Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore

The sequencing of individual DNA strands with nanopores is under investigation as a rapid, low-cost platform in which bases are identified in order as the DNA strand is transported through a pore under an electrical potential. Although the preparation of solid-state nanopores is improving, biological nanopores, such as alpha-hemolysin (alphaHL), are advantageous because they can be precisely manipulated by genetic modification. Here, we show that the transmembrane beta-barrel of an engineered alphaHL pore contains 3 recognition sites that can be used to identify all 4 DNA bases in an immobilized single-stranded DNA molecule, whether they are located in an otherwise homopolymeric DNA strand or in a heteropolymeric strand. The additional steps required to enable nanopore DNA sequencing are outlined.