We report on optical properties of gold deposited on SiO2 nanospheres randomly adsorbed on a thin gold layer. Extinction peaks with optical density of more than 2 are observed in the visible as well as near-IR regimes. The peak wavelength of the latter was affected exquisitely by the thickness of the top layer. A helium ion microscope (HIM) was used for careful observation of morphological transformation accompanying the change in the deposition thickness. Growth of grain structures into a capped-dimer structure was accompanied by slight blue-shift of the visible peak and significantly greater red-shift of the near-IR peak. Our finite-difference time-domain (FDTD) calculations show that these peaks in the visible and near-IR can be respectively attributed to dipole modes associated with transverse and longitudinal oscillations of free electrons in the gold-capped dimer. To investigate the refractive index sensitivity of these peaks, we used two approaches: immersion in solutions of varying refractive index and coating with an organic layer. With the first approach that characterizes the bulk sensitivity, the visible peak shows sensitivity of 122 nm/RIU, while the near-I peak shifts at the rate of 506 nm/RIU. With the second approach that reflects the local sensitivity, the surface was saturated with alkaline phosphatase (ALP), whose subsequent reaction led to formation of a thin insoluble organic layer, causing a relatively small blue-shift, under 7 nm, of the visible peak and much larger red-shift, over 50 nm, of the near-IR peak when measured in buffer. When the same reaction was measured at end points in the air, the shift was as large as 444 nm for the near-IR peak.