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

Greg Bashford, Don Lamb, Dan Grone, Bob Eckles, Kevin Kornelsen, Lyle Middendorf, John Williams

Research output: Contribution to journalArticle

6 Scopus citations

Abstract

We have been investigating a microfluidics platform for highspeed, low-cost sequencing of single DNA molecules using novel "chargeswitch" 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 singlemolecule 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.

Original languageEnglish (US)
Pages (from-to)3445-3455
Number of pages11
JournalOptics Express
Volume16
Issue number5
DOIs
StatePublished - Mar 3 2008

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

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    Bashford, G., Lamb, D., Grone, D., Eckles, B., Kornelsen, K., Middendorf, L., & Williams, J. (2008). Automated bead-trapping apparatus and control system for single-molecule DNA sequencing. Optics Express, 16(5), 3445-3455. https://doi.org/10.1364/OE.16.003445