Optical trapping assisted label-free and amplification-free detection of SARS-CoV-2 RNAs with an optofluidic nanopore sensor

Abstract

Ultrasensitive, versatile sensors for molecular biomarkers are a critical component of disease diagnostics and personalized medicine as the COVID-19 pandemic has revealed in dramatic fashion. Integrated electrical nanopore sensors can fill this need via label-free, direct detection of individual biomolecules, but a fully functional device for clinical sample analysis has yet to be developed. Here, we report amplification-free detection of SARS-CoV-2 RNAs with single molecule sensitivity from clinical nasopharyngeal swab samples on an electro-optofluidic chip. The device relies on optically assisted delivery of target carrying microbeads to the nanopore for single RNA detection after release. A sensing rate enhancement of over 2,000x with favorable scaling towards lower concentrations is demonstrated. The combination of target specificity, chip-scale integration and rapid detection ensures the practicality of this approach for COVID-19 diagnosis over the entire clinically relevant concentration range from 10 4 -10 9 copies/mL.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

“…Following this principle, the authors have demonstrated an almost two orders of magnitude increase in the analyte capture rate, which in turn illustrates the efficacy of their methodology. In a separate study, the lab has demonstrated a TACRE-based amplification-free detection of SARS-CoV-2 RNAs with a capture rate enhancement of over 2000× within the entire clinically relevant concentration range from 10 4 -10 9 copies/mL [428]. Therefore, it is probably safe to say that TACRE has particular relevance in clinical diagnostics, especially at ultra-low concentrations, paving the way toward early-stage disease detection.…”

Micro/nano biomedical devices for point-of-care diagnosis of infectious respiratory diseases

“…Yakoh et al reported a paper-based electrochemical biosensor for label-free detection of SARS-CoV-2 antibodies without the specific requirements of antibodies [ 164 ]. With optical assistance, Mohammad et al designed an electro-optofluidic chip that detected target SARS-CoV-2 RNAs without amplification, the detection limits up to 10 4 -10 9 copies/ml for swab samples [ 165 ]. A custom-made fidget spinner that rapidly concentrated pathogens in 1 ml samples of undiluted urine by more than 100-fold for the on-device colorimetric detection of bacterial load and pathogen identification was designed and fabricated ( Figure 5 c) [ 166 ].…”

Optofluidic Particle Manipulation: Optical Trapping in a Thin-Membrane Microchannel

“…This mechanism serves as a particle sorter and concentrator and can drastically increase particle concentration in the small protrusion cavities by collecting particles from a fluid flow stream. Once isolated in the cavity, these particles can be analyzed through a variety of mechanisms [ 13 , 14 ] or altered through chemical reactions, temperature, or mechanical stimulation [ 15 , 16 ].…”

“…One such application is the use of integrated solid-state nanopores as a means of particle identification when particles translocate the pore [ 21 ]. Thin membranes are required for focused ion beam (FIB) nanopore drilling in order to achieve tight pore dimensions [ 16 ]. The concentration and isolation functionality of this platform offers an excellent way to position high numbers of samples directly under the pore.…”