Examination on the orientation-dependent FRET by using DNA duplex

Abstract

Förster/Fluorescence resonance energy transfer (FRET) has been widely used as a molecular ruler since FRET efficiency varies depending on the distance and orientation between a donor and an acceptor. However, orientation dependence of FRET has not been fully utilized since it is difficult to control distance and orientation of dyes. On the other hand, DNA is an ideal scaffold to control the interaction between dyes since DNA can form a well-defined double helical structure. Distance and orientation can be strictly controlled by covalently introducing chromophores into DNA. Sequence can be easily controlled by using automated DNA synthesizer. In this review, we focus on the studies investigating orientation dependence of FRET by using DNA scaffolds. Orientation dependence of FRET can be used to analyze various DNA structures and DNA-drug interactions. Even homo-FRET can be investigated by using DNA scaffolds.