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Related Concept Videos

Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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Related Experiment Video

Updated: Jun 23, 2026

Determination of In Vitro and Cellular Turn-on Kinetics for Fluorogenic RNA Aptamers
08:11

Determination of In Vitro and Cellular Turn-on Kinetics for Fluorogenic RNA Aptamers

Published on: August 9, 2022

Fluorophore binding aptamers as a tool for RNA visualization.

Katja Eydeler1, Eileen Magbanua, Arne Werner

  • 1Department of Chemistry, Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.

Biophysical Journal
|May 6, 2009
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method using fluorescence correlation spectroscopy (FCS) to detect RNA in living cells. This technique allows for minimal invasive, single-molecule RNA detection within individual cells.

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Last Updated: Jun 23, 2026

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08:11

Determination of In Vitro and Cellular Turn-on Kinetics for Fluorogenic RNA Aptamers

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Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons
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Fluorescent End-Labeling and Encapsulation of Long RNAs for Single-Molecule FRET-TIRF Microscopy

Published on: October 18, 2024

Area of Science:

  • Molecular Biology
  • Biophysics
  • Cell Biology

Background:

  • Fluorescence correlation spectroscopy (FCS) is a powerful technique for analyzing fluorescent molecules in living cells.
  • Visualizing and quantifying mRNA within living cells is crucial for understanding gene expression and cellular processes.
  • Existing methods for RNA detection can be invasive or lack single-molecule resolution.

Purpose of the Study:

  • To develop a novel, minimal invasive method for detecting RNA at the single-molecule level in living cells.
  • To utilize fluorescence correlation spectroscopy (FCS) combined with RNA aptamers for RNA visualization.
  • To assess the binding affinity of RNA aptamers to fluorophores in cellular contexts.

Main Methods:

  • Genetically fused a fluorophore-specific RNA aptamer to green fluorescent protein (GFP) mRNA and noncoding sequences.
  • Employed fluorescence correlation spectroscopy (FCS) to determine the binding affinity (K(d)) of the aptamer-fluorophore complex.
  • Investigated aptamer binding in the context of total RNA extracts and using tandem aptamer constructs.

Main Results:

  • The RNA aptamer successfully bound the fluorophore in the nanomolar range, as confirmed by FCS measurements.
  • Aptamer-fluorophore binding was effective even within total RNA extracts.
  • A tandem construct of the RNA aptamer demonstrated a lower dissociation constant (K(d)) compared to the monomeric aptamer.

Conclusions:

  • This FCS-based approach provides a tool for minimal invasive, single-molecule detection of RNA in living cells.
  • The developed method enables the visualization of mRNA and noncoding RNA sequences.
  • RNA aptamers can be effectively used for quantitative RNA detection in biological systems.