Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications

Fluorogenic Labeling Strategies for Biological Imaging

(2017) Chenge Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

mRNA imaging in the chloroplast of Chlamydomonas reinhardtii using the light-up aptamer Spinach

(2017) Daniel Guzmán-Zapata et al.   JOURNAL OF BIOTECHNOLOGY

Development and characterization of Sindbis virus with encoded fluorescent RNA aptamer Spinach2 for imaging of replication and immune-mediated changes in intracellular viral RNA

(2017) Voraphoj Nilaratanakul et al.   JOURNAL OF GENERAL VIROLOGY

Fluoromodules Consisting of a Promiscuous RNA Aptamer and Red or Blue Fluorogenic Cyanine Dyes: Selection, Characterization, and Bioimaging

(2017) Xiaohong Tan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genetically Encoded Fluorescent RNA Sensor for Ratiometric Imaging of MicroRNA in Living Tumor Cells

(2017) Zhan-Ming Ying et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Recent Advances in Macrocyclic Fluorescent Probes for Ion Sensing

(2017) Joseph Wong et al.   MOLECULES

A homodimer interface without base pairs in an RNA mimic of red fluorescent protein

(2017) Katherine Deigan Warner et al.   Nature Chemical Biology

Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors

(2017) Ely B Porter et al.   Nature Chemical Biology

Imaging RNA polymerase III transcription using a photostable RNA–fluorophore complex

(2017) Wenjiao Song et al.   Nature Chemical Biology

Structural basis for high-affinity fluorophore binding and activation by RNA Mango

(2017) Robert J Trachman et al.   Nature Chemical Biology

FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs

(2017) Kun Huang et al.   NUCLEIC ACIDS RESEARCH

DNA mimics of red fluorescent proteins (RFP) based on G-quadruplex-confined synthetic RFP chromophores

(2017) Guangfu Feng et al.   NUCLEIC ACIDS RESEARCH

Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI

(2017) Pablo Fernandez-Millan et al.   RNA

Ribonucleoprotein purification and characterization using RNA Mango

(2017) Shanker Shyam S. Panchapakesan et al.   RNA

Structural Principles of Fluorescent RNA Aptamers

(2017) Robert J. Trachman et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Detection of human immunodeficiency virus RNAs in living cells using Spinach RNA aptamers

(2017) Brandon D. Burch et al.   VIRUS RESEARCH

RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes

(2017) Joseph Abatemarco et al.   Nature Communications

Cell-Free Translation Is More Variable than Transcription

(2017) Fabio Chizzolini et al.   ACS Synthetic Biology

A Fluorescent Split Aptamer for Visualizing RNA–RNA Assembly In Vivo

(2017) Khalid K. Alam et al.   ACS Synthetic Biology

Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria

(2017) Lieke A. van Gijtenbeek et al.   Frontiers in Microbiology

Ultrahigh-Throughput Improvement and Discovery of Enzymes Using Droplet-Based Microfluidic Screening

(2017) Alexis Autour et al.   Micromachines

Quadruplex-Flanking Stem Structures Modulate the Stability and Metal Ion Preferences of RNA Mimics of GFP

(2016) Eman A. Ageely et al.   ACS Chemical Biology

Live Cell Imaging of Endogenous mRNA Using RNA-Based Fluorescence “Turn-On” Probe

(2016) Wei Qiang Ong et al.   ACS Chemical Biology

Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules

(2016) Saki Inuzuka et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

In Vitro and In Vivo Enzyme Activity Screening via RNA-Based Fluorescent Biosensors for S-Adenosyl-l-homocysteine (SAH)

(2016) Yichi Su et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Super-resolution Imaging of Live Bacteria Cells Using a Genetically Directed, Highly Photostable Fluoromodule

(2016) Saumya Saurabh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Light-up and FRET aptamer reporters; evaluating their applications for imaging transcription in eukaryotic cells

(2016) Muslum Ilgu et al.   METHODS

Engineering a ribozyme cleavage-induced split fluorescent aptamer complementation assay

