Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel.
RNA and DNA strands produce ionic current signatures when driven through an alpha-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.
Vercoutere
W
W
Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.
Winters-Hilt
S
S
Olsen
H
H
Deamer
D
D
Haussler
D
D
Akeson
M
M
D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D020137:Base Pair Mismatch / Q000235:genetics; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D004553:Electric Conductivity; D029968:Escherichia coli Proteins; D006460:Hemolysin Proteins / Q000737:chemistry / Q000378:metabolism; D007473:Ion Channels / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D006460:Hemolysin Proteins; C036507:Hlya protein, E coli; D007473:Ion Channels; D008051:Lipid Bilayers; D004247:DNA