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Applied and Environmental Microbiology, October 2000, p. 4258-4265, Vol. 66, No. 10
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

A Bead-Based Method for Multiplexed Identification and Quantitation of DNA Sequences Using Flow Cytometry

Alexander Spiro,1 Mary Lowe,1,* and Drew Brown2,dagger

Physics Department, Loyola College in Maryland, Baltimore, Maryland 212101, and Center for Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 212022

Received 11 May 2000/Accepted 24 July 2000

A new multiplexed, bead-based method which utilizes nucleic acid hybridizations on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences is described. The method consists of three elements: beads (5.6-µm diameter) with oligomer capture probes attached to the surface, three fluorophores for multiplexed detection, and flow cytometry instrumentation. Two fluorophores are impregnated within each bead in varying amounts to create different bead types, each associated with a unique probe. The third fluorophore is a reporter. Following capture of fluorescent cDNA sequences from environmental samples, the beads are analyzed by flow cytometric techniques which yield a signal intensity for each capture probe proportional to the amount of target sequences in the analyte. In this study, a direct hybrid capture assay was developed and evaluated with regard to sequence discrimination and quantitation of abundances. The target sequences (628 to 728 bp in length) were obtained from the 16S/23S intergenic spacer region of microorganisms collected from polluted groundwater at the nuclear waste site in Hanford, Wash. A fluorescence standard consisting of beads with a known number of fluorescent DNA molecules on the surface was developed, and the resolution, sensitivity, and lower detection limit for measuring abundances were determined. The results were compared with those of a DNA microarray using the same sequences. The bead method exhibited far superior sequence discrimination and possesses features which facilitate accurate quantitation.

* Corresponding author. Mailing address: Physics Department, Loyola College in Maryland, Baltimore, MD 21210. Phone: (410) 617-2709. Fax: (410) 617-2646. E-mail: mlowe{at}loyola.edu.

dagger Present address: 719 Brinkwood Rd., Baltimore, MD 21229.

Applied and Environmental Microbiology, October 2000, p. 4258-4265, Vol. 66, No. 10
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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