Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore.

Protein nanopores are under investigation as key components of rapid, low-cost platforms to sequence DNA molecules. Previously, it has been shown that the α-hemolysin (αHL) nanopore contains three recognition sites, capable of discriminating between individual DNA bases when oligonucleotides are immobilized within the nanopore. However, the direct sequencing of RNA is also of critical importance. Here, we achieve sharply defined current distributions that enable clear discrimination of the four nucleobases, guanine, cytosine, adenine, and uracil, in RNA. Further, the modified bases, inosine, N(6)-methyladenosine, and N(5)-methylcytosine, can be distinguished.