Optimizing the plasmonic sensing of RNA folding based on local refractive index change of gold nanorod

In this paper, we investigate the spectroscopic sensing of RNA folding based on surface plasmon resonance (SPR) in coated gold nanorod. Theoretical calculations indicate that the folding and unfolding of coating RNA lead to the changing of local surrounding refractive index (RI) of gold nanorod, and then result in obvious SPR shift of absorption spectrum. The SPR shift is shown to be strongly influenced by the changing of the RNA length, environmental media and aspect ratio (AR) of gold nanorod. The high plasmonic sensitivity can be obtained with a long RNA length, great AR and large dielectric constant (DC) difference between RNA shell and environmental media. This new plasmonic sensing picture corresponding to folding and unfolding process of RNA is effective guide for the design and fabrication of nanometer scale biosensor for conformational probing of RNA.