Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells

Despite having many key roles in cellular biology, directly imaging biologically important RNAs has been hindered by a lack of fluorescent tools equivalent to the fluorescent proteins available to study cellular proteins. Ideal RNA labelling systems must preserve biological function, have photophysical properties similar to existing fluorescent proteins, and be compatible with established live and fixed cell protein labelling strategies. Here, we report a microfluidics-based selection of three new high-affinity RNA Mango fluorogenic aptamers. Two of these are as bright or brighter than enhanced GFP when bound to TO1-Biotin. Furthermore, we show that the new Mangos can accurately image the subcellular localization of three small non-coding RNAs (5S, U6, and a box C/D scaRNA) in fixed and live mammalian cells. These new aptamers have many potential applications to study RNA function and dynamics both in vitro and in mammalian cells. Many aptamer-fluorophore complexes suffer from low quantum yield and low extinction coefficients limiting their usability. Here the authors isolate new Mango aptamers with improved fluorescent properties for both fixed and live-cell imaging by using competitive ligand binding microfluidic selection.

• Publication year

  2018

• Venue

  Nature Communications

• Publication date

  2018-02-13

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1038/s41467-018-02993-8PMID 29440634PMCID 5811451
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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

  2017cited by this paper
• A homodimer interface without base pairs in an RNA mimic of red fluorescent protein

  2017cited by this paper
• Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex

  2017cited by this paper
• Ribonucleoprotein purification and characterization using RNA Mango

  2017cited by this paper
• Fluoromodules Consisting of a Promiscuous RNA Aptamer and Red or Blue Fluorogenic Cyanine Dyes: Selection, Characterization, and Bioimaging.

  2017cited by this paper
• Structural basis for high-affinity fluorophore binding and activation by RNA Mango

  2017cited by this paper
• Fluorophore‐binding RNA aptamers and their applications

  2016cited by this paper
• Fluorophore ligand binding and complex stabilization of the RNA Mango and RNA Spinach aptamers

  2016cited by this paper
• RNA Fluorescence with Light-Up Aptamers

  2016cited by this paper
• Single-Molecule DNA Polymerase Dynamics at a Bacterial Replisome in Live Cells.

  2016cited by this paper
• iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications

  2016cited by this paper
• Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions

  2015cited by this paper
• In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies.

  2015cited by this paper
• Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast

  2015cited by this paper
• Structure and Mechanism of RNA Mimics of Green Fluorescent Protein.

  2015cited by this paper
• Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

  2015cited by this paper
• The spinach RNA aptamer as a characterization tool for synthetic biology.

  2014cited by this paper
• Post-transcriptional modifications modulate conformational dynamics in human U2–U6 snRNA complex

  2014cited by this paper
• Structural basis for activity of highly efficient RNA mimics of green fluorescent protein

  2014cited by this paper
• Targeting vertebrate intron-encoded box C/D 2′-O-methylation guide RNAs into the Cajal body

  2014cited by this paper
• RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking.

  2014cited by this paper
• A G-Quadruplex-Containing RNA Activates Fluorescence in a GFP-Like Fluorophore

  2014cited by this paper
• Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

  2014cited by this paper
• Understanding the photophysics of the spinach-DFHBI RNA aptamer-fluorogen complex to improve live-cell RNA imaging.

  2013cited by this paper
• A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat RNA

  2013cited by this paper
• Optimized end-stacking provides specificity of N-methyl mesoporphyrin IX for human telomeric G-quadruplex DNA.

  2012cited by this paper
• RNA Mimics of Green Fluorescent Protein

  2011cited by this paper
• Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18.

  2011cited by this paper
• Single Molecule Analysis of Protein Free U2/U6 snRNAs

  2009cited by this paper
• Fluorogen-activating single-chain antibodies for imaging cell surface proteins

  2008cited by this paper
• Detection of intensity change points in time-resolved single-molecule measurements.

  2005cited by this paper
• A guide to choosing fluorescent proteins

  2005cited by this paper
• Aptamers switch on fluorescence of triphenylmethane dyes.

  2003cited by this paper
• Crystal structure of the specificity domain of ribonuclease P

  2003cited by this paper
• The human U6 snRNA intramolecular helix: structural constraints and lack of sequence specificity.

  1997cited by this paper
• In vitro selection of RNA aptamers specific for cyanocobalamin.

  1994cited by this paper
• Thiazole orange: a new dye for reticulocyte analysis.

  1986cited by this paper

• Fluorogenic CRISPR for DNA imaging in live mammalian cells.

  2026cites this paper
• Extending the Potential of Digital Droplet PCR by Expressing Amplified Genes and Assaying Their Phenotype.

  2026cites this paper
• pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing

  2026cites this paper
• T4 DNA ligase-mediated RAA coupled with RNA aptamer-driven cascade signal amplification for ultra-sensitive monkeypox virus detection.

