Perylene-Cy3 FRET System to Analyze Photoactive DNA Structures

We report a new Forster resonance energy transfer (FRET) system for structural analyses of DNA duplexes using perylene and Cy3 as donor and acceptor, respectively, linked at the termini of a DNA duplex via D-threoninol. Experimentally obtained FRET efficiencies were in good agreement with theoretical values calculated based on canonical B-form DNA. Due to the relatively long Forster radius, this system can be used to analyze large DNA structures, and duplexes containing photo-reactive molecules can be analyzed since perylene can be excited with visible light. The system was used to analyze a DNA duplex containing stilbene, demonstrating that in the region of the stilbene cluster the duplex adopts a ladder-like structure rather than helical one. Upon photodimerization between stilbene residues, FRET efficiencies indicated the reaction does not disturb DNA duplex. This FRET system will be useful for analysis of photoreactions of nucleobases as well as a wide range of nucleic acid structures.

Automated summary

A new FRET system using perylene and Cy3 as donor and acceptor, linked at the termini of a DNA duplex via D-threoninol, has been developed for structural analyses. The system shows good agreement between experimental FRET efficiencies and theoretical values, making it suitable for analyzing large DNA structures. Additionally, the system can be used to study photoreactions of nucleobases and a wide range of nucleic acid structures.