Chemical Physics Seminar: PCR-free sensing of Covid-19, metastatic mRNA biomarkers and towards single-cell proteomics using solid-state nanopore devices

Prof. Amit Meller, Technion

03 December 2020, 15:00 
Chemical Physics Seminar




The recent outbreak of the coronavirus disease (COVID-19) reinforced the acute need for extremely sensitive, accurate and point-of-care mRNA quantification sensors worldwide. In the past two decades our lab promoted solid-state nanopores as single-biomolecule sensors. In a nanopore device, an electrical field pulls the electrically charged analyte towards and through a nanometer-scale pore, allowing recognition of the molecule based on its ion-current signature. Here I will present results showing the ability to target mRNA biomarkers with sensitivity superseding the “gold-standard” RT-qPCR. Importantly, we developed and validated a purification-free biochemical assay to sense mRNAs from cell lines and from clinical samples, that allow single molecule multiplexed counting of the target RNAs. We applied our method for the sensing of cancer metastatic biomarkers MACC1 and S100A4 at early stage, and for PCR-free sensing of SARS-CoV-2 RNA molecules from clinical samples. Moving beyond nucleic acids, I will discuss our on-going efforts towards the use of plasmonic nanopore devices for the single protein molecules identification based on partial labelling of only two or three amino acids. This approach involves sophisticated signal analysis from each and every passage of the SDS-denatured protein through the nanopore. According to our simulations the noisy single-molecule signals can be robustly and uniquely associated with specific proteins using a custom deep learning strategy. This opens up a new route for single-cell proteomics of even rare proteins.



(1)           Rozevsky, Y.; Gilboa, T.; van Kooten, X. F.; Kobelt, D.; Huttner, D.; Stein, U.; Meller, A. Quantification of mRNA Expression Using Single-Molecule Nanopore Sensing. ACS Nano 2020, 14, 13964–13974.

(2)           Zrehen, A.; Ohayon, S.; Huttner, D.; Meller, A. On-Chip Protein Separation with Single-Molecule Resolution. Sci Rep 2020, 10, 15313–12.

(3)           Zrehen, A.; Huttner, D.; Meller, A. On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA. ACS Nano 2019, 13, 14388–14398.

(4)           Spitzberg, J. D.; Zrehen, A.; van Kooten, X. F.; Meller, A. Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection. Adv. Mater. 2019, 31, e1900422–18.

(5)           Ohayon, S.; Girsault, A.; Nasser, M.; Shen-Orr, S.; Meller, A. Simulation of Single-Protein Nanopore Sensing Shows Feasibility for Whole-Proteome Identification. PLoS Comput. Biol. 2019, 15, e1007067–21.

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