Nanowire based field effect transistors (FETs) have been extensively studied for their applications in biosensing. Due to the large surface to volume ratio of these structures, even a single biomolecule attached to the nanowire surface is able to change the electronic properties of the FET. Metal oxide nanowires such as CuO and ZnO are biocompatible, nontoxic, and stable when grown via thermal oxidation methods. However, the surface of the nanowire must be properly functionalized in order to fabricate a highly specific nanowire biosensor. We propose instead to use gold nanoparticles (GNPs) as the interface material between the nanowire and biomolecules of interest. In this study, we compare the performance between FETs with plain metal oxide nanowires and GNP-decorated nanowires fabricated using a cluster beam deposition (CBD) process via a magnetron sputtering system. These devices are used as DNA sensors. The CBD process allows us to exert size control over the GNPs to isolate and sense single DNA strands attached to the nanowire. We also show that GNP decoration increases the surface area to volume ratio of the nanowire and therefore the sensitivity of the device. This CBD process is integrated into a CMOS compatible procedure to fabricate arrays of nanowire DNA sensors.