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Nanopore detection using channel current cheminformatics
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Paper Abstract

A novel detector is used for analysis of single DNA molecules. The detector is based on current blockade measurements through a single, nanometer-scale, α-hemolysin ion channel. The biologically based alpha-hemolysin channel self-assembles in lipid bilayers, permitting highly reproducible experiments with Angstrom resolution. In previous work the spectrum of dsDNA blockade states could be explained in terms of the dsDNA-protein binding kinetics, and dsDNA terminus fraying (bond dissociation) kinetics. Results presented here strengthen the hypothesis that conformational dynamics can be observed as well, when the channel-captured dsDNA end is in an unbound state. Feature discovery methods: include a time-domain finite state automaton (FSA), a wavelet domain FSA, and a Hidden Markov Model (HMM). Classifier feature extraction methods: includes a time-domain FSA for signal acquisition and a generalized HMM with EM for features extraction. Classification method: Support Vector Machines (SVMs) are used with novel kernel designs. Kinetic feature extraction tool: a time-domain FSA projects current observations to a (small) set of blockade states. Those states are provided by the generalized HMM analysis. Noise sources limit the resolution of the nanopore device, and its multiclass scaling capabilities, and this is discussed in the context of ongoing refinements to the device.

Paper Details

Date Published: 25 May 2004
PDF: 13 pages
Proc. SPIE 5467, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II, (25 May 2004); doi: 10.1117/12.548551
Show Author Affiliations
Stephen Winters-Hilt, Univ. of New Orleans (United States)
Children's Hospital (United States)

Published in SPIE Proceedings Vol. 5467:
Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II
Derek Abbott; Sergey M. Bezrukov; Andras Der; Angel Sanchez, Editor(s)

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