Sequence specific recognition of ssDNA by fluorophore 3-hydroxyflavone

Area of Science:

• Chemical Biology
• Biophysical Chemistry
• Molecular Recognition

Background:

• 3-hydroxyflavone (3HF) derivatives are known for their interesting photophysical properties.
• Developing selective probes for nucleic acid detection is crucial in molecular diagnostics.
• Water-soluble fluorescent probes offer advantages for biological applications.

Purpose of the Study:

• To synthesize and characterize a water-soluble 3HF derivative, N-(3-hydroxy-4'-flavonyl)-N,N,N-trimethylammonium sulfate (3HFNMe3).
• To investigate the photophysical properties of 3HFNMe3 in aqueous solution.
• To explore the potential of 3HFNMe3 as a sensor for distinguishing single-stranded DNA (ssDNA) sequences.

Main Methods:

• Synthesis of the 3HFNMe3 derivative.
• Spectroscopic analysis (emission spectra) of 3HFNMe3 in ultrapure water.
• Titration experiments with various ssDNA sequences.
• Analysis of emission band intensity ratios (A*/T*) to establish characteristic curves.

Main Results:

• 3HFNMe3 exhibits three distinct emission bands: normal (N*), anionic (A*), and tautomeric (T*).
• Binding with ssDNA causes selective quenching of the A* emission band, while the T* band remains largely unaffected.
• The ratiometric change (A*/T*) generates unique characteristic curves for different ssDNA sequences.
• This ratiometric response allows for the differentiation of ten distinct ssDNA chains based on their nucleotide sequences.

Conclusions:

• 3HFNMe3 is a versatile water-soluble fluorescent probe with distinct emission properties.
• The probe demonstrates effective sequence-specific recognition of ssDNA through ratiometric fluorescence changes.
• This method provides a promising approach for identifying and differentiating ssDNA sequences in solution.