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. 1999 Dec;77(6):3227–3233. doi: 10.1016/S0006-3495(99)77153-5

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

M Akeson 1, D Branton 1, J J Kasianowicz 1, E Brandin 1, D W Deamer 1
PMCID: PMC1300593  PMID: 10585944

Abstract

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.

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Selected References

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  1. Adler A. J., Grossman L., Fasman G. D. Circular dichroism of cytosine dinucleoside monophosphates containing arabinose, ribose, and deoxyribose. Biochemistry. 1968 Nov;7(11):3836–3841. doi: 10.1021/bi00851a008. [DOI] [PubMed] [Google Scholar]
  2. Adler B. A., Grossman L., Fasman G. D. Single-stranded oligomers and polymers of cytidylic and 2'-deoxycytidylic acids: comparative optical rotatory studies. Proc Natl Acad Sci U S A. 1967 Feb;57(2):423–430. doi: 10.1073/pnas.57.2.423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arnott S., Chandrasekaran R., Leslie A. G. Structure of the single-stranded polyribonucleotide polycytidylic acid. J Mol Biol. 1976 Sep 25;106(3):735–748. doi: 10.1016/0022-2836(76)90262-x. [DOI] [PubMed] [Google Scholar]
  4. Bezrukov S. M., Vodyanoy I., Parsegian V. A. Counting polymers moving through a single ion channel. Nature. 1994 Jul 28;370(6487):279–281. doi: 10.1038/370279a0. [DOI] [PubMed] [Google Scholar]
  5. Brahms J., Michelson A. M., Van Holde K. E. Adenylate oligomers in single- and double-strand conformation. J Mol Biol. 1966 Feb;15(2):467–488. doi: 10.1016/s0022-2836(66)80122-5. [DOI] [PubMed] [Google Scholar]
  6. Brutyan R. A., DeMaria C., Harris A. L. Horizontal 'solvent-free' lipid bimolecular membranes with two-sided access can be formed and facilitate ion channel reconstitution. Biochim Biophys Acta. 1995 Jun 14;1236(2):339–344. doi: 10.1016/0005-2736(95)00089-l. [DOI] [PubMed] [Google Scholar]
  7. Bustamante J. O., Oberleithner H., Hanover J. A., Liepins A. Patch clamp detection of transcription factor translocation along the nuclear pore complex channel. J Membr Biol. 1995 Aug;146(3):253–261. doi: 10.1007/BF00233945. [DOI] [PubMed] [Google Scholar]
  8. Evans F. E., Sarma R. H. Nucleotide rigidity. Nature. 1976 Oct 14;263(5578):567–572. doi: 10.1038/263567a0. [DOI] [PubMed] [Google Scholar]
  9. FASMAN G. D., LINDBLOW C., GROSSMAN L. THE HELICAL CONFORMATIONS OF POLYCYTIDYLIC ACID: STUDIES ON THE FORCES INVOLVED. Biochemistry. 1964 Aug;3:1015–1021. doi: 10.1021/bi00896a002. [DOI] [PubMed] [Google Scholar]
  10. Inners L. D., Felsenfeld G. Conformation of polyribouridylic acid in solution. J Mol Biol. 1970 Jun 14;50(2):373–389. doi: 10.1016/0022-2836(70)90199-3. [DOI] [PubMed] [Google Scholar]
  11. Kasianowicz J. J., Brandin E., Branton D., Deamer D. W. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13770–13773. doi: 10.1073/pnas.93.24.13770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Leng M., Felsenfeld G. A study of polyadenylic acid at neutral pH. J Mol Biol. 1966 Feb;15(2):455–466. doi: 10.1016/s0022-2836(66)80121-3. [DOI] [PubMed] [Google Scholar]
  13. Saenger W., Riecke J., Suck D. A structural model for the polyadenylic acid single helix. J Mol Biol. 1975 Apr 25;93(4):529–534. doi: 10.1016/0022-2836(75)90244-2. [DOI] [PubMed] [Google Scholar]
  14. Song L., Hobaugh M. R., Shustak C., Cheley S., Bayley H., Gouaux J. E. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science. 1996 Dec 13;274(5294):1859–1866. doi: 10.1126/science.274.5294.1859. [DOI] [PubMed] [Google Scholar]
  15. Wonderlin W. F., Finkel A., French R. J. Optimizing planar lipid bilayer single-channel recordings for high resolution with rapid voltage steps. Biophys J. 1990 Aug;58(2):289–297. doi: 10.1016/S0006-3495(90)82376-6. [DOI] [PMC free article] [PubMed] [Google Scholar]

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