Realizing plasmonic nanogaps with a refractive index (n = 1) environment in metallic nanoparticle (NP) structures are highly attractive for wide range of applications. So far in self-assembly-based approaches, without surface functionalization of metallic NPs, achieving such extremely small nanogaps is challenging. Surface functionalization introduces changes in refractive index at nanogap, which in turn deteriorates desired plasmonic properties. Add to this, fabrication of low-density dimer NP designs with smaller nanogaps poses a big challenge. Here, we introduce a simple and straight forward self-assembly-based strategy in fabrication of low-density, isolated dimer gold nanoparticles in nano-particle-on-metallic-mirror (NPoM) platform. A minimum interparticle gap distance between NPs of ~ 3 nm is achieved without surface functionalization. This is possible by utilizing M13 bacteriophage as spacer layer instead of SiO2 in NPoM. Density functional theory calculations on Au atom adsorption on SiO2 and M13 bacteriophage surface constituents trace the NP assembly on the latter to a comparatively weak interaction with substrate. Our study offers an attractive route in fabricating low density plasmonic dimer structures featuring small nanogaps and will enrich structure specific/isolated studies benefitting variety of optical, actuator, and sensing applications.