Urea Facilitates the Translocation of Single-Stranded DNA and RNA Through the alpha-Hemolysin Nanopore

D Japrung, M Henricus, QH Li, Giovanni Maglia, Hagan Bayley

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The staphylococcal a-hemolysin (alpha HL) protein nanopore is under investigation as a fast, cheap detector for nucleic acid analysis and sequencing. Although discrimination of all four bases of DNA by the alpha HL pore has been demonstrated, analysis of single-stranded DNAs and RNAs containing secondary structure mediated by basepairing is prevented because these nucleic acids cannot be translocated through the pore. Here, we show that a structured 95-nucleotide single-stranded DNA and its RNA equivalent are translocated through the alpha HL pore in the presence of 4 M urea, a concentration that denatures the secondary structure of the polynucleotides. The alpha HL pore is functional even in 7 M urea, and therefore it is easily stable enough for analyses of challenging DNA and RNA species.
Original languageEnglish
Pages (from-to)1856-1863
Number of pages8
JournalBiophysical Journal
Issue number9
Publication statusPublished - 5-May-2010
Externally publishedYes


  • nanometer-scale pore
  • polynucleotide molecules
  • secondary structure
  • hairpin molecules
  • aqueos solutions
  • protein pore
  • discrimination
  • viscosity
  • database

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