Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules

Biophys J. 1999 Dec;77(6):3227-33. doi: 10.1016/S0006-3495(99)77153-5.


Single molecules of DNA or RNA can be detected as they are driven through an alpha-hemolysin channel by an applied electric field. During translocation, nucleotides within the polynucleotide must pass through the channel pore in sequential, single-file order because the limiting diameter of the pore can accommodate only one strand of DNA or RNA at a time. Here we demonstrate that this nanopore behaves as a detector that can rapidly discriminate between pyrimidine and purine segments along an RNA molecule. Nanopore detection and characterization of single molecules represent a new method for directly reading information encoded in linear polymers, and are critical first steps toward direct sequencing of individual DNA and RNA molecules.

Publication types

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

MeSH terms

  • Bacterial Toxins
  • Base Sequence
  • Biophysical Phenomena
  • Biophysics
  • DNA, Single-Stranded / chemistry
  • Hemolysin Proteins
  • Ion Channels
  • Lipid Bilayers
  • Models, Molecular
  • Nucleic Acid Conformation
  • Poly A / chemistry*
  • Poly C / chemistry*
  • Poly U / chemistry*
  • RNA / chemistry*


  • Bacterial Toxins
  • DNA, Single-Stranded
  • Hemolysin Proteins
  • Ion Channels
  • Lipid Bilayers
  • staphylococcal alpha-toxin
  • Poly A
  • Poly U
  • Poly C
  • RNA