Viral RNA detection through DNA-based biosensing

COVID-19 outbreak has spread rapidly, resulting in a worldwide critical health situation. RT-PCR is the standard method to diagnose SARS-CoV-2 infection, but faster and cheaper diagnostic tools are needed and continuously developing. We focus on an optical DNA-based biosensor, where DNA strands immobilized on gold are used to detect specific SARS-CoV-2 RNA sequences through hybridization. DNA self-assembled monolayers are studied by a multi-technique approach to optimize the sensing platform, by tuning ssDNA immobilization time, concentration of ssDNA and molecular spacer and solution ionic strength. The target RNA sequence is detected by measuring changes in the film thickness (by spectroscopic ellipsometry (SE) and AFM nanolithography), in the film molecular UV-Vis absorption (by SE), and coverage (by X-ray photoemission spectroscopy (XPS) and quartz crystal microbalance (QCM)). SE allows to monitor the hybridization in situ, in a non-destructive and extremely fast way. Hybridization experiments carried on by SE and QCM as a function of the concentration of RNA indicate, at present, a detection limit of 10 nmol/L, which is expected to decrease through an ongoing upgrade of the optical setup.