Attomolar-level detection of respiratory virus long-chain oligonucleotides based on FRET biosensor with upconversion nanoparticles and Au-Au dimer

Upconversion nanoparticles (UCNPs) are promising nanoprobes in DNA/RNA detection, such as respiratory viral RNAs, and siRNA in cancer. However, recent studies have indicated that the sensitivity of UCNP-based biosensors is restricted, ranging from picomolar to femtomolar level. Moreover, most of existing UCNP-based probes are only able to detect short-chain oligonucleotides, which are not suitable for detection of long-chain oligonucleotides in many real applications. In this work, we introduced a new UCNP-based fluorescence resonance energy transfer (FRET) nanoprobe design composed of NaGdF4:Yb3+, Er3+@NaGdF4 core-shell UCNPs (csUCNPs) linking with Au-Au dimer to detect long-chain oligonucleotides of SARS-CoV-2 N-gene. Compared with typical single gold nanoparticles (AuNPs) in FRET biosensors, our theoretical investigation shows that a stronger electromagnetic field is generated in the Au-Au dimer where the plasmon resonance can enhance FRET efficiency and increase the working distance. Thus, the synergetic effect of plasmonic resonance and FRET enables a greater quenching efficiency (QE) of Au-Au dimer to UCNPs, which leads to more remarkable upconversion luminescence (UCL) recovery for each target gene recognition. Importantly, our design significantly improved the limit of detection (LOD) to attomolar level, with a linear response ranging from 2 aM to 2 fM. Moreover, the clinical detection with inactivated SARS-CoV-2 samples was successfully performed with excellent specificity within 30 min using the developed UCNPs biosensors incorporated with Au-Au dimer. This UCNP biosensor based on Au-Au dimer strategy with ultra-sensitivity and good selectivity opens a new path for clinical diagnosis without target amplification and plays an instructive role in other virus diagnosis.