A gold nanoparticle based fluorescent probe for simultaneous recognition of single-stranded DNA and double-stranded DNA

A fluorescent method is described for simultaneous recognition of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). It is based on the quenching of the fluorescence of fluorophore labeled DNA probes by gold nanoparticles (AuNPs). To demonstrate feasibility, two DNA probes labeled with spectrally different fluorophores were designed. The first DNA probe (P-1) was modified with 6-carboxyfluorescein (FAM; with green fluorescence, peaking at 518 nm), while the second (P-2) was modified with carboxy-X-rhodamine (ROX; with yellow fluorescence, 610 nm). The fluorescence signals of the labels are quenched if P-1 or P-2 are adsorbed on AuNPs. Upon addition of ssDNA and dsDNA, hybridization occurs between P-1 and ssDNA to form a dsDNA. In contrast, P-2 hybridizes with dsDNA such that a triplex DNA is formed. As a result, the dsDNA and the triplex DNA, respectively, are desorbed from the surface of the AuNPs so that quenching no longer can occur and strong fluorescence can be observed. Under the optimal conditions, ssDNA and dsDNA can be detected simultaneously via the green and yellow fluorescence, respectively. The detection limits can be as low as 330 pM. In particular, the method has excellent selectivity for the target DNAs over control DNAs.