Soft and hard multiway FRET-based investigation of interaction between drug and QD labeled DNA

Abstract

Interaction of 7-aminoactinomycin D (7AAD) with duplex form of quantum dot (QD) conjugated DNA, is the subject of this report. Excitation emission fluorescence measurements based on FRET mechanism offer a powerful means of studying this process. During titration experiments of DNA with 7AAD, three-way data are obtained—fluorescence measurements as a function of excitation and emission wavelengths at different 7AAD concentrations. The PARAFAC algorithm is applied to resolve the recorded data array. Upon inspection of the results, however, deviation from trilinearity as an intrinsic property of FRET data is observed that results in chemically less meaningful profiles from PARAFAC. This difficulty is addressed by using the restricted Tucker3 algorithm. The restricted Tucker3 shows a better performance compared to PARAFAC in resolving the data sets. Whereas this approach is more flexible in the modeling of profiles, the non-unique resolution is the major disadvantage of the algorithm. Therefore, to assess complete analysis of the FRET data hard trilinear decomposition is tried. It is shown that HTD algorithm has succeeded in the unique calculation of concentration profiles and pure spectra of all species. Also, equilibrium constants for the hybridization (3.1×106M−1) and the intercalation equilibrium (1.4×107M−1) are estimated in a unique way using hard modeling.