Bridging the gap between in vitro and in vivo RNA folding

Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR

(2016) Chelsea M. Hull et al.   ACS Chemical Biology

RNA Hairpin Folding in the Crowded Cell

(2016) Mimi Gao et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Computational modeling of RNA 3D structures and interactions

(2016) Wayne K Dawson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg2+, Nucleotides, and RNA

(2016) Erica A. Frankel et al.   LANGMUIR

Structure and Mechanism of RNA Mimics of Green Fluorescent Protein

(2015) Mingxu You et al.   Annual Review of Biophysics

Challenge of Mimicking the Influences of the Cellular Environment on RNA Structure by PEG-Induced Macromolecular Crowding

(2015) Jillian Tyrrell et al.   BIOCHEMISTRY

StructureFold: genome-wide RNA secondary structure mapping and reconstructionin vivo

(2015) Yin Tang et al.   BIOINFORMATICS

Effects of Cosolvents on the Folding and Catalytic Activities of the Hammerhead Ribozyme

(2015) Shu-ichi Nakano et al.   CHEMBIOCHEM

Fast kinetics of calcium signaling and sensor design

(2015) Shen Tang et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA

(2015) Chelsea M. Hull et al.   JOURNAL OF MOLECULAR BIOLOGY

Kinetic and Thermodynamic Origins of Osmolyte-Influenced Nucleic Acid Folding

(2015) Erik D. Holmstrom et al.   JOURNAL OF PHYSICAL CHEMISTRY B

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

(2015) Yiliang Ding et al.   Nature Protocols

Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data

(2015) Yang Wu et al.   NUCLEIC ACIDS RESEARCH

The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication

(2015) Chringma Sherpa et al.   NUCLEIC ACIDS RESEARCH

Imaging metabolite dynamics in living cells using a Spinach-based riboswitch

(2015) Mingxu You 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

RNA-PuzzlesRound II: assessment of RNA structure prediction programs applied to three large RNA structures

(2015) Zhichao Miao et al.   RNA

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

(2015) Chun Kit Kwok et al.   TRENDS IN BIOCHEMICAL SCIENCES

TGF-β1 conjugated chitosan collagen hydrogels induce chondrogenic differentiation of human synovium-derived stem cells

(2015) Jinku Kim et al.   Journal of Biological Engineering

Methods for SAXS-Based Structure Determination of Biomolecular Complexes

(2014) Sichun Yang   ADVANCED MATERIALS

Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes

(2014) Sean R. Eddy   Annual Review of Biophysics

Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA

(2014) Tian Jiang et al.   BIOCHEMISTRY

Genetically encoded reactive oxygen species (ROS) and redox indicators

(2014) Sandrine Pouvreau   Biotechnology Journal

Engineering lead-sensing GFP through rational designing

(2014) Saravanan Prabhu Nadarajan et al.   CHEMICAL COMMUNICATIONS

Macro-/micro-environment-sensitive chemosensing and biological imaging

(2014) Zhigang Yang et al.   CHEMICAL SOCIETY REVIEWS

Mitochondrial biosensors

(2014) Roberto De Michele et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Folding Pathways of the Tetrahymena Ribozyme

(2014) David Mitchell et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Crowding Accelerates Ribozyme Docking and Catalysis

(2014) Bishnu P. Paudel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Dynalign II: common secondary structure prediction for RNA homologs with domain insertions

(2014) Yinghan Fu et al.   NUCLEIC ACIDS RESEARCH

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

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

(2014) C. A. Strulson et al.   RNA

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

(2014) J. Talkish et al.   RNA

HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism

(2014) Sebastien M. Weyn-Vanhentenryck et al.   Cell Reports

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

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

(2013) Christopher A. Strulson et al.   BIOCHEMISTRY

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

(2013) Jillian Tyrrell et al.   BIOCHEMISTRY

Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure

(2013) Elizabeth J. Denning et al.   BIOPHYSICAL CHEMISTRY

A FRET ratiometric fluorescence sensing system for mercury detection and intracellular colorimetric imaging in live Hela cells

(2013) Bo Hu et al.   BIOSENSORS & BIOELECTRONICS

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

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

The Long-Range P3 Helix of the Tetrahymena Ribozyme Is Disrupted during Folding between the Native and Misfolded Conformations

