College of Veterinary Medicine

Veterinary Microbiology & Pathology

Microarrays and Applications

A “classic” microarray is composed of a collection of unique DNA probes that are arranged in a regular lattice on a solid substrate (e.g., glass). Each probe is composed of a DNA sequence that is complementary to the sequence of interest. Nucleic acid “targets” are applied to these probes in a hybridization fluid. Targets will anneal to complementary probes and unhybridized target is washed away. The probe:target duplex is then detected using some type of direct or indirect reporter system combined with a laser or white-light based scanner system. The resulting image usually resembles a lattice of spots with varying intensities or colors depending on the application. Differential color or signal intensity correlates with target abundance. For readers familiar with basic techniques in molecular biology, you may recognize a microarray as being a high-density, miniaturized, reverse-dot-blot. 

The type of probe that is used will depend on the particular application, substrate, reporter molecule and image detection system. Generally, synthetic DNA (oligonucleotides) between 9 and 100 bases long are used or longer PCR products (300-3,000 bases) are used as probes. The oligonucleotides can be mechanically deposited onto the substrate or generated in situ using lithographic or “virtual-well” technologies. PCR products are usually deposited mechanically onto silanized glass or nylon membranes.

Microarrays have been coupled with PCR to detect single nucleotide polymorphisms (SNPs) or to detect and genotype pathogenic organisms. Arrays are commonly used to assess gene expression for a large number of genes (10-1000’s) and have been used to some success for sequencing DNA. Arrays have also been used to directly detect RNA or DNA from environmental samples or to characterize single bacterial isolates such as with genomic arrays.

Our lab focuses on low and high density arrays printed on Teflon masked and unmasked, glass slides. We take advantage of epoxy-silane attachment procedures and use direct fluorescent labels, biotin-streptavidin labeling systems, and enzymatic amplification systems to detect probe:target duplexes.

Additional information and a general description of microarrays can be found at the following <link>

Last Edited: Dec 26, 2007 4:52 PM
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