Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy
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 …
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
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 …
(WC) bps and can play unique functional roles in duplex DNA. Here, we use structural …
Visualizing spatially correlated dynamics that directs RNA conformational transitions
RNAs fold into three-dimensional (3D) structures that subsequently undergo large,
functionally important, conformational transitions in response to a variety of cellular signals …
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 …
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
Biomolecules form dynamic ensembles of many inter-converting conformations which are
key for understanding how they fold and function. However, determining ensembles is …
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) …
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
We describe a strategy for constructing atomic resolution dynamical ensembles of RNA
molecules, spanning up to millisecond timescales, that combines molecular dynamics (MD) …
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 …
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 …
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
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 …
secondary structure level significantly restrict the orientation of RNA helices across two-way …