(2016) Simon Ausländer et al.   NUCLEIC ACIDS RESEARCH

Engineering and characterization of fluorogenic glycine riboswitches

(2016) Simon Ketterer et al.   NUCLEIC ACIDS RESEARCH

Use of Baby Spinach and Broccoli for imaging of structured cellular RNAs

(2016) Maho Okuda et al.   NUCLEIC ACIDS RESEARCH

Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP

(2016) Xin C. Wang et al.   NUCLEIC ACIDS RESEARCH

iSpinach: a fluorogenic RNA aptamer optimized forin vitroapplications

(2016) Alexis Autour et al.   NUCLEIC ACIDS RESEARCH

A genetically encoded fluorescent tRNA is active in live-cell protein synthesis

(2016) Isao Masuda et al.   NUCLEIC ACIDS RESEARCH

A conformation-induced fluorescence method for microRNA detection

(2016) Sherry S. Aw et al.   NUCLEIC ACIDS RESEARCH

Hybrid promiscuous (Hypr) GGDEF enzymes produce cyclic AMP-GMP (3′, 3′-cGAMP)

(2016) Zachary F. Hallberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluorophore ligand binding and complex stabilization of the RNA Mango and RNA Spinach aptamers

(2016) Sunny C.Y. Jeng et al.   RNA

Fluorophore-binding RNA aptamers and their applications

(2016) Elena V. Dolgosheina et al.   Wiley Interdisciplinary Reviews-RNA

RNA Fluorescence with Light-Up Aptamers

(2016) Jonathan Ouellet   Frontiers in Chemistry

Structure and Mechanism of RNA Mimics of Green Fluorescent Protein

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

Spinach RNA aptamer detects lead(ii) with high selectivity

(2015) Saurja DasGupta et al.   CHEMICAL COMMUNICATIONS

In-Gel Imaging of RNA Processing Using Broccoli Reveals Optimal Aptamer Expression Strategies

(2015) Grigory S. Filonov et al.   CHEMISTRY & BIOLOGY

Genetically encoded tools for RNA imaging in living cells

(2015) Anna K. Rath et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fluorescence imaging using synthetic GFP chromophores

(2015) Christopher L Walker et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Selection of Intracellularly Functional RNA Mimics of Green Fluorescent Protein Using Fluorescence-Activated Cell Sorting

(2015) Jiawei Zou et al.   JOURNAL OF MOLECULAR EVOLUTION

RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messenger Cyclic di-AMP

(2015) Colleen A. Kellenberger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers

(2015) Ankita Arora et al.   NUCLEIC ACIDS RESEARCH

Systematic reconstruction of binding and stability landscapes of the fluorogenic aptamer spinach

(2015) Simon Ketterer 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

GEMM-I riboswitches fromGeobactersense the bacterial second messenger cyclic AMP-GMP

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

Metazoan tRNA introns generate stable circular RNAs in vivo

(2015) Zhipeng Lu et al.   RNA

Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions

(2015) Michael Ryckelynck et al.   RNA

Segmented GFP-like aptamer probes for functional imaging of viral genome trafficking

(2015) Irina B. Tsvetkova et al.   VIRUS RESEARCH

Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast

(2015) David Guet et al.   Nature Communications

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

(2015) Jichuan Zhang et al.   Scientific Reports

RNA Mango Aptamer-Fluorophore: A Bright, High-Affinity Complex for RNA Labeling and Tracking

(2014) Elena V. Dolgosheina et al.   ACS Chemical Biology

Live-Cell Imaging of Endogenous mRNAs with a Small Molecule

(2014) Shin-ichi Sato et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Live-cell reporters for fluorescence imaging

(2014) Ivan R Corrêa   CURRENT OPINION IN CHEMICAL BIOLOGY

Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

(2014) Grigory S. Filonov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Plug-and-Play Fluorophores Extend the Spectral Properties of Spinach

(2014) Wenjiao Song et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A G-quadruplex–containing RNA activates fluorescence in a GFP-like fluorophore

(2014) Hao Huang et al.   Nature Chemical Biology

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural basis for activity of highly efficient RNA mimics of green fluorescent protein

(2014) Katherine Deigan Warner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters

(2014) Ilchung Shin et al.   NUCLEIC ACIDS RESEARCH

Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers

(2014) Sanchita Bhadra et al.   NUCLEIC ACIDS RESEARCH

A Spinach molecular beacon triggered by strand displacement

(2014) Sanchita Bhadra et al.   RNA

A Fluorescent Nucleic Acid Nanodevice Quantitatively Images Elevated Cyclic Adenosine Monophosphate in Membrane-Bound Compartments

