Abstract: Assays using nanoparticle probes can be used to detect a target oligonucleotide with digital resolution by measuring the peak wavelengths and/or peak intensities of resonantly reflected light from locations on the surface of a photonic crystal (PC). The PC is functionalized with a capture oligonucleotide that binds to a nanoparticle probe that has bound to the target analyte. The binding of the nanoparticle probe to the PC shifts the peak wavelength and reduces the peak intensity of the resonantly reflected light at the binding location. An example nanoparticle probe includes a metallic nanoparticle conjugated to a probe oligonucleotide bound to a protector oligonucleotide. The probe oligonucleotide includes a first portion complementary to the target oligonucleotide and a second portion complementary to the capture oligonucleotide.