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Published on: October 6, 2022
A binary Cy3 aptamer probe composed of folded modules.
1Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.
Analytical Biochemistry
|January 23, 2010
Summary
Researchers developed a novel RNA aptamer, Cy3_apt, for detecting the fluorescent dye Cy3. This aptamer can be used as a binary probe for real-time detection of nucleic acids and RNA interactions.
Area of Science:
- Molecular Biology
- Biochemistry
- Biotechnology
Background:
- Aptamers are short nucleic acid sequences with high target affinity.
- Dye-binding aptamers enable real-time detection of biomolecules.
- Cy3 is a common, non-toxic fluorescent dye used in biological research.
Purpose of the Study:
- To isolate and characterize an RNA aptamer specific to the fluorescent dye Cy3.
- To develop a novel aptamer-based detection system for nucleic acids and RNA interactions.
Main Methods:
- In vitro selection (SELEX) to isolate RNA aptamers against Cy3.
- Sequence optimization to enhance aptamer affinity and reduce length.
- Surface Plasmon Resonance (SPR) assay to monitor binding kinetics.
- Development of a binary aptamer probe system.
Main Results:
- Aptamer Cy3_apt was selected and optimized to 49 nucleotides.
- The optimized Cy3_apt showed high affinity for Cy3, confirmed by SPR.
- Binding of Cy3 to Cy3_apt enhanced Cy3's fluorescence.
- A binary aptamer probe was constructed from two modules of Cy3_apt.
Conclusions:
- The developed Cy3_apt is a high-affinity binder for the fluorescent dye Cy3.
- The binary aptamer probe system demonstrates potential for detecting target oligonucleotides and RNA-RNA interactions.
- This work introduces a novel tool for sensitive and real-time molecular detection.
