Rank Annihilation Factor Analysis for estimating of Förster Resonance Energy Transfer (FRET) profile in hybridization studies

Förster resonance energy transfer (FRET) is a mechanism describing energy transfer between two light-sensitive molecules (chromophores) labeled as suitable donor or acceptor. A donor chromophore, initially in its electronic excited state, may transfer energy to an acceptor chromophore through non-radiative dipole–dipole coupling when the distance between them is close enough to energy transfer occurs. This distance dependence means that FRET data provide valuable information about the structure and conformation of bio-macromolecules and their interactions including protein-protein interactions, protein–DNA interactions, and protein conformational changes. The FRET efficiency is measured through spectral changes and used to identify interactions between the labeled complexes and hence accurate resolution of the chromophores spectral profiles is of importance. There are several ways of measuring the FRET efficiency by monitoring changes in the fluorescence emitted by the donor or the acceptor [1, 2].In this work a new solution for accurate extraction of FRET profiles and consequently determination of FRET efficiency is proposed. Rank Annihilation Factor Analysis [3, 4] was used in two modes for eliminating the donor and acceptor pure contributions from data and accurate profile related to component (hybrid component making FRET phenomenon) retained. The efficiency of proposed method was evaluated by simulating several datasets at different degrees of spectral overlapping and in the presence of noise. The advantage of the proposed method is its simplicity toward the extraction of true FRET profiles of desired component from a complex data without need to complicated chemometrics analysis.