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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...
FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
In-situ Hybridization02:31

In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...

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Related Experiment Video

Updated: Jun 25, 2026

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes
07:44

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes

Published on: July 6, 2016

Fluorogenic Sydnones for Bioorthogonal Labeling of DNA.

Kerstin Müller1, Hans-Achim Wagenknecht1

  • 1Institut of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.

Chemistry (Weinheim an Der Bergstrasse, Germany)
|June 24, 2026
PubMed
Summary
This summary is machine-generated.

New fluorescent dyes conjugated to sydnones offer bioorthogonal reactivity for cell imaging. These novel cyanine-styryl dyes enable efficient and selective labeling of DNA and RNA, enhancing cellular visualization through fluorescence turn-on and spectral shifts.

Keywords:
DNARNAcyanine dyefluorescencesynthesis

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Specific Labeling of Mitochondrial Nucleoids for Time-lapse Structured Illumination Microscopy
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Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells
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Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells

Published on: April 9, 2018

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Last Updated: Jun 25, 2026

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07:44

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Published on: July 6, 2016

Specific Labeling of Mitochondrial Nucleoids for Time-lapse Structured Illumination Microscopy
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Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells
14:02

Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells

Published on: April 9, 2018

Area of Science:

  • Organic Chemistry
  • Chemical Biology
  • Biochemistry

Background:

  • Bioorthogonal chemistry enables selective labeling of biomolecules within living systems.
  • Fluorescent dyes are crucial tools for visualizing cellular processes.
  • Sydnone-based click chemistry offers unique reactivity for bioconjugation.

Purpose of the Study:

  • To synthesize novel cyanine-styryl dyes conjugated to sydnones.
  • To investigate the fluorogenicity and reaction kinetics of strain-promoted sydnone-alkyne cycloaddition (SPSAC) reactions.
  • To evaluate the utility of these dyes for bioorthogonal labeling of nucleic acids in cells.

Main Methods:

  • Heck couplings were used for synthesizing cyanine-styryl sydnone conjugates.
  • Spectroscopic methods were employed to study SPSAC reaction kinetics and fluorescence.
  • HeLa cells were used to assess bioorthogonal labeling of BCN-modified DNA.

Main Results:

  • Novel cyanine-styryl sydnone dyes were synthesized with significant Stokes shifts.
  • SPSAC reactions showed fluorescence turn-on up to 8-fold with nucleosides.
  • BCN-modified DNA templating significantly enhanced SPSAC kinetics (k2 up to 2,300 M-1s-1) and fluorescence turn-on (up to 17-fold).
  • Bioorthogonal labeling in HeLa cells demonstrated the utility for distinguishing modified nucleosides and DNA.

Conclusions:

  • The developed cyanine-styryl sydnone dyes combine fluorogenicity with bioorthogonal reactivity.
  • DNA templating significantly boosts the efficiency of SPSAC reactions.
  • These dyes are promising tools for metabolic labeling of RNA and DNA with distinct fluorescence readouts.