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Proceedings Paper

Effect of target and probe concentrations on hybridization in DNA microarrays
Author(s): Lili Wang; Adolfas K. Gaigalas; Yaping Zong; Shannon Zhang; Jennifer Shi; Youxiang Wang
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Paper Abstract

Efficient hybridization of complementary strands of DNA is the underlying principle of all microarray-based techniques for gene expression analysis. Recently studies have been published to assess oligonucleotide (55-70 bases) performance on glass-slide microarrays and stress advantages over the cDNA arrays. Importantly the oligo arrays eliminate possible failure in PCR amplifications and attain sequence optimization. In the present study, we have used 60mer oligo microarrays to investigate the effect of target (immobilized on the glass slides) and probe concentrations and possible probe interactions on hybridization. Scanner calibration slides (manufactured by Full Moon BioSystems) were used to concert the fluorescence signals into fluorophore per μm2 in order to eliminate possible variation from scanner. The retention of the target was determined based on mock hybridization using Cy3-labeled oligonucleotide. We found that hybridization signals fell within the linear response range when the target concentration (printing solution) was equal or less than 2.5 μM. With fixed target concentrations, there is a non-linear relationship between the probe concentration and the hybridization signal. Dual-probe hybridization measurements suggest that hybridization of probes is not ideally independent. In this study, hybridization signal from Cy5 is consistently lower than that from Cy3.

Paper Details

Date Published: 22 June 2004
PDF: 11 pages
Proc. SPIE 5328, Microarrays and Combinatorial Techniques: Design, Fabrication, and Analysis II, (22 June 2004); doi: 10.1117/12.528245
Show Author Affiliations
Lili Wang, National Institute of Standards and Technology (United States)
Adolfas K. Gaigalas, National Institute of Standards and Technology (United States)
Yaping Zong, Full Moon BioSystems, Inc. (United States)
Shannon Zhang, Full Moon BioSystems, Inc. (United States)
Jennifer Shi, Full Moon BioSystems, Inc. (United States)
Youxiang Wang, Full Moon BioSystems, Inc. (United States)


Published in SPIE Proceedings Vol. 5328:
Microarrays and Combinatorial Techniques: Design, Fabrication, and Analysis II
Dan V. Nicolau; Ramesh Raghavachari, Editor(s)

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