Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids

NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function

(2021) T. Reid Alderson et al.   CELL

4′-Fluorinated RNA: Synthesis, Structure, and Applications as a Sensitive 19F NMR Probe of RNA Structure and Function

(2020) Qiang Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods

(2020) Anita Kotar et al.   METHODS

A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR

(2020) Mihajlo Novakovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing RNA Conformational Equilibria within the Functional Cellular Context

(2020) Laura R. Ganser et al.   Cell Reports

Extending the Sensitivity of CEST NMR Spectroscopy to Micro‐to‐Millisecond Dynamics in Nucleic Acids Using High‐Power Radio‐Frequency Fields

(2020) Atul Rangadurai et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA

(2020) Lorenzo Baronti et al.   NATURE

Integrating NMR and simulations reveals motions in the UUCG tetraloop

(2020) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans

(2020) Oliver Binas et al.   NUCLEIC ACIDS RESEARCH

A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle

(2020) Gili Abramov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aromatic 19 F– 13 C TROSY—[ 19 F, 13 C]‐Pyrimidine Labeling for NMR Spectroscopy of RNA

(2020) Felix Nußbaumer et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

5′-fluoro(di)phosphate-labeled oligonucleotides are versatile molecular probes for studying nucleic acid secondary structure and interactions by 19F NMR

(2020) Marek R Baranowski et al.   NUCLEIC ACIDS RESEARCH

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

(2020) Romeo C A Dubini et al.   NUCLEIC ACIDS RESEARCH

FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds

(2020) Andrew Martin Watkins et al.   STRUCTURE

Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage

(2020) Yu Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Visualizing a protonated RNA state that modulates microRNA-21 maturation

(2020) Jared T. Baisden et al.   Nature Chemical Biology

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

(2020) Hala Abou Assi et al.   NUCLEIC ACIDS RESEARCH

Solution NMR readily reveals distinct structural folds and interactions in doubly 13C- and 19F-labeled RNAs

(2020) Owen B. Becette et al.   Science Advances

Using quantum chemistry to estimate chemical shifts in biomolecules

(2020) David A. Case   BIOPHYSICAL CHEMISTRY

Parallel reaction pathways accelerate folding of a guanine quadruplex

(2020) Robert W Harkness et al.   NUCLEIC ACIDS RESEARCH

Aromatic 19F-13C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics

(2019) Andras Boeszoermenyi et al.   NATURE METHODS

Defining the Role of Nucleotide Flipping in Enzyme Specificity Using 19F NMR

(2019) Blaine J. Dow et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA dynamics by NMR

(2019) Maja Marušič et al.   CHEMBIOCHEM

Fitting Corrections to an RNA Force Field Using Experimental Data

(2019) Andrea Cesari et al.   Journal of Chemical Theory and Computation

The roles of structural dynamics in the cellular functions of RNAs

(2019) Laura R. Ganser et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The roles of DNA, RNA and histone methylation in ageing and cancer

(2019) Ewa M. Michalak et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site

(2019) Chia-Chieh Chu et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Atul Rangadurai et al.   PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy

(2019) Owen Becette et al.   MOLECULES

Direct evidence for (G)O6···H2-N4(C)+ hydrogen bonding in transient G(syn)-C+ and G(syn)-m5C+ Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R1ρ relaxation dispersion measurements

(2019) Atul Rangadurai et al.   JOURNAL OF MAGNETIC RESONANCE

Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing

(2019) Raphael Plangger et al.   NUCLEIC ACIDS RESEARCH

Determination of a Structural Ensemble Representing the Dynamics of a G-Quadruplex DNA

(2019) Guillem Portella et al.   BIOCHEMISTRY

Enhancing NMR derived ensembles with kinetics on multiple timescales

(2019) Colin A. Smith et al.   JOURNAL OF BIOMOLECULAR NMR

Probing excited conformational states of nucleic acids by nitrogen CEST NMR spectroscopy

(2019) Bo Zhao et al.   JOURNAL OF MAGNETIC RESONANCE

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

(2019) Honglue Shi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exposing Hidden High-Affinity RNA Conformational States

(2019) Nicole I. Orlovsky et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational Dynamics of Strand Register Shifts in DNA G-Quadruplexes

(2019) J. Tassilo Grün et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data

(2019) Sabine Reißer et al.   NUCLEIC ACIDS RESEARCH

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach

(2018) Judith Schlagnitweit et al.   CHEMISTRY-A EUROPEAN JOURNAL

NMR probing of invisible excited states using selectively labeled RNAs

(2018) Regan M. LeBlanc et al.   JOURNAL OF BIOMOLECULAR NMR

Isotope labeling for studying RNA by solid-state NMR spectroscopy

(2018) Alexander Marchanka et al.   JOURNAL OF BIOMOLECULAR NMR

Atomic structures of excited state A–T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations

(2018) Honglue Shi et al.   JOURNAL OF BIOMOLECULAR NMR

Accurate Measurement of Residual Dipolar Couplings in Large RNAs by Variable Flip Angle NMR

(2018) Jan Marchant et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble

(2018) Laura R. Ganser et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA force field with accuracy comparable to state-of-the-art protein force fields

(2018) Dazhi Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Life times of metastable states guide regulatory signaling in transcriptional riboswitches

(2018) Christina Helmling et al.   Nature Communications

High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble

(2018) Laura R. Ganser et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations

(2018) Sandro Bottaro et al.   Science Advances

Dynamic basis for dG•dT misincorporation via tautomerization and ionization

(2018) Isaac J. Kimsey et al.   NATURE

Regulation of microRNA function in animals

(2018) Luca F. R. Gebert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Coupling Between Conformational Dynamics and Catalytic Function at the Active Site of the Lead-Dependent Ribozyme

(2018) Neil A White et al.   RNA

5-Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson-Crick like cmo5 U-G Base Pairs

(2018) Elisabeth Strebitzer et al.   CHEMISTRY-A EUROPEAN JOURNAL

Structure modeling of RNA using sparse NMR constraints

(2017) Benfeard Williams et al.   NUCLEIC ACIDS RESEARCH

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

(2017) Bharathwaj Sathyamoorthy et al.   NUCLEIC ACIDS RESEARCH

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop

(2017) Aditi N. Borkar et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Characterizing excited conformational states of RNA by NMR spectroscopy

(2015) Bo Zhao et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

(2015) Jason Swails et al.   JOURNAL OF BIOMOLECULAR NMR

A Simple and Fast Approach for Predicting 1H and 13C Chemical Shifts: Toward Chemical Shift-Guided Simulations of RNA

(2014) Aaron T. Frank et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

(2014) Parin Sripakdeevong et al.   NATURE METHODS

Characterizing RNA ensembles from NMR data with kinematic models

(2014) Rasmus Fonseca et al.   NUCLEIC ACIDS RESEARCH

Visualizing transient low-populated structures of RNA

(2012) Elizabeth A. Dethoff et al.   NATURE

Isotope labeling strategies for NMR studies of RNA

(2009) Kun Lu et al.   JOURNAL OF BIOMOLECULAR NMR

Exact Distances and Internal Dynamics of Perdeuterated Ubiquitin from NOE Buildups

(2009) Beat Vögeli et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology