Fluorogenic Sydnones for Bioorthogonal Labeling of DNA

Area of Science:

• Organic Chemistry
• Chemical Biology
• Biochemistry

Background:

• Bioorthogonal chemistry enables selective labeling of biomolecules within living systems.
• Fluorescent dyes are crucial tools for visualizing cellular processes.
• Sydnone-based click chemistry offers unique reactivity for bioconjugation.

Purpose of the Study:

• To synthesize novel cyanine-styryl dyes conjugated to sydnones.
• To investigate the fluorogenicity and reaction kinetics of strain-promoted sydnone-alkyne cycloaddition (SPSAC) reactions.
• To evaluate the utility of these dyes for bioorthogonal labeling of nucleic acids in cells.

Main Methods:

• Heck couplings were used for synthesizing cyanine-styryl sydnone conjugates.
• Spectroscopic methods were employed to study SPSAC reaction kinetics and fluorescence.
• HeLa cells were used to assess bioorthogonal labeling of BCN-modified DNA.

Main Results:

• Novel cyanine-styryl sydnone dyes were synthesized with significant Stokes shifts.
• SPSAC reactions showed fluorescence turn-on up to 8-fold with nucleosides.
• BCN-modified DNA templating significantly enhanced SPSAC kinetics (k2 up to 2,300 M-1s-1) and fluorescence turn-on (up to 17-fold).
• Bioorthogonal labeling in HeLa cells demonstrated the utility for distinguishing modified nucleosides and DNA.

Conclusions:

• The developed cyanine-styryl sydnone dyes combine fluorogenicity with bioorthogonal reactivity.
• DNA templating significantly boosts the efficiency of SPSAC reactions.
• These dyes are promising tools for metabolic labeling of RNA and DNA with distinct fluorescence readouts.