We describe the efficiency of deoxyribonucleic acid (DNA) immobilization onto a nanowire (NW) after employing various surface cleaning methods. From surface tension measurements and fluorescence microscopy images of the silicon oxide surfaces, we determined that the effectiveness of surface cleaning using an acetone/ethanol mixture was similar to that of piranha solution (sulfuric acid/hydrogen peroxide). Thus, we employed surface cleaning with an acetone/ethanol mixture en route toward the fabrication of a series of label-free, back-gated, 60-nm nanowire field-effect transistor (NWFET) sensors for the detection of the BRAFV599E oncogene. We applied the NWFET sensor to the successful detection of the hybridization and dehybridization processes of the BRAFV599E mutation gene.