Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery

(2019) Sai Shashank Chavali et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure

(2019) Colleen M. Connelly et al.   Nature Communications

Nucleobase mutants of a bacterial preQ1-II riboswitch that uncouple metabolite sensing from gene regulation

(2019) Debapratim Dutta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure

(2019) Paul E Lund et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Kaiming Zhang et al.   Nature Communications

Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria

(2018) Debapratim Dutta et al.   BIOCHEMISTRY

SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation

(2018) Jeremy D. Schmit et al.   Journal of Chemical Theory and Computation

Principles for targeting RNA with drug-like small molecules

(2018) Katherine Deigan Warner et al.   NATURE REVIEWS DRUG DISCOVERY

Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription

(2018) Ivan A Belashov et al.   NUCLEIC ACIDS RESEARCH

Structure–Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch

(2018) Quentin Vicens et al.   ACS Chemical Biology

ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands

(2018) Alla Peselis et al.   Nature Chemical Biology

Ribosome-induced RNA conformational changes in a viral 3′-UTR sense and regulate translation levels

(2018) Erik W. Hartwick et al.   Nature Communications

Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes

(2017) Joseph E. Wedekind et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

(2017) J. R. Stagno et al.   NATURE

Riboswitch diversity and distribution

(2017) Phillip J. McCown et al.   RNA

Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated

(2016) Marina Frener et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Characterizing RNA structures in vitro and in vivo with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2016) Kyle E. Watters et al.   METHODS

Mg2+ions: do they bind to nucleobase nitrogens?

(2016) Filip Leonarski et al.   NUCLEIC ACIDS RESEARCH

The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts

(2016) Arlie J. Rinaldi et al.   Nature Communications

Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model

(2015) Pengfei Li et al.   Journal of Chemical Theory and Computation

Force Field for Mg2+, Mn2+, Zn2+, and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids

(2015) Maria T. Panteva et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Selective small-molecule inhibition of an RNA structural element

(2015) John A. Howe et al.   NATURE

Structural analysis of a class III preQ1riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

(2015) Joseph A. Liberman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface

(2015) Anita C. Jones et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics

(2015) Asaminew H. Aytenfisu et al.   RNA

Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch

(2015) Aiming Ren et al.   Cell Reports

The purine riboswitch as a model system for exploring RNA biology and chemistry

(2014) Ely B. Porter et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations

(2014) Tod D. Romo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Structure and function of pseudoknots involved in gene expression control

(2014) Alla Peselis et al.   Wiley Interdisciplinary Reviews-RNA

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure

(2013) Krishna C. Suddala et al.   NUCLEIC ACIDS RESEARCH

Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study

(2012) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Mechanisms of RNA SHAPE Chemistry

(2012) Jennifer L. McGinnis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

Linking Crystallographic Model and Data Quality

(2012) P. A. Karplus et al.   SCIENCE

Ultraviolet Shadowing of RNA Can Cause Significant Chemical Damage in Seconds

(2012) Wipapat Kladwang et al.   Scientific Reports

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world

(2011) Joseph A Liberman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Comparison of a PreQ1Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation

(2011) Jermaine L. Jenkins et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection

(2011) Quentin Vicens et al.   NUCLEIC ACIDS RESEARCH

Modeling and automation of sequencing-based characterization of RNA structure

(2011) S. Aviran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms

(2011) Jean-François Lemay et al.   PLoS Genetics

Riboswitch structure in the ligand-free state

(2011) Joseph A. Liberman et al.   Wiley Interdisciplinary Reviews-RNA

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch

(2010) Lili Huang et al.   MOLECULAR CELL

Folding of a transcriptionally acting PreQ1 riboswitch

(2010) U. Rieder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for recognition of S-adenosylhomocysteine by riboswitches

(2010) A. L. Edwards et al.   RNA

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

(2010) Colby D. Stoddard et al.   STRUCTURE

Riboswitches: Structures and Mechanisms

(2010) A. D. Garst et al.   Cold Spring Harbor Perspectives in Biology

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Structural and Functional Diversity of Metabolite-Binding Riboswitches

(2009) Adam Roth et al.   Annual Review of Biochemistry

Amino acid recognition and gene regulation by riboswitches

(2009) Alexander Serganov et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A partial nudged elastic band implementation for use with large or explicitly solvated systems

(2009) Christina Bergonzo et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

The Structural Basis for Recognition of the PreQ0Metabolite by an Unusually Small Riboswitch Aptamer Domain

(2009) Robert C. Spitale et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA

(2009) Mijeong Kang et al.   MOLECULAR CELL

Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch

(2009) Alexander Serganov et al.   NATURE

Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase

(2009) Daniel J Klein et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Deciphering Deazapurine Biosynthesis: Pathway for Pyrrolopyrimidine Nucleosides Toyocamycin and Sangivamycin

(2008) Reid M. McCarty et al.   CHEMISTRY & BIOLOGY

Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element

(2008) Andrew D. Garst et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch

(2008) Stéphane Thore et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Strong Correlation between SHAPE Chemistry and the Generalized NMR Order Parameter (S2) in RNA

(2008) Costin M. Gherghe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural insights into amino acid binding and gene control by a lysine riboswitch

(2008) Alexander Serganov et al.   NATURE