A spectroscopic ruler for intermediate-zone FRET measurements

It is well known that Fluorescence Resonance Energy Transfer (FRET), the most common mechanism for electronic energy to migrate between molecular chromophores, has a predominantly inverse sixth power dependence on the rate of transfer as a function of the distance R between the chromophores. However, the unified theory of electronic energy transfer, derived from quantum electrodynamics, predicts an additional contribution with an R-4 dependence on distance. This intermediate-zone term becomes especially important when the chromophore spacing is similar in magnitude to the reduced wavelength (ƛ= λ 2π ) associated with the mediated energy. In previous theoretical studies we have suggested that inclusion of the intermediate term, through rate equation and quantum dynamical calculations, may be important for describing the exciton diffusion process in some circumstances, and in particular when the distance between the chromophores exceeds 5 nm. In this paper, we focus of the role of the intermediate-zone contribution to distance measurements between chromophores made through the application of spectroscopic ruler techniques. One of the major assumptions made in employing these experimental techniques is that the R−6dependence is valid. In this work, we reformulate the spectroscopic ruler principles for intermediate distances to include the inverse fourth power rate component, and compare the results of this reformulation to experimental FRET results from the literature. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.