Effect of Target and Probe Concentrations on Hybridization in DNA Microarrays

Published

June 1, 2004

Author(s)

Lili Wang, Adolfas K. Gaigalas, Y Zong, S Zhang, J Shi, Yunda Wang

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 mm2 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 mM. 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.

Proceedings Title

Progress in Biomedical Optics and Imaging; Microarrays and Combinatorial Techniques: Design, Fabricatoin, and Analysis II

Volume

5

Issue

17

Conference Dates

January 25-26, 2004

Conference Location

San Jose, CA

Conference Title

Conference on Microarrays and Combinatorial Techniques: Design, Fabrication and Analysis II

Pub Type

Conferences

Keywords

calibration, concentration, Cy3, Cy5, hybridization, oligo microarray, probe interaction, retention

Citation

Wang, L. , Gaigalas, A. , Zong, Y. , Zhang, S. , Shi, J. and Wang, Y. (2004), Effect of Target and Probe Concentrations on Hybridization in DNA Microarrays, Progress in Biomedical Optics and Imaging; Microarrays and Combinatorial Techniques: Design, Fabricatoin, and Analysis II, San Jose, CA (Accessed April 26, 2024)