(2014) Suruchi Sharma et al.   Small

Background free imaging of single mRNAs in live cells using split fluorescent proteins

(2014) Bin Wu et al.   Scientific Reports

RNA Signal Amplifier Circuit with Integrated Fluorescence Output

(2014) Farhima Akter et al.   ACS Synthetic Biology

Fluorescent Monitoring of RNA Assembly and Processing Using the Split-Spinach Aptamer

(2014) Tucker A. Rogers et al.   ACS Synthetic Biology

Contact-Mediated Quenching for RNA Imaging in Bacteria with a Fluorophore-Binding Aptamer

(2013) Murat Sunbul et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Unbiased Tracking of the Progression of mRNA and Protein Synthesis in Bulk and in Liposome-Confined Reactions

(2013) Pauline van Nies et al.   CHEMBIOCHEM

Understanding the Photophysics of the Spinach–DFHBI RNA Aptamer–Fluorogen Complex To Improve Live-Cell RNA Imaging

(2013) Kyu Young Han et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Universal Aptamer-Based Real-Time Monitoring of Enzymatic RNA Synthesis

(2013) Katharina Höfer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messengers Cyclic di-GMP and Cyclic AMP-GMP

(2013) Colleen A. Kellenberger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Directed evolution of genetic parts and circuits by compartmentalized partnered replication

(2013) Jared W Ellefson et al.   NATURE BIOTECHNOLOGY

Imaging bacterial protein expression using genetically encoded RNA sensors

(2013) Wenjiao Song et al.   NATURE METHODS

A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat–containing RNA

(2013) Rita L Strack et al.   NATURE METHODS

Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor

(2013) Dan Shu et al.   NUCLEIC ACIDS RESEARCH

Gene Position More Strongly Influences Cell-Free Protein Expression from Operons than T7 Transcriptional Promoter Strength

(2013) Fabio Chizzolini et al.   ACS Synthetic Biology

The Spinach RNA Aptamer as a Characterization Tool for Synthetic Biology

(2013) Georgios Pothoulakis et al.   ACS Synthetic Biology

The Art of Fluorescence Imaging with Chemical Sensors

(2012) Michael Schäferling   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Malachite Green Derivatives for Two-Photon RNA Detection

(2012) Jacques Lux et al.   CHEMBIOCHEM

Nanomolar fluorescent detection of c-di-GMP using a modular aptamer strategy

(2012) Shizuka Nakayama et al.   CHEMICAL COMMUNICATIONS

Fluorescence Imaging of Cellular Metabolites with RNA

(2012) Jeremy S. Paige et al.   SCIENCE

Small-molecule fluorescent probes for specific RNA targets

(2011) Asako Murata et al.   CHEMICAL COMMUNICATIONS

Thermodynamically stable RNA three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics

(2011) Dan Shu et al.   Nature Nanotechnology

Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods

(2011) Bingling Li et al.   NUCLEIC ACIDS RESEARCH

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Combining SELEX Screening and Rational Design to Develop Light-Up Fluorophore−RNA Aptamer Pairs for RNA Tagging

(2010) Jungjoon Lee et al.   ACS Chemical Biology

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues

(2010) Dmitriy M. Chudakov et al.   PHYSIOLOGICAL REVIEWS

Fluorophore Binding Aptamers as a Tool for RNA Visualization

(2009) Katja Eydeler et al.   BIOPHYSICAL JOURNAL

TokenRNA: A New Type of Sequence-Specific, Label-Free Fluorescent Biosensor for Folded RNA Molecules

(2008) Kirill A. Afonin et al.   CHEMBIOCHEM

Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA

(2008) Shinsuke Sando et al.   CHEMICAL COMMUNICATIONS

Fluorinated Analogs of Malachite Green: Synthesis and Toxicity

(2008) George Kraus et al.   MOLECULES

Synthesis of New Fluorogenic Cyanine Dyes and Incorporation into RNA Fluoromodules

(2008) Tudor P. Constantin et al.   ORGANIC LETTERS