SHAPE Directed Discovery of New Functions in Large RNAs

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

(2021) Nicholas C. Huston et al.   MOLECULAR CELL

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

(2020) Phillip J. Tomezsko et al.   NATURE

Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA

(2020) Jeffrey E. Ehrhardt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Advances in RNA 3D Structure Modeling Using Experimental Data

(2020) Bing Li et al.   Frontiers in Genetics

Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies

(2020) Ilaria Manfredonia et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid

(2020) Christiane Iserman et al.   MOLECULAR CELL

A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

(2020) Tycho Marinus et al.   NUCLEIC ACIDS RESEARCH

The RNA Architecture of the SARS-CoV-2 3′-Untranslated Region

(2020) Junxing Zhao et al.   Viruses-Basel

Using SHAPE-MaP to probe small molecule-RNA interactions

(2019) Sarah Martin et al.   METHODS

SHAPE Probing Reveals Human rRNAs Are Largely Unfolded in Solution

(2019) Catherine A. Giannetti et al.   BIOCHEMISTRY

Effects of Refolding on Large-Scale RNA Structure

(2019) Elizabeth A. Dethoff et al.   BIOCHEMISTRY

Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies

(2019) Steven Busan et al.   BIOCHEMISTRY

Physical and Functional Analysis of Viral RNA Genomes by SHAPE

(2019) Mark A. Boerneke et al.   Annual Review of Virology

Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells

(2019) Arnab Sengupta et al.   PLOS BIOLOGY

RNA base-pairing complexity in living cells visualized by correlated chemical probing

(2019) Anthony M. Mustoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA structure regulates protein expression through changes in functional half-life

(2019) David M. Mauger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing RNA structure in vivo

(2019) David Mitchell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans

(2018) Anthony M. Mustoe et al.   BIOCHEMISTRY

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

(2018) Anthony M. Mustoe et al.   CELL

In-cell RNA structure probing with SHAPE-MaP

(2018) Matthew J Smola et al.   Nature Protocols

Principles for targeting RNA with drug-like small molecules

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

Tapping the RNA world for therapeutics

(2018) Judy Lieberman   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tapping the RNA world for therapeutics

(2018) Judy Lieberman   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies

(2018) Jason W. Rausch et al.   Frontiers in Microbiology

High-throughput determination of RNA structures

(2018) Eric J. Strobel et al.   NATURE REVIEWS GENETICS

Pervasive tertiary structure in the dengue virus RNA genome

(2018) Elizabeth A. Dethoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression

(2017) Meredith Corley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization of RNA structure models within the Integrative Genomics Viewer

(2017) Steven Busan et al.   RNA

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

(2017) Steven Busan et al.   RNA

Decoding the RNA structurome

(2016) Zhipeng Lu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity

(2016) Pablo Garcia-Miranda et al.   JOURNAL OF VIROLOGY

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Cotranscriptional folding of a riboswitch at nucleotide resolution

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

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across theXistlncRNA in living cells

(2016) Matthew J. Smola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct identification of base-paired RNA nucleotides by correlated chemical probing

(2016) Andrey Krokhotin et al.   RNA

Cotranscriptional folding of a riboswitch at nucleotide resolution

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

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

(2015) Jillian Tyrrell et al.   BIOCHEMISTRY

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

Review toward all RNA structures, concisely

(2015) Kevin M. Weeks   BIOPOLYMERS

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state

(2015) Jennifer L. McGinnis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functionally conserved architecture of hepatitis C virus RNA genomes

(2015) David M. Mauger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

(2015) Christopher A. Lavender et al.   PLoS Computational Biology

Structure and Dynamics of the HIV-1 Frameshift Element RNA

(2014) Justin T. Low et al.   BIOCHEMISTRY

Ribosome RNA Assembly Intermediates Visualized in Living Cells

(2014) Jennifer L. McGinnis et al.   BIOCHEMISTRY

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

(2014) Thomas R. Cech et al.   CELL

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically

(2014) Katherine Deigan Warner et al.   CHEMISTRY & BIOLOGY

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Single-molecule correlated chemical probing of RNA

(2014) P. J. Homan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of Context in RNA Structure: Flanking Sequences Reconfigure CAG Motif Folding in Huntingtin Exon 1 Transcripts

(2013) Steven Busan et al.   BIOCHEMISTRY

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

(2013) Jillian Tyrrell et al.   BIOCHEMISTRY

Long-Range Architecture in a Viral RNA Genome

(2013) Eva J. Archer et al.   BIOCHEMISTRY

The genetic code as expressed through relationships between mRNA structure and protein function

(2013) David M. Mauger et al.   FEBS LETTERS

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

A Guanosine-Centric Mechanism for RNA Chaperone Function

(2013) J. K. Grohman et al.   SCIENCE

Targeting frameshifting in the human immunodeficiency virus

(2012) Léa Brakier-Gingras et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity

(2012) Kady-Ann Steen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis

(2012) F. Karabiber et al.   RNA

Exploring RNA Structural Codes with SHAPE Chemistry

(2011) Kevin M. Weeks et al.   ACCOUNTS OF CHEMICAL RESEARCH

Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target

(2011) W. J. Krzyzosiak et al.   NUCLEIC ACIDS RESEARCH

RNA structure probing dash seq

(2011) K. M. Weeks   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain

(2010) Christopher A. Lavender et al.   BIOCHEMISTRY

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain

(2009) S. A. Mortimer 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

Complex Ligand-Induced Conformational Changes in tRNAAspRevealed by Single-Nucleotide Resolution SHAPE Chemistry†

(2008) Bin Wang et al.   BIOCHEMISTRY

Slow Conformational Dynamics at C2′-endo Nucleotides in RNA

(2008) Costin M. Gherghe 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

Time-Resolved RNA SHAPE Chemistry

(2008) Stefanie A. Mortimer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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