The roles of structural dynamics in the cellular functions of RNAs

RNA structure maps across mammalian cellular compartments

(2019) Lei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit

(2018) Ambadas B. Rode et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

(2018) Anthony M. Mustoe et al.   CELL

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

(2018) Sarah Knight Denny et al.   CELL

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

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

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics

(2018) Yang Qi et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

(2018) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin 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

Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics

(2018) Dawn K Merriman et al.   RNA

RNA buffers the phase separation behavior of prion-like RNA binding proteins

(2018) Shovamayee Maharana et al.   SCIENCE

mRNA structure determines specificity of a polyQ-driven phase separation

(2018) Erin M. Langdon et al.   SCIENCE

Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes

(2018) Hua Li et al.   Nature Communications

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis

(2018) Ryota Yamagami et al.   Nature Communications

Life times of metastable states guide regulatory signaling in transcriptional riboswitches

(2018) Christina Helmling et al.   Nature Communications

A potentially abundant junctional RNA motif stabilized by m6A and Mg2+

(2018) Bei Liu 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

2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

(2018) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Hidden Structural Modules in a Cooperative RNA Folding Transition

(2018) Brant Gracia et al.   Cell Reports

Mimicking Co-Transcriptional RNA Folding Using a Superhelicase

(2018) Boyang Hua et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamic basis for dG•dT misincorporation via tautomerization and ionization

(2018) Isaac J. Kimsey et al.   NATURE

Challenges and Approaches to Predicting RNA with Multiple Functional Structures

(2018) Susan J Schroeder   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

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

(2018) Sunny Y. Yang et al.   Nature Communications

Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA

(2017) Benjamin E. Allred et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations

(2017) Christina Helmling et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

Ensemble cryo-EM elucidates the mechanism of translation fidelity

(2017) Anna B. Loveland et al.   NATURE

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

Chemical and structural effects of base modifications in messenger RNA

(2017) Emily M. Harcourt et al.   NATURE

An excited state underlies gene regulation of a transcriptional riboswitch

(2017) Bo Zhao et al.   Nature Chemical Biology

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Distributed biotin–streptavidin transcription roadblocks for mapping cotranscriptional RNA folding

(2017) Eric J. Strobel et al.   NUCLEIC ACIDS RESEARCH

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

(2017) Aleksandar Spasic et al.   NUCLEIC ACIDS RESEARCH

Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch

(2017) Heesoo Uhm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination

(2017) Arjun Prabhakar et al.   PROTEIN SCIENCE

Pseudouridine and N 6 -methyladenosine modifications weaken PUF protein/RNA interactions

(2017) Pavanapuresan P. Vaidyanathan et al.   RNA

Slow molecular recognition by RNA

(2017) Kristin R. Gleitsman et al.   RNA

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation

(2017) Hannah Steinert et al.   eLife

Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells

(2016) Jessica L. Childs-Disney et al.   Annual Review of Pharmacology and Toxicology

Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales

(2016) Dawn K. Merriman et al.   BIOCHEMISTRY

RNA assemblages orchestrate complex cellular processes

(2016) Finn Cilius Nielsen et al.   BIOESSAYS

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

(2016) Guanghong Wei et al.   CHEMICAL REVIEWS

RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation

(2016) J. Matthew Taliaferro et al.   MOLECULAR CELL

RNA Remodeling Activity of DEAD Box Proteins Tuned by Protein Concentration, RNA Length, and ATP

(2016) Younghoon Kim et al.   MOLECULAR CELL

The solution structural ensembles of RNA kink-turn motifs and their protein complexes

(2016) Xuesong Shi et al.   Nature Chemical Biology

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

(2016) Huiqing Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cotranscriptional folding of a riboswitch at nucleotide resolution

(2016) Kyle E Watters et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics

(2016) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Opportunities in the design and application of RNA for gene expression control

(2016) Maureen McKeague et al.   NUCLEIC ACIDS RESEARCH

Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway

(2016) Namita Bisaria et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NMR detection of intermolecular interaction sites in the dimeric 5′-leader of the HIV-1 genome

(2016) Sarah C. Keane et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of a low-population binding intermediate in protein-RNA recognition

(2016) Aditi N. Borkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bridging the gap between in vitro and in vivo RNA folding

(2016) Kathleen A. Leamy et al.   QUARTERLY REVIEWS OF BIOPHYSICS

RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria

(2016) J. U. Guo et al.   SCIENCE

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch

(2016) Yi Xue et al.   Nature Communications

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

(2016) Huiqing Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cotranscriptional folding of a riboswitch at nucleotide resolution

(2016) Kyle E Watters et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics

(2016) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

(2016) Emily J. Hawkes et al.   Cell Reports

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

(2015) Magdalena Gebala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Noncanonical Secondary Structure Stabilizes Mitochondrial tRNASer(UCN) by Reducing the Entropic Cost of Tertiary Folding

(2015) Anthony M. Mustoe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes

(2015) Wenwen Fang et al.   MOLECULAR CELL

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

Visualizing transient Watson–Crick-like mispairs in DNA and RNA duplexes

(2015) Isaac J. Kimsey et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics

(2015) Mario R Blanco et al.   NATURE METHODS

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple conformations are a conserved and regulatory feature of theRB15′ UTR

(2015) Katrina M. Kutchko et al.   RNA

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

(2015) Pablo Cordero et al.   PLoS Computational Biology

A Toxic RNA Catalyzes the In Cellulo Synthesis of Its Own Inhibitor

(2014) Suzanne G. Rzuczek et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Hierarchy of RNA Functional Dynamics

(2014) Anthony M. Mustoe et al.   Annual Review of Biochemistry

Understanding Nucleic Acid–Ion Interactions

(2014) Jan Lipfert et al.   Annual Review of Biochemistry

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

Global analysis of riboswitches by small-angle X-ray scattering and calorimetry

(2014) Jinwei Zhang et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2014) Thomas R. Cech et al.   CELL

Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme

(2014) Hui-Ting Lee et al.   NUCLEIC ACIDS RESEARCH

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

(2014) Anthony M. Mustoe et al.   NUCLEIC ACIDS RESEARCH

Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble

(2014) Emily Rogers et al.   NUCLEIC ACIDS RESEARCH

Invisible RNA state dynamically couples distant motifs

(2014) Janghyun Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics

(2014) N. F. Dupuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states

(2014) Siqi Tian et al.   RNA

Advances in the Determination of Nucleic Acid Conformational Ensembles

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

Molecular Crowding Favors Reactivity of a Human Ribozyme Under Physiological Ionic Conditions

(2013) Christopher A. Strulson et al.   BIOCHEMISTRY

Ensemble Analysis of Primary MicroRNA Structure Reveals an Extensive Capacity To Deform near the Drosha Cleavage Site

(2013) Kaycee A. Quarles et al.   BIOCHEMISTRY

Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids

(2013) Shu-ichi Nakano et al.   CHEMICAL REVIEWS

Increased Ribozyme Activity in Crowded Solutions

(2013) Ravi Desai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed

(2013) Loïc Salmon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Three-state mechanism couples ligand and temperature sensing in riboswitches

(2013) Anke Reining et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

(2013) Justin Ritz et al.   PLoS Computational Biology

Visualizing transient low-populated structures of RNA

(2012) Elizabeth A. Dethoff et al.   NATURE

Functional complexity and regulation through RNA dynamics

(2012) Elizabeth A. Dethoff et al.   NATURE

RNA catalysis through compartmentalization

(2012) Christopher A. Strulson et al.   Nature Chemistry

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

(2012) Raheleh Salari et al.   NUCLEIC ACIDS RESEARCH

Assembly of Bacterial Ribosomes

(2011) Zahra Shajani et al.   Annual Review of Biochemistry

Molecular Basis for Interaction of let-7 MicroRNAs with Lin28

(2011) Yunsun Nam et al.   CELL

Prospects for Riboswitch Discovery and Analysis

(2011) Ronald R. Breaker   MOLECULAR CELL

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

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

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

Compact Intermediates in RNA Folding

(2010) Sarah A. Woodson   Annual Review of Biophysics

Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect

(2010) Duncan Kilburn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

(2010) M. H. Bailor et al.   SCIENCE

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

Maternally Expressed Gene 3 (MEG3) Noncoding Ribonucleic Acid: Isoform Structure, Expression, and Functions

(2009) Xun Zhang et al.   ENDOCRINOLOGY

Germline mutation of microRNA-125a is associated with breast cancer

(2009) W Li et al.   JOURNAL OF MEDICAL GENETICS

Facilitation of RNA Enzyme Activity in the Molecular Crowding Media of Cosolutes

(2009) Shu-ichi Nakano 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

RNA granules: post-transcriptional and epigenetic modulators of gene expression

(2009) Paul Anderson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2009) Aaron T. Frank et al.   NUCLEIC ACIDS RESEARCH

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

(2009) V. B. Chu et al.   RNA

A repulsive field: advances in the electrostatics of the ion atmosphere

(2008) Vincent B Chu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

RNA misfolding and the action of chaperones

(2007) Rick Russell   Frontiers in Bioscience-Landmark