We report the effect of surface coverage and sequence on the performance of 5' thiolated, 3' fluorophore-labeled DNA hairpin probes bound to Au/Ag striped ("barcoded") metal nanowires. Coverage was controlled by varying probe concentration, buffer ionic strength, and by addition of short hydroxy-terminated alkanethiol diluent molecules during probe assembly onto the nanowire surface. Surface dilution of the surface-bound probes with a (omega-hydroxyl alkanethiol, a commonly accepted practice in the surface-bound DNA literature, did not appreciably improve sensor performance as compared to similar probe coverages without hydroxyalkanethiol diluents; this finding underscores the differences between the molecular beacon probes used here and more traditional nonfluorescent, random coil probes. We found that intermediate probe coverage of similar to 10(12) Molecules/cm(2) gave the best discrimination between presence and absence of a target sequence. Because we are interested in multiplexed assays, we also compared several beacon probe sequences having different stabilities for secondary structure formation in solution; we found that both probe surface coverage and sensor performance varied for different probe sequences. When five different molecular beacon probes, each bound to barcoded nanowires, were used in a multiplexed, wash-free assay for target oligonucleotides corresponding to viral nucleic acid sequences, these differences in probe performance did not prevent accurate target identification. We anticipate that the findings described here will also be relevant to other applications involving molecular beacons or other structured nucleic acid probes immobilized on metal surfaces.