Sequence-specific detection of individual DNA strands using engineered nanopores

Nat Biotechnol. 2001 Jul;19(7):636-9. doi: 10.1038/90236.


We describe biosensor elements that are capable of identifying individual DNA strands with single-base resolution. Each biosensor element consists of an individual DNA oligonucleotide covalently attached within the lumen of the alpha-hemolysin (alphaHL) pore to form a "DNA-nanopore". The binding of single-stranded DNA (ssDNA) molecules to the tethered DNA strand causes changes in the ionic current flowing through a nanopore. On the basis of DNA duplex lifetimes, the DNA-nanopores are able to discriminate between individual DNA strands up to 30 nucleotides in length differing by a single base substitution. This was exemplified by the detection of a drug resistance-conferring mutation in the reverse transcriptase gene of HIV. In addition, the approach was used to sequence a complete codon in an individual DNA strand tethered to a nanopore.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Pair Mismatch
  • Biosensing Techniques
  • Biotechnology / methods
  • Cell Membrane / chemistry
  • DNA / analysis*
  • DNA / metabolism
  • HIV / enzymology
  • Lipid Bilayers / metabolism
  • Models, Biological
  • Mutation
  • Nevirapine / pharmacology
  • Nucleic Acid Hybridization / methods*
  • RNA-Directed DNA Polymerase / genetics
  • Reverse Transcriptase Inhibitors / pharmacology
  • Sequence Analysis, DNA / methods*
  • Time Factors


  • Lipid Bilayers
  • Reverse Transcriptase Inhibitors
  • DNA
  • Nevirapine
  • RNA-Directed DNA Polymerase