Rhodamine analogs for molecular ruler applications

• Extended rigid rhodamines were designed via molecular simulations.
• The trend of spectral properties of rhodamines agreed with TDDFT calculations.
• Amine-reactive probes for bioconjugation were synthesized.
• To be used as molecular ruler to study pore dilation in cationic channels.

A series of geometrically well-defined cationic fluorophores were designed based on molecular mechanics. They contain biaryl linkers to impart rigidity preventing intramolecular folding between a conjugated biomolecule and fluorophore. All probes have absorption and emission maxima within 20 nm from Texas Red, as predicted by TDDFT calculations and validated experimentally.

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