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The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold

Journal Article · · Nat. Chem. Biol.

Research Organization:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
DOE - Office Of Science; National Institutes of Health (NIH)
OSTI ID:
1844622
Journal Information:
Nat. Chem. Biol., Vol. 18
Country of Publication:
United States
Language:
ENGLISH

References (50)

Illuminating RNA Biology: Tools for Imaging RNA in Live Mammalian Cells journal August 2020
RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers journal November 2018
Fluorogenic Aptasensors with Small Molecules journal March 2021
In vitro selection of RNA molecules that bind specific ligands journal August 1990
Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA journal March 1990
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase journal August 1990
Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution journal November 2014
iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications journal March 2016
Structure and functional reselection of the Mango-III fluorogenic RNA aptamer journal April 2019
RNA Mimics of Green Fluorescent Protein journal July 2011
Understanding the Photophysics of the Spinach–DFHBI RNA Aptamer–Fluorogen Complex To Improve Live-Cell RNA Imaging journal December 2013
A G-quadruplex–containing RNA activates fluorescence in a GFP-like fluorophore journal June 2014
Structural basis for activity of highly efficient RNA mimics of green fluorescent protein journal July 2014
A homodimer interface without base pairs in an RNA mimic of red fluorescent protein journal September 2017
Imaging RNA polymerase III transcription using a photostable RNA–fluorophore complex journal September 2017
Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine journal June 2021
2.8 Å crystal structure of the malachite green aptamer 1 1Edited by J. A. Doudna journal August 2000
Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif journal October 2018
The emerging structural complexity of G-quadruplex RNAs journal January 2021
Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag journal December 2021
Structural Basis for Discriminative Regulation of Gene Expression by Adenine- and Guanine-Sensing mRNAs journal December 2004
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif journal April 2001
Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence journal August 2019
Anion−π Interactions with Fluoroarenes journal August 2015
Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening journal April 2016
Fluorotyrosine Alkaline Phosphatase from Escherichia coli: Preparation, Properties, and Fluorine-19 Nuclear Magnetic Resonance Spectrum journal February 1974
The purine riboswitch as a model system for exploring RNA biology and chemistry journal October 2014
Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET journal December 2020
Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI journal September 2017
From fluorescent proteins to fluorogenic RNAs: Tools for imaging cellular macromolecules journal May 2019
In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold journal August 2016
A divalent cation-dependent variant of the glmS ribozyme with stringent Ca 2+ selectivity co-opts a preexisting nonspecific metal ion-binding site journal December 2016
Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors journal January 2017
Three-way RNA junctions with remote tertiary contacts: A recurrent and highly versatile fold journal September 2009
Long-Range Interactions in Riboswitch Control of Gene Expression journal May 2017
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch journal May 2006
Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand journal May 2006
Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition journal September 2006
Structural basis of ligand binding by a c-di-GMP riboswitch journal November 2009
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch journal November 2009
Structural Basis for Specific, High-Affinity Tetracycline Binding by an In Vitro Evolved Aptamer and Artificial Riboswitch journal October 2008
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography journal November 2016
Geometric nomenclature and classification of RNA base pairs journal April 2001
XDS journal January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Coot model-building tools for molecular graphics journal November 2004
Phaser crystallographic software journal July 2007
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions journal June 2017
High-Precision Isothermal Titration Calorimetry with Automated Peak-Shape Analysis journal June 2012
SEDPHAT – A platform for global ITC analysis and global multi-method analysis of molecular interactions journal April 2015