(2013) David Mitchell et al.   JOURNAL OF MOLECULAR BIOLOGY

Crowders Perturb the Entropy of RNA Energy Landscapes to Favor Folding

(2013) Duncan Kilburn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In Vivo X-Ray Footprinting of Pre-30S Ribosomes Reveals Chaperone-Dependent Remodeling of Late Assembly Intermediates

(2013) Sarah F. Clatterbuck Soper et al.   MOLECULAR CELL

MagFRET: The First Genetically Encoded Fluorescent Mg2+ Sensor

(2013) Laurens H. Lindenburg et al.   PLoS One

Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core

(2013) D. M. Truong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Denaturation of RNA Secondary and Tertiary Structure by Urea: Simple Unfolded State Models and Free Energy Parameters Account for Measured m-Values

(2012) Dominic Lambert et al.   BIOCHEMISTRY

Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference

(2012) Pablo Cordero et al.   BIOCHEMISTRY

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots

(2012) Matthew G. Seetin et al.   BIOINFORMATICS

PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data

(2012) Z. Sukosd et al.   BIOINFORMATICS

Analysis of energy-based algorithms for RNA secondary structure prediction

(2012) Monir Hajiaghayi et al.   BMC BIOINFORMATICS

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

(2012) Z. Ouyang et al.   GENOME RESEARCH

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

RNA catalysis through compartmentalization

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

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

(2012) Stefan Washietl et al.   NUCLEIC ACIDS RESEARCH

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

(2012) F. Li et al.   PLANT CELL

High-resolution imaging of Ca2+, redox status, ROS and pH using GFP biosensors

(2012) Won-Gyu Choi et al.   PLANT JOURNAL

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction

(2012) Kourosh Zarringhalam et al.   PLoS One

Fluorescence Imaging of Cellular Metabolites with RNA

(2012) Jeremy S. Paige et al.   SCIENCE

In Vivo Imaging of Ca2+, pH, and Reactive Oxygen Species Using Fluorescent Probes in Plants

(2011) Sarah J. Swanson et al.   Annual Review of Plant Biology

Time resolved SAXS and RNA folding

(2011) Lois Pollack   BIOPOLYMERS

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

(2011) Arif O Harmanci et al.   BMC BIOINFORMATICS

Molecular cloning, characterization, genomic organization and promoter analysis of the α1,6-fucosyltransferase gene (fut8) expressed in the rat hybridoma cell line YB2/0

(2011) Béatrice Teylaert et al.   BMC BIOTECHNOLOGY

Imaging Intracellular pH in Live Cells with a Genetically Encoded Red Fluorescent Protein Sensor

(2011) Mathew Tantama et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Peptide–nucleotide microdroplets as a step towards a membrane-free protocell model

(2011) Shogo Koga et al.   Nature Chemistry

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters

(2010) Biao Liu et al.   BIOCHEMISTRY

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences

(2010) Zhenjiang Xu et al.   BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Multiple Unfolding Events during Native Folding of the Tetrahymena Group I Ribozyme

(2010) Yaqi Wan et al.   JOURNAL OF MOLECULAR BIOLOGY

The Osmolyte TMAO Stabilizes Native RNA Tertiary Structures in the Absence of Mg2+: Evidence for a Large Barrier to Folding from Phosphate Dehydration

(2010) Dominic Lambert et al.   JOURNAL OF MOLECULAR BIOLOGY

Multistage Collapse of a Bacterial Ribozyme Observed by Time-Resolved Small-Angle X-ray Scattering

(2010) Joon Ho Roh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect

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

Multiple native states reveal persistent ruggedness of an RNA folding landscape

(2010) Sergey V. Solomatin et al.   NATURE

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots

(2009) Biao Liu et al.   BIOCHEMISTRY

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

(2009) Shu-ichi Nakano et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

Reactive oxygen species in abiotic stress signaling

(2009) Pinja Jaspers et al.   PHYSIOLOGIA PLANTARUM

Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators

(2009) H. Imamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

(2008) C. B. Do et al.   BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Tertiary Interactions Determine the Accuracy of RNA Folding

(2008) Seema Chauhan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

A practical guide to single-molecule FRET

(2008) Rahul Roy et al.   NATURE METHODS

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

(2008) Arif Ozgun Harmanci et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA