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Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel

A Corrigendum to this article was published on 01 July 2001


RNA and DNA strands produce ionic current signatures when driven through an α-hemolysin channel by an applied voltage. Here we combine this nanopore detector with a support vector machine (SVM) to analyze DNA hairpin molecules on the millisecond time scale. Measurable properties include duplex stem length, base pair mismatches, and loop length. This nanopore instrument can discriminate between individual DNA hairpins that differ by one base pair or by one nucleotide.

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Figure 1: Blockade of the α-hemolysin nanopore by a DNA hairpin.
Figure 2: Standard free energy of hairpin formation versus shoulder blockade duration.
Figure 3: Discrimination between DNA hairpins at single-base pair resolution.
Figure 4: Detection of single-nucleotide differences between DNA hairpins.
Figure 5: Typical current blockade signatures caused by 7, 8, and 9 bp hairpins obtained using a voltage pulse routine.

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This work was supported by NRHGI grant HG01826-01. We wish to thank Laura Steinmann for thoughtful comments on the manuscript.

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Correspondence to Mark Akeson.

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Vercoutere, W., Winters-Hilt, S., Olsen, H. et al. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol 19, 248–252 (2001).

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