Fast and Sensitive Detection of the Specific DNA Sequences Using Magnetically Modulated Biosensors

Background: Modern biomedical research extensively relies on detection of specific nucleic acid targets. The most widely used technique for DNA/RNA detection is based on the polymerase chain reaction (PCR). PCR is highly sensitive, but also time consuming, laborious, and requires highly purified samples in which the target sequence is intact, and no polymerase inhibitors are present. In some applications (e.g., environmental, industrial, forensic), PCR is not directly applicable. Fast and sensitive detection of the specific DNA/RNA sequences requires development of new detection method.

Methods: Recently introduced Magnetic Modulation Biosensing (MMB) technology allows detection of biomarkers at very low concentrations. Here, we present two MMB-based methods for specific detection of DNA sequences. The first is based on Sandwich Hybridization Assay (SHA) methodology, which allows detection of DNA fragments without target amplification. The second method is based on a conventional qPCR protocols, with the MMB as a detection device.

Results: MMB-assisted SHA is capable of directly detecting as low as 1.4 pM of the DNA target in human serum, without enzymatic target/signal amplification. Using the MMB-based qPCR approach, we demonstrated detection of the highly repetitive female-specific XhoI sequence of the domestic chicken (Gallus gallus) in-ovo within 13 minutes, with 100% sensitivity and specificity. This is 4-9 times faster than conventional qPCR.

Conclusion: MMB-based methods allow rapid and precise detection of DNA targets either without enzymatic target/signal amplification, or with a minimal number of amplification cycles.