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The interactions between a cationic polymer, poly(2- dimethylamino)ethyl methacrylate (pDMAEMA), and negatively charged rhodaminelabeled 25-mer phosphodiester oligonucleotides (RhONs) were studied by fluorescence fluctuation spectroscopy and other techniques. The composition of the pDMAEMA/Rh ON complexes was investigated as a function of the charge ratio (+/) by increasing the pDMAEMA concentration and keeping the RhON concentration constant. We applied two different methods for analyzing the fluorescence fluctuation profiles of the pDMAEMA/RhON complexes, which depended on their composition. First, we analyzed the data with the photon counting histogram (PCH) technique, which determines the molecular brightness and the concentration of fluorophores (Chen et al., 1999). A particular challenge for the data analysis is the occurrence of sudden fluorescence bursts in the fluorescence fluctuation profiles, which are linked to the appearance of multimolecular complexes (i. e. when several RhONs were present in one complex). A quantitative interpretation of the analysis for the complexes remains challenging and is connected to the rarity of the fluorescent bursts, which do not provide sufficient data statistics. To specifically address the problem of the fluorescent bursts we employed a method described by Van Craenenbroeck et al. 1999). This method, applicable only when data were integrated over much longer time bins, allowed us to estimate the number of fluorescence bursts which could be considered as a relative measure of the amount of multimolecular complexes present. When monomolecular complexes were formed, i. e. at high values of the charge ratio, highly intense fluorescence peaks were not present and the interpretation of the PCH analysis was more straightforward. The molecular brightness of the species (e), as revealed from PCH analysis, was greater than e for the free Rh ONs, indicating that the RhONs were attached to pDMAEMA chains.

Fluorescence Fluctuation Analysis for the Study of Interactions between Oligonucleotides and Polycationic Polymers