PME SPECIAL INTERDISCIPLINARY SEMINAR: Nanopores and nanofluidics for single molecule DNA and protein profiling

Nanopores are single-molecule biosensors that utilize electrokinetic forces to focus, linearize and detect individual biopolymers, such as DNA and proteins.1 Solid-state nanopores are mechanically robust, versatile sensors, that lend themselves for integration in sophisticated devices designed to process and detect biological samples. Our lab is pursuing this technology to advance a wide range of biomedical needs. Here I will provide several recent examples, including: (i) Threading of an extremely long genomic DNA (~0.5 Mbp) into solid-state nanopores, and engineering the Electro Osmotic Forces (EOF) to facilitate the sensing of extremely short DNA (<50 bp) in sub 5 nm pores. (ii) An amplification- free mRNA quantification sensors to replace RT-qPCR for SARS-CoV-2 and for quantification of the early-stage Colorectal cancer marker MACC1. (iii) On-chip focusing of sub pM nucleic acid samples using Isotacophoresis (ITP) for an efficient single-molecule counting. Moving beyond nucleic acids, I will discuss our latest efforts towards the use of electrophoretic single protein molecule separation by mass/charge ratio in sub-wavelength, nanometric channels.2 Two color sensing and dynamical tracking of dually labeled proteins enable proteins identification using 4D information. This antibody-free sensing methodology permits discrete quantification of a cytokine panel, for the discrimination among viral versus bacterial infections host’s response. Moreover, we show that this method allows identification of close VEGF protein isoforms, with diverse biological role, but can evade immuno sensing. This method can be integrated upstream of the many other single-molecule methods, including nanopore sensors and fluorosequencing for enhanced, high-throughput proteome profiling.

Host: Allison Squires | asquires@uchicago.edu