Chair: Oliver Otto
Speaker: Ulrich F. Keyser, 

Cavendish Laboratory, University of Cambridge, UK

Biosensing with nanopores is developing rapidly with commercial DNA and RNA sequencing platforms challenging established next generation sequencing technologies. Nanopores offer the unique ability to translate molecular structure directly into electrical signals without the need of fluorescent labels. Beyond sequencing of nucleic acids and proteins, many other applications are enabled by counting single molecules with nanopores.

First, I will describe the identification of long transcript isoforms at the single-molecule level using solid-state nanopore microscopy. We refold target RNA into RNA identifiers (IDs) with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colours. The sequence of structural colours of RNA identifiers enables simultaneous identification and relative quantification of multiple RNA targets without prior amplification. RNA IDs discriminate circular and linear transcript isoforms in a one-step, enzyme-free reaction in a complex human transcriptome with single-molecule resolution [1]. We will show recent results on detection of RNA modifications like 5mC, Inosine and MeC using RNA nanotechnology in ribosomal RNA (rRNA) from pathogenic bacteria like A. baumannii [2]. Finally, I will discuss how the technique may enable single-cell RNA detection by adapting the process for integration into droplet microfluidics.  

References:

1. Bošković and U. F. Keyser. Nanopore microscope identifies RNA isoforms with structural colors. Nature Chemistry, 14:1258-1264, 2022.
2. Li, S. C. Meng, Y. Wang, C. M. Platnich, M. K. Earle, E. Mylona, P. Naydenova, S. Baker, J. Zhu and U. F. Keyser. Nanopore detection of single-nucleotide RNA mutations and modifications with programmable nanolatches. Nature Nanotechnology, published online, 2025.