Orientation control of fluorescence resonance energy transfer using DNA as a helical scaffold.

The efficiency of fluorescence resonance energy transfer (FRET) between two chromophores positioned at opposite ends of DNA base pair domains has been investigated. The base pair domain serves as a helical scaffold which defines both the distance between chromophores and the dihedral angle between their electronic transition dipole moments, each incremental base pair increasing the distance and stepping the dihedral angle. Fluorescence quantum yields and lifetimes have been determined for both the donor and acceptor chromophores. The experimental data are found to be in excellent accord with an oriented dipole model, rather than with the averaged dipole model conventionally assumed for FRET.