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 Citations (Scopus)

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

Fingerprint

sequencing
beads
deoxyribonucleic acid
trapping
nucleotides
molecules
plenum chambers
fluidics
classifying
pressure gradients
positioning
signal processing
platforms
traps
fluorescence
requirements

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

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

Automated bead-trapping apparatus and control system for single-molecule DNA sequencing. / Bashford, Greg; Lamb, Don; Grone, Dan; Eckles, Bob; Kornelsen, Kevin; Middendorf, Lyle; Williams, John.

In: Optics Express, Vol. 16, No. 5, 03.03.2008, p. 3445-3455.

Research output: Contribution to journalArticle

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, vol. 16, no. 5, pp. 3445-3455. https://doi.org/10.1364/OE.16.003445
Bashford, Greg ; Lamb, Don ; Grone, Dan ; Eckles, Bob ; Kornelsen, Kevin ; Middendorf, Lyle ; Williams, John. / Automated bead-trapping apparatus and control system for single-molecule DNA sequencing. In: Optics Express. 2008 ; Vol. 16, No. 5. pp. 3445-3455.
@article{f3b61a7b04ce4e3bafca18bbabda70ea,
title = "Automated bead-trapping apparatus and control system for single-molecule DNA sequencing",
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.",
author = "Greg Bashford and Don Lamb and Dan Grone and Bob Eckles and Kevin Kornelsen and Lyle Middendorf and John Williams",
year = "2008",
month = "3",
day = "3",
doi = "10.1364/OE.16.003445",
language = "English (US)",
volume = "16",
pages = "3445--3455",
journal = "Optics Express",
issn = "1094-4087",
publisher = "The Optical Society",
number = "5",

}

TY - JOUR

T1 - Automated bead-trapping apparatus and control system for single-molecule DNA sequencing

AU - Bashford, Greg

AU - Lamb, Don

AU - Grone, Dan

AU - Eckles, Bob

AU - Kornelsen, Kevin

AU - Middendorf, Lyle

AU - Williams, John

PY - 2008/3/3

Y1 - 2008/3/3

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=40349091387&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=40349091387&partnerID=8YFLogxK

U2 - 10.1364/OE.16.003445

DO - 10.1364/OE.16.003445

M3 - Article

C2 - 18542436

AN - SCOPUS:40349091387

VL - 16

SP - 3445

EP - 3455

JO - Optics Express

JF - Optics Express

SN - 1094-4087

IS - 5

ER -