Comparative examination of probe labeling methods for microarray hybridization

David I. Burke; Karen Woodward; Robert A. Setterquist; Ernest S. Kawasaki

doi:10.1117/12.427979

4 June 2001 Comparative examination of probe labeling methods for microarray hybridization

David I. Burke, Karen Woodward, Robert A. Setterquist, Ernest S. Kawasaki

Proceedings Volume 4266, Microarrays: Optical Technologies and Informatics; (2001) https://doi.org/10.1117/12.427979
Event: BiOS 2001 The International Symposium on Biomedical Optics, 2001, San Jose, CA, United States

Abstract

For detection of differential gene expression, confocal laser based scanners are now capable of analyzing microarrays using one to five wavelengths. This allows investigators to choose among several labeling methods. Here we compare direct incorporation and indirect methods (amino-allyl and dendrimers) for labeling cDNA probes. We assessed reproducible sensitivity of each probe preparation method in two ways. First, by comparing hybridization intensities for limit of signal detection and second by measuring the lowest detectable concentration of a known ratio of mixed DNA (spikes). Limit of detection assay was done using arrays of mixed targets consisting of a serially diluted human specific gene fragment (HU1) and an undiluted DNA of chloramphenicol acetyl tranferase (CAT) gene. Then, individual single target arrays of CAT and HU1 DNA were used to determine the lowest detectable spike ratio of each labeling method. The results of this study will be presented and their significance for the analysis of microarrays will be discussed.

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David I. Burke, Karen Woodward, Robert A. Setterquist, and Ernest S. Kawasaki "Comparative examination of probe labeling methods for microarray hybridization", Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); https://doi.org/10.1117/12.427979

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KEYWORDS

Computed tomography

Dendrimers

Bioalcohols

Glasses

Signal detection

Target detection

Laser scanners

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