Palladium–iridium nanocubes modified with a high-affinity DNA aptamer as paired viral diagnostic and therapeutic tools

The COVID-19 pandemic emphasizes the need for the development of molecular tools that can be used as effective diagnostic and therapeutic agents. Herein we investigate the potential of aptamer-dressed nanomaterials both as diagnostics and therapeutics using SARS-CoV-2 as a model. The nanomaterials are based on the palladium-iridium (Pd–Ir) nanocubes modified with monomeric, dimeric or trimeric aptamers that exhibit varying affinities for the spike protein of SARS-CoV-2. These nanomaterials were first examined for diagnostic potential through the creation of a nanozyme-linked aptamer assay (NLAA) that takes advantage of the peroxidase-mimicking activity of Pd–Ir nanocubes. The trimeric aptamer-based NLAA demonstrated a limit of detection (LOD) of 9.3×103 cp/mL for pseudoviruses expressing the spike protein of SARS-CoV-2, 172- and 12.9-fold lower than that of the monomeric and dimeric aptamer-based NLAAs, respectively. Upon testing with 60 clinical saliva samples, the trimeric aptamer-based NLAA achieved a specificity of 100% and a sensitivity of 86.7%. The same nanomaterials were also examined for the ability to block viral entry to host cells. The trimeric aptamer-conjugated nanocubes exhibited a superior neutralizing ability, with an IC50 value of 6.4 pM, 2.7-fold and 10.1-fold lower than that of the dimeric and monomeric aptamer nanocubes. Moreover, the trimeric aptamer-conjugated nanocubes exhibited excellent biostability and biocompatibility. Overall, our study provides a framework for combating future viral pandemics through the development of a paired biosensor and neutralizing agent made of the same aptamer-modified nanomaterial that recognizes an important viral surface protein like the spike protein of SARS-CoV-2.