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How it works: Nanopore-based DNA sequencing

How it works: Nanopore-based DNA sequencing

Ion channels are membrane proteins allowing ions such as sodium and chloride to cross the lipid (fat molecule) layers forming the cell membrane. Some channels have wider pores, allowing larger molecules to pass through the membranes. About 30 years ago, scientists discovered that specific channels (protein nanopores) from bacteria are wide enough to allow single-stranded molecules of DNA to pass through them. Based on this observation, several companies have developed technologies to sequence DNA. How does it work? Single nanopores are embedded in a synthetic membrane that separates two fluid-filled compartments, in one of which DNA molecules are dissolved. Using sophisticated micro-engineering techniques, an electric potential difference is imposed across the nanopores and electrical current flowing through them is recorded. When a DNA molecule permeates the nanopore, fluctuations of this current are recorded. These fluctuations, which depend on the DNA sequence, i.e., the A, T, G, C nucleobases, are then analysed to determine the sequence in a process called “base-calling”. This approach has several advantages compared to other technologies: it can sequence very long DNA fragments (up to several millions of bases), genomic DNA can be directly sequenced (no need for amplification), chemical modifications of the bases (important for epigenetics) can also be identified, RNA molecules can also be sequenced, and, finally, it is possible to produce relatively cheap and portable sequencing devices. This nanopore DNA sequencing technology has been widely used to sequence the genome of the different variants of the SARS-CoV-2 virus.

Hugues Abriel
NCCR TransCure Director and PI