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Nat Biotechnol. 2001 Jul;19(7):636-9.

Sequence-specific detection of individual DNA strands using engineered nanopores.

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  • 1Department of Medical Biochemistry and Genetics, The Texas A&M University System Health Science Center, 440 Reynolds Medical Building, College Station, TX 77843-1114, USA.


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.

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