Four different conjugated polymer nanoparticles (CPNs) were used to differentiate structurally similar glycosaminoglycans (GAGs) in a urine simulant. challenged by the structural similarity of GAGs and interferences of the concomitant biomolecules commonly present in biological fluids. Conventional GAG detection methods require sample preparation steps followed by complicated instrumental analysis or biochemical assays.5-9 Recently several Nodakenin researchers have developed conceptually important detection methods on the basis of pattern recognition using nanoparticles conjugated polyelectrolytes and liposomes.10-14 In those examples differentiation of GAGs was demonstrated by using multivariate statistical methods including linear discriminant analysis (LDA). While current sensory systems perform well in a simplified solution (i.e. highly diluted media with buffers) few sensory systems have been reported for sensitive detection of GAGs in complicated biological fluids. Development of simple and sensitive sensory systems of GAGs in biological media is highly important and practical for future disease diagnostics. Owing to their excellent photophysical properties conjugated polymers (CPs) have attracted much attention for optical detection of chemicals metal ions and biological substances.15-18 Many synthetic and fabrication methods have been developed to increase aqueous compatibility of CPs to achieve necessary sensitivity for specific analytes in aqueous environments.19 Depending on the aqueous solubility of CPs Nodakenin and the nature of interaction between CPs and analytes structural changes can occur in individual CP chains or multiple chain aggregates which correspond to changes in CP optical properties.20 21 Previously we have fabricated positively charged conjugated polymer nanoparticles (CPNs) by treating a non-aqueous soluble primary amine-containing CP [i.e. poly(p-phenyleneethynylene) (PPE)] with KLHL1 antibody organic acids followed by dialysis.22 The aggregation structures and sizes of CPNs were dependent on the nature of organic acid treatment. Furthermore we found that CPNs fabricated with a semi-flexible CP [i.e. a flexible linker containing poly(p-phenylenebutadiynylene) (PPB)] exhibited backbone reorganization to maximize hydrophobic chain interaction when treated with an anionic linear polysaccharide hyaluronic acid (HA).23 24 The structural reorganization of CPNs was evident by photophysical changes including a new sharp absorption peak at longer wavelength and decreased fluorescence intensity. The physical change was observed as an elongated particle shape shown in atomic force microscopic images. From these observations we hypothesized that the aggregation status of cationic CPNs will be different upon interaction with GAGs due to the differences in ionic strength of the GAGs exhibiting different degrees of acetylation and sulfonation in the repeating disaccharide units [see Electronic Supporting Information (ESI) for chemical structures of GAGs]. While the hydrophobic interaction among non-aqueous soluble CPs provides the structural integrity of CPNs in a biological medium the loosely aggregated CPNs will undergo backbone reorganization under polyelectrolyte interactions with GAGs. Depending on the strength of ionic interactions the aggregation properties of CPNs will change accordingly resulting in measurable spectral changes. In this report we use four different CPNs that act as both an analyte receptor and a signal transducer and analyze their differential responses to each GAG in a urine simulant. A systematic investigation of the aggregation properties of CPNs that vary by side chain amine density backbone flexibility and type of backbone structure in response to GAGs was conducted by monitoring changes in absorption/emission profiles and size/size distributions. Finally entire spectral responses of the structurally diverse CPNs were analyzed by Nodakenin Nodakenin LDA to differentiate structurally similar GAGs Nodakenin at a physiologically relevant concentration25 in a urine simulant. We found that side chain and backbone flexibility strongly affects both the physical and photophysical properties of CPN/GAG complexes. A clear differentiation of recognition patterns was observed in a Nodakenin LDA plot supporting that structurally diverse CPNs are effective at.