Application of supramolecular complexes of DNA-fragments biotinylated at both ends with streptavidin demonstrated ultrasensitive detection of three microbial toxins (Vibrio cholerae toxin, Staphylococcus aureus toxic shock syndrome toxin and S. aureus enterotoxin A) by real-time immuno-PCR. Bisbiotinylated DNA probes of various types were employed to design DNA-streptavidin complexes, i.e. single-stranded DNA of 60 n., double-stranded DNA of 150, 300, and 750 bp-long at different DNA-streptavidin ratio. The test systems displayed the following sensitivities: for SEA - 1 pg/ml, TSST – 0.1 pg/ml, CHT – 1 pg/ml composing 300, 2000, and 200-fold higher sensitivity, respectively, as compared to the corresponding ELISA tests. Interestingly, a high sensitivity can be reached regardless of a DNA probe size. However, the most precise results were observed with a short single chain probe at the DNA-streptavidin ratio 1/1.