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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.
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Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
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Related Experiment Video

Updated: May 7, 2026

Fluorescent End-Labeling and Encapsulation of Long RNAs for Single-Molecule FRET-TIRF Microscopy
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Fluorescent End-Labeling and Encapsulation of Long RNAs for Single-Molecule FRET-TIRF Microscopy

Published on: October 18, 2024

Fluorescently labeling synthetic RNAs.

Max Greenfeld1, Daniel Herschlag

  • 1Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Department of Biochemistry, Stanford University, Stanford, CA, USA.

Methods in Enzymology
|September 17, 2013
PubMed
Summary

This protocol details labeling synthetic RNA oligonucleotides with N-hydroxysuccinamide (NHS) functionalized fluorophores. This versatile method enables direct use, targeting, or ligation of labeled RNA for various applications.

Keywords:
Fluorescence resonance energy transfer (FRET)Gel purificationLarge-scale labeling reactionNHS-activated fluorophoresPrecipitate unlabeled oligonucleotideSynthetic RNAs

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Published on: August 6, 2014

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Organic Chemistry

Background:

  • Synthetic RNA oligonucleotides are crucial tools in molecular biology.
  • Labeling RNA with fluorophores enhances its utility in various biological assays.
  • N-hydroxysuccinamide (NHS) chemistry provides a reliable method for bioconjugation.

Purpose of the Study:

  • To provide a detailed protocol for labeling synthetic RNA with primary amine residues using NHS-functionalized fluorophores.
  • To highlight the versatility of this RNA labeling technique for different applications.
  • To acknowledge the existence and potential need for alternative labeling strategies.

Main Methods:

  • Modification of synthetic RNA to incorporate a primary amine residue.
  • Coupling of N-hydroxysuccinamide (NHS) functionalized fluorophores to the primary amine on RNA.
  • Purification and characterization of the labeled RNA.

Main Results:

  • Successful incorporation of NHS-functionalized fluorophores into synthetic RNA.
  • Demonstration of the general applicability of the labeling method.
  • Established a foundation for diverse applications of labeled RNA.

Conclusions:

  • The described protocol offers a robust method for fluorescent labeling of synthetic RNA.
  • This technique supports direct use, hybridization-based targeting, and ligation of labeled RNA.
  • Researchers should remain aware of alternative labeling strategies for specific experimental needs.