Environment-responsive fluorescent nucleoside analogue probe for studying oligonucleotide dynamics in a model...

Area of Science:

• Biophysical Chemistry
• Nucleic Acid Research
• Fluorescent Probes

Background:

• Conventional fluorescent nucleoside analogues are unsuitable for cell-based assays due to UV excitation and low quantum yields.
• Studying nucleic acids in confined, cell-like environments requires specialized probes and methodologies.
• Reverse micelles (RM) serve as effective biological membrane models and are UV-transparent.

Purpose of the Study:

• To photophysically characterize a novel fluorescent uridine analogue (1) in micelles and reverse micelles (RM).
• To evaluate the potential of this analogue as a probe for nucleic acids in a cell-mimicking environment.
• To assess the suitability of RM for studying labeled oligonucleotides.

Main Methods:

• Synthesis and photophysical characterization of a novel fluorescent uridine analogue (1) based on a 5-(benzo[b]thiophen-2-yl)pyrimidine core.
• Incorporation of the nucleoside analogue into an RNA oligonucleotide.
• Hybridization of the labeled oligonucleotide with complementary DNA and RNA strands.
• Measurement of fluorescence intensity, lifetime, and anisotropy in aqueous buffer versus RM.

Main Results:

• The fluorescent nucleoside analogue (1) is sensitive to polarity and viscosity, reporting on its microenvironment.
• Oligonucleotides labeled with nucleoside 1 exhibited significantly higher fluorescence intensity, lifetime, and anisotropy in RM compared to aqueous buffer.
• The observed fluorescence changes in RM are consistent with the expected properties of this confined, cell-like environment.

Conclusions:

• Nucleoside analogue 1 demonstrates promising photophysical properties for use as a fluorescent label.
• Reverse micelles provide a suitable model system for studying nucleic acid behavior in a confined milieu.
• This fluorescent probe can be utilized for investigating nucleic acid function in model cellular environments.