Nanopore sequencing technology

Nano? Pore?

Idea: Push DNA through a small gap (pore) in a membrane and detect each nucleotide as it passes by.

One upon a time …

Idea for Nanopore sequenced in the 1980s…

Year
1980 Nobel prize for chain termination method (Sanger sequencing)
1980 to mid 2000 Improvement of Sanger sequencing technique
1990 Idea of using reversible fluorescent labeled nucleotides for sequencing
1998 Formatino of Solexa (sequencing by synthesis) and other companies
2007 Illumina acquires Solexa
2021 Sequencing by synthesis is an essential technique and Illumina is market leader

First pores were based on alpha-hemolysin

…a cell toxin from Staphylococcus aureus

Nanopores allow ssDNA to pass

Nanopores allow ssDNA to pass

Nanopores allow ssDNA to pass

The blockade of the ion current is detectable

dsDNA preparation for Nanopore sequencing

Unwinding the dsDNA helix

Long-reads with Nanopore



Technique Max read length
Sanger sequencing ~1000 nt
Illumina sequencing 50–400 nt
Nanopore sequencing unlimited?

Take-home message


  • Sequencing of single DNA molecules (no PCR amplification!)
  • Theoretically unlimited read length
  • Real-Time data
  • Portable device
  • But: Lower per-base accuracy (higher error rate)