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Detection of DNA sequences is of great importance for food control, pathogen determination, cancer diagnostics and forensic analysis. DNA detection techniques are often based on hybridization reaction. Although homogeneous methods are more rapid and simple, heterogeneous methods are more sensitive and less prone to matrix effect in real samples analysis. In our work some formats of microplate sandwich assay for DNA detection with different capture and reporter conjugates have been developed. Since the surface of microtiter plate wells is limited, the highly sensitive detection system based on HRP-catalysed chemiluminescence with the use of phenothiazine enhancers (3-(10’-phenothiazinyl)propionic acid and 3-(10’-phenothiazinyl)propane-1-sulfonate) in combination with N-morpholinopyridine was applied.