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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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Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Updated: May 9, 2026

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization
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Published on: April 3, 2014

Oligodeoxynucleotides containing multiple thiophene-modified isomorphic fluorescent nucleosides.

Mary S Noé1, Renatus W Sinkeldam, Yitzhak Tor

  • 1Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, USA.

The Journal of Organic Chemistry
|July 18, 2013
PubMed
Summary

Researchers incorporated a fluorescent nucleoside analogue into DNA strands. Oligonucleotides with multiple fluorescent nucleosides showed enhanced, sequence-dependent signals for DNA duplex formation or dissociation with minimal structural impact.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Nucleic Acid Chemistry

Background:

  • Nucleoside analogues are crucial tools in molecular biology and diagnostics.
  • Fluorescent nucleosides enable real-time monitoring of nucleic acid interactions.
  • Developing analogues with minimal structural perturbation is essential for accurate biological insights.

Purpose of the Study:

  • To investigate the incorporation of 5-(Thien-2-yl)-2'-deoxyuridine, a fluorescent nucleoside analogue, into oligodeoxynucleotides.
  • To evaluate the impact of this analogue on DNA duplex stability and structure.
  • To assess the utility of modified oligonucleotides in generating sequence-dependent fluorescent signals for nucleic acid dynamics.

Main Methods:

  • Chemical synthesis of oligodeoxynucleotides containing 5-(Thien-2-yl)-2'-deoxyuridine at various positions.
  • Spectroscopic analysis to detect fluorescence changes.
  • Biophysical techniques to assess DNA duplex formation and dissociation kinetics.
  • Structural analysis to confirm minimal impact on oligonucleotide conformation.

Main Results:

  • Successful incorporation of the isomorphic fluorescent nucleoside analogue into single-stranded oligodeoxynucleotides.
  • Oligonucleotides with three identical fluorescent nucleosides exhibited enhanced on-signals.
  • The observed signals were sequence-dependent and correlated with duplex formation or dissociation.
  • Minimal impact on the overall stability and structure of the DNA duplexes was observed.

Conclusions:

  • 5-(Thien-2-yl)-2'-deoxyuridine can be effectively incorporated into DNA, creating functional fluorescent probes.
  • Modified oligonucleotides provide sensitive, sequence-specific detection of nucleic acid interactions.
  • This approach offers a valuable tool for studying DNA dynamics and developing novel diagnostic or research applications.