The promise of cryo-EM to explore RNA structural dynamics

Thoughts on how to think (and talk) about RNA structure

(2022) Quentin Vicens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of cryo-EM cooling on structural ensembles

(2022) Lars V. Bock et al.   Nature Communications

Cryo-EM reveals an entangled kinetic trap in the folding of a catalytic RNA

(2022) Steve L. Bonilla et al.   Science Advances

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

(2021) Ellen D. Zhong et al.   NATURE METHODS

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM

(2021) Ali Punjani et al.   JOURNAL OF STRUCTURAL BIOLOGY

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

(2021) Zhaoming Su et al.   NATURE

Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

(2021) Kaiming Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles

(2021) Mattia Bernetti et al.   NUCLEIC ACIDS RESEARCH

High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs

(2021) Steve L. Bonilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A roadmap for rRNA folding and assembly during transcription

(2021) Margaret L. Rodgers et al.   TRENDS IN BIOCHEMICAL SCIENCES

A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments

(2021) Julian Giraldo-Barreto et al.   Scientific Reports

A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure

(2021) Steve L. Bonilla et al.   SCIENCE

Determination of RNA structural diversity and its role in HIV-1 RNA splicing

(2020) Phillip J. Tomezsko et al.   NATURE

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

(2020) Kalli Kappel et al.   NATURE METHODS

How low can we go? Structure determination of small biological complexes using single-particle cryo-EM

(2020) Mengyu Wu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy

(2019) Huaqun Zhang et al.   Wiley Interdisciplinary Reviews-RNA

The roles of structural dynamics in the cellular functions of RNAs

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

Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation

(2019) Joseph D. Yesselman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution

(2019) Kaiming Zhang et al.   Nature Communications

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

(2018) Massimiliano Bonomi et al.   BIOPHYSICAL JOURNAL

High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding

(2018) Sarah Knight Denny et al.   CELL

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

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Revealing the distinct folding phases of an RNA three-helix junction

(2018) Alex Plumridge et al.   NUCLEIC ACIDS RESEARCH

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

(2018) Takanori Nakane et al.   eLife

Reducing effects of particle adsorption to the air–water interface in cryo-EM

(2018) Alex J. Noble et al.   NATURE METHODS

Long Non-coding RNA Structure and Function: Is There a Link?

(2018) Anna Zampetaki et al.   Frontiers in Physiology

The Story of RNA Folding, as Told in Epochs

(2018) Daniel Herschlag et al.   Cold Spring Harbor Perspectives in Biology

Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway

(2017) Steve Bonilla et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

(2017) Aleksandar Spasic et al.   NUCLEIC ACIDS RESEARCH

Shape change in crystallization of biological macromolecules

(2016) Peter G. Vekilov et al.   MRS BULLETIN

How cryo-EM is revolutionizing structural biology

(2015) Xiao-chen Bai et al.   TRENDS IN BIOCHEMICAL SCIENCES

Distinguishing induced fit from conformational selection

(2014) Stefano Gianni et al.   BIOPHYSICAL CHEMISTRY

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

Cryo-EM enters a new era

(2014) Werner Kühlbrandt   eLife

Advances in the Determination of Nucleic Acid Conformational Ensembles

(2013) Loïc Salmon et al.   Annual Review of Physical Chemistry

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Molecular recognition and function of riboswitches

(2012) Alexander Serganov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Dynamic Nature of RNA as Key to Understanding Riboswitch Mechanisms

(2011) Andrea Haller et al.   ACCOUNTS OF CHEMICAL RESEARCH

Time resolved SAXS and RNA folding

(2011) Lois Pollack   BIOPOLYMERS

Conformational capture of the SAM-II riboswitch

(2011) Andrea Haller et al.   Nature Chemical Biology

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

(2011) Andrew C Stelzer et al.   Nature Chemical Biology

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure

(2009) P. V. Burra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison and functional implications of the 3D architectures of viral tRNA-like structures

(2009) J. A. Hammond et al.   RNA

A Molecular Ruler for Measuring Quantitative Distance Distributions

(2008) Rebecca S. Mathew-Fenn et al.   PLoS One