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Optics Express

Optics Express

  • Editor: C. Martijn de Sterke
  • Vol. 16, Iss. 5 — Mar. 3, 2008
  • pp: 3445–3455

Automated bead-trapping apparatus and control system for single-molecule DNA sequencing

Greg Bashford, Don Lamb, Dan Grone, Bob Eckles, Kevin Kornelsen, Lyle Middendorf, and John Williams  »View Author Affiliations


Optics Express, Vol. 16, Issue 5, pp. 3445-3455 (2008)
http://dx.doi.org/10.1364/OE.16.003445


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Abstract

We have been investigating a microfluidics platform for high-speed, low-cost sequencing of single DNA molecules using novel “charge-switch” nucleotides. A significant challenge is the design of a flowcell suitable for manipulating bead-DNA complexes and sorting labeled polyphosphate molecules by charge. The flowcell is part of a single-molecule detection instrument, creating fluorescence images from labeled polyphosphates. These images would ultimately be analyzed by signal processing algorithms to identify specific nucleotides in a DNA sequence.Here we describe requirements of the fluidics system for loading, identifying, tracking, and positioning beads. By dynamically modulating pressure gradients in the plenum chambers of a multi-channel network, we could guide individual beads with high precision to any desired coordinate and reversibly trap them in stepped channels. We show that DNA immobilized on pressure-trapped beads can be physically extended into a downstream channel under electric force for analysis. Custom dynamic algorithms for automated bead control are described.

© 2008 Optical Society of America

OCIS Codes
(070.0070) Fourier optics and signal processing : Fourier optics and signal processing
(100.0100) Image processing : Image processing
(120.0120) Instrumentation, measurement, and metrology : Instrumentation, measurement, and metrology
(170.0170) Medical optics and biotechnology : Medical optics and biotechnology
(180.0180) Microscopy : Microscopy

ToC Category:
Instrumentation, Measurement, and Metrology

History
Original Manuscript: December 6, 2007
Revised Manuscript: January 23, 2008
Manuscript Accepted: January 25, 2008
Published: February 29, 2008

Virtual Issues
Vol. 3, Iss. 4 Virtual Journal for Biomedical Optics

Citation
Greg Bashford, Don Lamb, Dan Grone, Bob Eckles, Kevin Kornelsen, Lyle Middendorf, and John Williams, "Automated bead-trapping apparatus and control system for single-molecule DNA sequencing," Opt. Express 16, 3445-3455 (2008)
http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-16-5-3445


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