DNA Sensing by Amplifying the Number of Near-Infrared Emitting, Oligonucleotide-Encapsulated Silver Clusters

A bifunctional oligonucleotide integrates <i>in situ</i> synthesis of a fluorogenic silver cluster with recognition of a target DNA sequence. With the template C<sub>3</sub>AC<sub>3</sub>AC<sub>3</sub>GC<sub>3</sub>A, a complex forms with 10 silver atoms that possesses electronic transitions in the near-infrared and that is detected at nanomolar concentrations using diode laser excitation. Pendant to this cluster encoding region, the recognition component binds a target DNA strand through hybridization, and decoupling of these two regions of the composite sensor renders a modular sensor for specific oligonucleotides. A target is detected using a quencher strand that bridges the cluster template and recognition components and disturbs cluster binding, as indicated by static quenching. Competitive displacement of the quencher by the target strand restores the favored cluster environment, and our key finding is that this exchange enhances emission through a proportional increase in the number of emissive clusters. DNA detection is also accomplished in serum-containing buffers by taking advantage of the high brightness of this fluorophore and the inherently low endogenous background in the near-infrared spectral region. Cluster stability in this biological environment is enhanced by supplementing the solutions with Ag<sup>+</sup>.