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Published on: July 8, 2025
Development of dansyl-modified oligonucleotide probes responding to structural changes in a duplex
Yoshio Suzuki1, Keiko Kowata, Yasuo Komatsu
1Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
Bioorganic & Medicinal Chemistry Letters
|October 3, 2013
Summary
Dansyl-modified oligonucleotides (ONTs) offer sequence-specific fluorescent detection of DNA and RNA. Their fluorescence changes based on guanosine proximity and hybridization, enabling precise probing.
Area of Science:
- Biochemistry
- Molecular Biology
- Organic Chemistry
Background:
- Oligonucleotides (ONTs) are crucial in molecular biology.
- Fluorescent probes enhance detection sensitivity.
- Dansyl fluorophores offer unique optical properties.
Purpose of the Study:
- To synthesize dansyl-modified oligonucleotides (ONTs) for fluorescent detection.
- To investigate the fluorescence response of dansyl-ONTs to DNA and RNA hybridization.
- To evaluate the potential of dansyl-ONTs as sequence-specific probes.
Main Methods:
- Synthesis of a nonnucleoside amidite block containing a dansyl fluorophore.
- Preparation of dansyl-modified oligonucleotides (ONTs).
- Spectroscopic analysis of fluorescence intensity changes upon hybridization with DNA and RNA targets.
Main Results:
- Dansyl-ONT fluorescence intensity increased with adjacent guanosine residues.
- Fluorescence significantly decreased in a dansyl-flipping duplex due to solvatochromism.
- Increased fluorescence observed at equimolar concentrations of target DNA.
- Dansyl-ONT duplexes exhibited higher melting temperatures.
- Similar fluorescence changes detected upon hybridization with complementary RNAs.
Conclusions:
- Dansyl-modified ONTs act as effective sequence-specific fluorescent probes for DNA and RNA.
- The observed fluorescence changes are influenced by guanine content and the microenvironment.
- This method provides a sensitive approach for nucleic acid detection and characterization.
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