Thermodynamic Investigation into the Binding Properties of DNA Functionalized Gold Nanoparticle Probes and Molecular Fluorophore Probes*

Oligonucleotide functionalized gold nanoparticles, or nanoparticle probes, have become the basis for an increasing number of diagnostic applications that compete with molecular fluorophores in certain settings. Several studies have qualitatively determined that the presence of gold nanoparticle probes results in cooperative melting properties of the probe/target complex, which both sharpen and increase the melting transition of DNA-linked nanoparticle aggregates. Binding of nanoparticle probes to a complementary target sequence modified with a molecular fluorophore resulted in quenching and decreased fluorescence intensity. At room temperature, this translates to binding of the nanoparticles at concentrations as low as 20 fmol. Nanoparticle probes have a higher binding constant, which increases the sensitivity of assays based upon them, as compared with their molecular counterparts. As the length of the recognition sequence increases, the enhancement of the binding strength diminishes. In designing an effective probe, a balance must be maintained between binding strength and selectivity.