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Horseradish peroxidase is one of the widely used enzymes in analytical biochemistry. However efficient use of peroxidase in clinical, nutritional and environmental analysis still has to overcome a number of limitations, particularly the low operation stability of the biocatalyst in organic media that is necessary for the determination of poorly water-soluble analytes in water-insoluble samples. In the present work to overcome the above mentioned limitations we propose the approach based on the inclusion of peroxidase into the nanostructured self-assembled complex with a natural polyelectrolyte - chitosan. The novel biocatalyst is characterized by a narrow distribution of average hydrodynamic radius of particles (25-30 nm) and is twice more active than the native enzyme in the presence of 30% dimethylsulfoxide (DMSO), and acts as a native enzyme in the presence of 60 % DMSO. The self-assembled enzyme-polyelectrolyte complex was used as a basis for the design of optical sensors for the determination of physiologically active compounds (phenolic compounds and organic peroxides) – the substrates of peroxidase. The technology of the formation of the transparent films from water-organic media on the surface of optical glasses and in wells of polystyrene plates was developed. It was shown that biorecognizing films generated from water-DMSO are characterized by a higher transparency than the films generated from water solutions. The morphology of the films on the basis of peroxidase-chitosan complex was studied by atomic force spectroscopy method. The sensors based on the self-assembled peroxidase-chitosan complex were used for the determination of phenolic compounds and organic peroxides in different matri