Poly cytosine (C)/poly adenine (A) modified probe for signal “on-off-on” assay of single-base mismatched dsDNA by a competitive mechanism

Direct discrimination of single-base mismatched dsDNA by a simple method or strategy would provide enormous opportunities for applications in the fields of life sciences and disease diagnosis. Herein, the peroxidase-mimicking activity of a metal-organic framework nanoprobe (MOF) was well exploited for the direct discrimination of single-base mismatched dsDNA based on a competition-induced signal on-off-on mechanism. The single-base mismatched dsDNA related with FecB gene (usually guanine (G)/thymine (T) mismatch) and MIL-88B-NH2 were used as target and MOF model, respectively. Firstly, polyA/polyC were loosely adsorbed onto the MOFs via the weak interaction to block the peroxidase activity of MOF, inducing the signal transition from on to off. Unexpectedly, the single-base mismatched (GT) dsDNA could reverse the signal response of MOF probe from off to on. But it could not occur for other nonspecific mismatches, such as CT and TT-mismatched dsDNA. A synergistic interaction mechanism between multiple GT mismatches and polyA/polyC was attempted to explain the competitive dissociation of polyA/polyC from MOF for the recovery of peroxidase activity. With it, a wide linear detection ranges from 10-9 M-10-5 M of GT mismatched dsDNA and a low detection limit of 0.247 nM could be achieved, even in the real samples. The effect of mismatched base number or position was also studied. Such a simple, rapid, cost-effective, and one-step mixing and checking method for single-base mismatched dsDNA discrimination eliminates the complex sample pretreatment, special DNA probe design, exclusive amplification or signal readout means. It thus offers a simple and effective route for direct discrimination of mismatched dsDNA and might hold a huge potential for the applications in gene analysis, disease diagnosis, and elementary research in life sciences.