Model-based approaches to investigate the interactions between unmodified gold nanoparticles and DNA strands

Model-based techniques were used to resolve fluorescence datasets related to the interactions of two complementary oligonucleotides (which were tagged by fluorescein and Texas red respectively) in the presence of 13 nm gold nanoparticles (AuNPs). This system was selected as an example to demonstrate the advantages of model-based techniques in studying interactions of nanoparticles and biomolecules, and providing better insight to such nano-bio systems which is in turn helpful for designing more efficient sensor/delivery systems. The adsorption isotherms were analyzed by model-based Scatchard and Langmuir methods and the results were the adsorption constants of the oligonucleotides on AuNPs and the number of binding sites on AuNPs. This is the first reported application of Scatchard method where DNA is the adsorbate. The main part of the study is focused on the application of more sophisticated model-based techniques to analyze complex three-way excitation-emission fluorescence data sets recorded through the adsorption/hybridization process. A novel model-based restricted Tucker3 method is also proposed to estimate the hybridization constant. An advantage of this technique is the estimation of the concentration profiles of all involving chemical components, even those without a fluorescence signal.