  2026cites this paper
• Synthesis of long and functionally active RNAs facilitated by acetal levulinic ester chemistry

  2026cites this paper
• Dynamic regulation of neuronal vault trafficking and RNA cargo by the noncoding RNA, Vaultrc5

  2026cites this paper
• Evaluating Linker Architecture in RNA-Detecting Riboglow Probes and Effects on Fluorescence Turn-On.

  2026cites this paper
• Structure-guided engineering of modular RNA aptamer biosensors for one-pot, multiplex detection of CircRNAs.

  2026cites this paper
• Engineered mitochondria in diseases: mechanisms, strategies, and applications

  2025cites this paper
• Developing Orthogonal Fluorescent RNAs for Photoactive Dual-color Imaging of RNAs in Live Cells.

  2025cites this paper
• Biochemical Characterization of a Non-G4-Type RNA Aptamer That Lights Up a GFP-like Fluorogenic Ligand

  2025cites this paper
• A genetically encoded Mango II-based system with increased brightness and selectivity for imaging RNAs in live cells.

  2025cites this paper
• Possible Direction of Drug Discovery Based on Single-Molecule Live Imaging.

  2025cites this paper
• De Novo Development of Fluorogenic RNA-Based Biosensors Using Capture-SELEX in Tandem with Droplet Microfluidics.

  2025cites this paper
• Chemical Synthesis and Poly(ethylene glycol)-Like Conjugation of the Mango-II Fluorogenic RNA Aptamer.

  2025cites this paper
• Orthogonal RNA-regulated destabilization domains for three-color RNA imaging with minimal RNA perturbation

  2025cites this paper
• Cryo-EM structure of a natural RNA nanocage

  2025cites this paper
• 3D Histology visualizing hypoxia-induced upregulation of N-terminal cysteine using de novo fluorophore generation

  2025cites this paper
• Nicked RCA-assisted self-assembling MNAzyme coupled with fluorogenic aptamer for label-free detection of miRNA

  2025cites this paper
• Advanced CRISPR Technologies for RNA Imaging in Live Cells

  2025cites this paper
• Hydrogel-Bead Particles Enable Activity-Based Identification of Nucleic Acid Aptamer Enzyme Inhibitors.

  2025cites this paper
• The catalytic hairpin assembly induces a conformational change of the RNA aptamer enabled in situ imaging of circRNAs in tumor cells.

  2025cites this paper
• Information Theory-Guided Detection of Biomarkers Using Programmable Aptamer Arrays

  2025cites this paper
• Rapid Isothermal DNA Amplification in Microchambers Detected by Fluorescence RNA Aptamer Transcription

  2025cites this paper
• oShark: A Modified Nuclease-Resistant Light-Up Aptamer.

  2025cites this paper
• Human polynucleotide phosphorylase in mitochondrial RNA metabolism

  2025cites this paper
• RNA aptamers as tools for the purification and analysis of in vivo assembled ribonucleoproteins

  2025cites this paper
• Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli.

  2025cites this paper
• Imaging and Tracking RNA in Live Mammalian Cells via Fluorogenic Photoaffinity Labeling.

  2025cites this paper
• Illuminating Diverse Cellular Contents with Fluorogenic RNA Aptamer-Based Biosensors: From Standardization to Innovation

  2025cites this paper
• Challenges in observing transcription–translation for bottom-up synthetic biology

  2025cites this paper
• Fluorescent RNAs: new opportunities for drug discovery.

  2025cites this paper
• Design and Characterization of a Micro RNA‐200c Detecting Broccoli Fluorescent Light‐up Aptamer

  2025cites this paper
• Structure-informed design of an ultrabright RNA-activated fluorophore

  2025cites this paper
• Photochemical synthesis of natural lipids in artificial and living cells

  2025cites this paper
• RNA Mango-based Sensors for Lead

  2025cites this paper
• Decoding the structure and translational promise of ROOL RNA nanocages

  2025cites this paper
• Developments of the mDZ-RhoBAST Probe for Super-Resolution Imaging of FTO Demethylation in Live Cells.

  2025cites this paper
• Capabilities and challenges for the use of fluorescent RNAs in RNA dynamics research.

  2025cites this paper
• Rolling circle transcription-based fluorescent aptasensor for highly sensitive and onsite detection of microcystin-LR

  2025cites this paper
• Live Imaging and Interactome Analysis of Zika and Chikungunya Viral RNAs Via Dual-Action Aptamer Tag

  2025cites this paper
• In vivo CRISPR biosensing.

  2025cites this paper
• Evolution Driven Microscale Combinatorial Chemistry in Intracellular Mimicking Droplets to Engineer Thermostable RNA for Cellular Imaging

  2025cites this paper
• Programmable fluorescent aptamer-based RNA switches for rapid identification of point mutations

  2025cites this paper
• Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA

  2024cites this paper
• Identification of the Binding Site between Aptamer sgc8c and PTK7.

  2024cites this paper
• Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches.

  2024cites this paper
• Multiplexed sequential imaging in living cells with orthogonal fluorogenic RNA aptamer/dye pairs

  2024cites this paper
• CRISPR/RNA Aptamer System Activated by an AND Logic Gate for Biomarker-Driven Theranostics.

