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Updated: Jun 21, 2026
07:44
Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes
Published on: July 6, 2016
DNA sequence-dependent enhancement of Cy3 fluorescence
Billie Jo Harvey1, Claudia Perez, Marcia Levitus
1Biodesign Institute, Arizona State University, Arizona State University, Tempe, AZ, USA.
Summary
The fluorescence of Cy3 (a cyanine dye) attached to DNA depends on the DNA sequence. Specific DNA interactions with Cy3 enhance its fluorescence by limiting photoisomerization, a process that typically quenches the signal.
Area of Science:
- Molecular Biology
- Biophysics
- Biochemistry
Background:
- Cyanine dyes, such as Cy3, are widely employed as fluorescent probes in various scientific disciplines.
- Understanding the photophysical properties of these dyes is crucial for their effective application.
Purpose of the Study:
- To investigate the fluorescent properties of Cy3 when covalently attached to DNA oligonucleotides.
- To determine how DNA sequence influences the fluorescence efficiency and lifetime of Cy3.
Main Methods:
- Covalent attachment of Cy3 dye to the 5' terminus of DNA oligonucleotides.
- Analysis of fluorescence efficiency and lifetime measurements.
- Correlation of photophysical properties with DNA sequence and structure.
Main Results:
- Fluorescence efficiency and lifetime of Cy3 are highly dependent on the DNA sequence.
- DNA sequence dictates the extent and nature of Cy3-DNA base interactions.
- These interactions lead to an unusual enhancement in Cy3 fluorescence for many oligonucleotide sequences.
Conclusions:
- The observed fluorescence enhancement is linked to a photoisomerization mechanism that competes with fluorescence emission.
- Cy3-DNA interactions that restrict rotation around double bonds decrease photoisomerization, increasing the excited state lifetime.
- The interaction capability of Cy3 with DNA is influenced by oligonucleotide flexibility and the presence of purine bases.
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