Rapid Detection of Specific DNA Sequences at Low Concentrations

Repetitive DNA sequences are an extremely common phenomena in the genome of most biological species. Current methods to detect specific DNA sequences are based on the quantitative polymerase chain reaction (PCR), which relies on target amplification by Taq polymerase and uses a fluorescent resonance energy transfer (FRET)-based probe. Here, to rapidly detect a repetitive DNA sequence, we combine a highly sensitive magnetic modulation biosensing (MMB) system and a modified double-quenched FRET-based probe. The high numbers of copies of the female-specific XhoI sequence of the domestic chicken, combined with the low background fluorescence levels of the modified double-quenched probe and the high sensitivity of the MMB system, allow us to determine the chick sex in ovo within 13 minutes, with 100% sensitivity and specificity. Compared to quantitative PCR, which requires 1-2 hours for the same task, the presented assay is 4–9 times faster. By specifically tailoring the primers and probe, the proposed assay can detect any target DNA sequence, either repetitive or non-repetitive.