Sensitive and label-free shell isolated Ag NPs@Si architecture based SERS active substrate: FDTD analysis and in-situ cellular DNA detection

•SiO2 capping over-layered on Ag NPs@Si by low energy e-beam irradiation method.•The local electromagnetic field distribution for the SiO2 capped non-identical trimer Ag NPs on Si substrate was evaluated by FDTD analysis.•The SERS substrate exhibits good stability and achieved the low detection limit up to 10−10 M concentration.•Fingerprint of DNA was detected in a cellular level by label free method.