Triphenylmethane dyes as fluorescent probes for G-quadruplex recognition

Area of Science:

• Biophysical Chemistry
• Molecular Biology
• Analytical Chemistry

Background:

• Triphenylmethane (TPM) dyes typically exhibit weak fluorescence due to vibrational deexcitation.
• G-quadruplexes are unique nucleic acid structures with potential roles in various biological processes.

Purpose of the Study:

• To investigate the potential of TPM dyes as fluorescent probes for G-quadruplex DNA.
• To explore the factors influencing the interaction between TPM dyes and G-quadruplexes.

Main Methods:

• Comparative analysis of fluorescence and energy transfer spectra of five TPM dyes.
• Testing dye interactions with intramolecular G-quadruplexes, intermolecular G-quadruplexes, single-stranded DNA, and double-stranded DNA.
• Evaluating the impact of dye charge and substituent size on binding stability.

Main Results:

• Four TPM dyes demonstrated distinct fluorescence spectra capable of differentiating intramolecular G-quadruplexes from other DNA structures.
• Energy transfer fluorescence spectra and titration successfully distinguished all G-quadruplexes from single- and double-stranded DNA.
• TPM dye charge and substituent size were identified as key factors affecting binding stability.

Conclusions:

• TPM dyes can be effectively utilized as sensitive fluorescent probes for G-quadruplex detection.
• Spectroscopic methods involving TPM dyes offer reliable discrimination between different DNA structures.
• Understanding dye properties is crucial for optimizing G-quadruplex-TPM dye interactions.