  2024cites this paper
• Precise intracellular uptake and endosomal release of diverse functional mRNA payloads via glutathione-responsive nanogels

  2024cites this paper
• Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD

  2024cites this paper
• Bright and Stable Cyan Fluorescent RNA Enables Multicolor RNA Imaging in Live Escherichia coli.

  2024cites this paper
• Deep generative design of RNA aptamers using structural predictions

  2024cites this paper
• Structural basis of mRNA decay by the human exosome–ribosome supercomplex

  2024cites this paper
• Localization of RNAs to the mitochondria—mechanisms and functions

  2024cites this paper
• Design of an intracellular aptamer-based fluorescent biosensor to track burden in E. coli

  2024cites this paper
• Quencher-Free Fluorescence Monitoring of G-Quadruplex Folding

  2024cites this paper
• Synergically Remodeling Human Telomeric G-Quadruplexes into DNA Mimics of GFP with a Na+ Selectivity.

  2024cites this paper
• Real-time single-molecule imaging of transcriptional regulatory networks in living cells

  2024cites this paper
• Ultrahigh-throughput discovery of modified aptamers as specific and potent enzyme inhibitors

  2024cites this paper
• Aggregation-Induced Emission Luminogens: A New Possibility for Efficient Visualization of RNA in Plants

  2024cites this paper
• A rapid and sensitive one-pot platform integrating fluorogenic RNA aptamers and CRISPR-Cas13a for visual detection of monkeypox virus.

  2024cites this paper
• Illuminating RNA through fluorescent light-up RNA aptamers.

  2024cites this paper
• Turn-on RNA Mango Beacons for trans-acting fluorogenic nucleic acid detection

  2024cites this paper
• Imaging of endogenous RNA in live cells using sequence-activated fluorescent RNA probes

  2024cites this paper
• Bioorthogonal Cyclopropenones for Investigating RNA Structure

  2024cites this paper
• Structure-Informed Design of an Ultra Bright RNA-activated Fluorophore

  2024cites this paper
• In Vitro Selection and Characterization of a Light‐up DNA Aptamer for Thiazole Orange

  2024cites this paper
• Accelerated, high-quality photolithographic synthesis of RNA microarrays in situ

  2024cites this paper
• Isolation of novel fluorogenic RNA aptamers via in vitro compartmentalization using microbead-display libraries.

  2024cites this paper
• Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform

  2024cites this paper
• Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives

  2024cites this paper
• Fluorogenic RNA-based biomaterials for imaging and tracking the cargo of extracellular vesicles.

  2024cites this paper
• Structure-based insights into fluorogenic RNA aptamers

  2024cites this paper
• SAM-III aptamer enables detection of enzymatic SAM analogue generation.

  2024cites this paper
• Primer exchange reaction-coupled transcription isothermal amplification as a sensitive biomolecular assay.

  2024cites this paper
• Bioorthogonal cyclopropenones for investigating RNA structure

  2024cites this paper
• Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies

  2023cites this paper
• Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging.

  2023cites this paper
• Multiplexed Sequential Imaging in Living Cells with Orthogonal Fluorogenic RNA Aptamer/Dye Pairs

  2023cites this paper
• Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells

  2023cites this paper
• Boronic Acid Assisted Self-Assembly of Functional RNAs.

  2023cites this paper
• At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring

  2023cites this paper
• Avidity-based bright and photostable light-up aptamers for single-molecule mRNA imaging

  2023cites this paper
• Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting

  2023cites this paper
• Tracking the Message: Applying Single Molecule Localization Microscopy to Cellular RNA Imaging

  2023cites this paper
• Characterizing Fluorescence Properties of Turn-on RNA Aptamers.

  2023cites this paper
• Conformational preferences of modified nucleobases in RNA aptamers and their effect on Förster resonant energy transfer.

  2023cites this paper
• A universal orthogonal imaging platform for living-cell RNA detection using fluorogenic RNA aptamers

  2023cites this paper
• Enzyme Reaction-Assisted Programmable Transcriptional Switches for Bioactive Molecule Detection.

  2023cites this paper
• Evaluating DFHBI-Responsive RNA Light-Up Aptamers as Fluorescent Reporters for Gene Expression

  2023cites this paper
• Implication of polymerase recycling for nascent transcript quantification by live cell imaging

  2023cites this paper
• Centromeric and pericentric transcription and transcripts: their intricate relationships, regulation, and functions

  2023cites this paper
• Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function

  2023cites this paper
• Visualization of direct and diffusion-assisted RAD51 nucleation by full-length human BRCA2 protein

  2023cites this paper
• Biogenic Imaging Contrast Agents

  2023cites this paper
• Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches

  2023cites this paper
• Harmonizing the growing fluorogenic RNA aptamer toolbox for RNA detection and imaging.

  2023cites this paper
• Droplet-based microfluidics

  2023cites this paper
• Cell-Free Production Systems in Droplet Microfluidics.

  2023cites this paper