Multiway investigation of interaction between fluorescence labeled DNA strands and unmodified gold nanoparticles

The single stranded DNA can be adsorbed on the negatively charged surface of gold nanoparticles (AuNPs), but the rigid structure of double stranded DNA prevents it from adsorption. Signal of a tagged single stranded DNA will be quenched by the plasmon effect of the AuNP surface after its adsorption. This phenomenon has been used to study the DNA hybridization and interactions of two complementary 21mer oligonucleotides each tagged with a different fluorescent dye in the presence of 13 nm gold nanoparticles. The DNA strands used in this study belong to the genome of HIV. The obtained rank deficient three-way fluorescence data sets were resolved by both PARAFAC and restricted Tucker3 models. This is the first successful application of a multiway chemometric technique to analyze multidimensional nanobiological data. The restricted Tucker3 showed a better performance compared to PARAFAC in resolving the data sets. The advantages of restricted Tucker3 analysis over the unrestricted one, i.e., the limited rotational freedom (more unique results) and better interpretability of the obtained results, were experienced in this study. The resolved excitation, emission, and concentration profiles and specially fluorescence resonance energy transfer (FRET) profiles obtained by restricted Tucker3 were chemically more meaningful than those obtained from PARAFAC.