GeneChips - Best Technology Product Reviews

GeneChips - Best Technology Product Reviews

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Welcome to the DNA Microarray (Genome Chip) Web site! You'll find the basics on DNA microarray technology and a list of academic and industrial links related to this exciting new technology. Your comments, corrections, and suggestions are welcome. Please help me make this site more useful to you and many other visitors.

DNA Microarrays - A technology that is reshaping molecular biology


It is widely believed that thousands of genes and their products (i.e., RNA and proteins) in a given living organism function in a complicated and orchestrated way that creates the mystery of life. However, traditional methods in molecular biology generally work on a "one gene in one experiment" basis, which means that the throughput is very limited and the "whole picture" of gene function is hard to obtain. In the past several years, a new technology, called DNA microarray, has attracted tremendous interests among biologists. This technology promises to monitor the whole genome on a single chip so that researchers can have a better picture of the interactions among thousands of genes simultaneously.



Terminologies that have been used in the literature to describe this technology include, but not limited to: biochip, DNA chip, DNA microarray, and gene array. Affymetrix, Inc. owns a registered trademark, GeneChip®, which refers to its high density, oligonucleotide-based DNA arrays. However, in some articles appeared in professional journals, popular magazines, and the WWW the term "gene chip(s)" has been used as a general terminology that refers to the microarray technology. Affymetrix strongly opposes such usage of the term "gene chip(s)". More recently, I prefer the term "genome chip", indicating that this technology is meant to monitor the whole genome on a single chip. GenomeChip would also include the increasingly important and feasible protein chip technology.



Base-pairing (i.e., A-T and G-C for DNA; A-U and G-C for RNA) or hybridization is the underlining principle of DNA microarray.



An array is an orderly arrangement of samples. It provides a medium for matching known and unknown DNA samples based on base-pairing rules and automating the process of identifying the unknowns. An array experiment can make use of common assay systems such as microplates or standard blotting membranes, and can be created by hand or make use of robotics to deposit the sample. In general, arrays are described as macroarrays or microarrays, the difference being the size of the sample spots. Macroarrays contain sample spot sizes of about 300 microns or larger and can be easily imaged by existing gel and blot scanners. The sample spot sizes in microarray are typically less than 200 microns in diameter and these arrays usually contains thousands of spots. Microarrays require specialized robotics and imaging equipment that generally are not commercially available as a complete system.



DNA microarray, or DNA chips are fabricated by high-speed robotics, generally on glass but sometimes on nylon substrates, for which probes* with known identity are used to determine complementary binding, thus allowing massively parallel gene expression and gene discovery studies. An experiment with a single DNA chip can provide researchers information on thousands of genes simultaneously - a dramatic increase in throughput. (*Note: In the literature there exist at least two confusing nomenclature systems for referring to hybridization partners. Both use common terms: "probes" and "targets". According to the nomenclature recommended by B. Phimister of Nature Genetics, a "probe" is the tethered nucleic acid with known sequence, whereas a "target" is the free nucleic acid sample whose identity/abundance is being detected. This site follows that recommendation. See Nature Genetics volume 21 supplement pp 1 - 60, 1999, which is freely accessable.



There are two major application forms for the DNA microarray technology: 1) Identification of sequence (gene / gene mutation); and 2) Determination of expression level (abundance) of genes.



There are two variants* of the DNA microarray technology, in terms of the property of arrayed DNA sequence with known identity:



Format I: probe cDNA (500~5,000 bases long) is immobilized to a solid surface such as glass using robot spotting and exposed to a set of targets either separately or in a mixture. This method, "traditionally" called DNA microarray, is widely considered as developed at Stanford University. A recent article by R. Ekins and F.W. Chu (Microarrays: their origins and applications. Trends in Biotechnology, 1999, 17, 217-218) seems to provide some generally forgotten facts.



Format II: an array of oligonucleotide (20~80-mer oligos) or peptide nucleic acid (PNA) probes is synthesized either in situ (on-chip) or by conventional synthesis followed by on-chip immobilization. The array is exposed to labeled sample DNA, hybridized, and the identity/abundance of complementary sequences are determined. This method, "historically" called DNA chips, was developed at Affymetrix, Inc. , which sells its photolithographically fabricated products under the GeneChip® trademark. Many companies are manufacturing oligonucleotide based chips using alternative in-situ synthesis or depositioning technologies.



In the preparation of this Web site, "DNA microarray(s)" and "DNA chip(s)" are used interchangeably. But viewers should aware this technical difference.



* In addition, microfluidics-based chip or laboratory-on-a-chip systems are also listed in this Web site.



The microarray (DNA chip) technology is having a significant impact on genomics study. Many fields, including drug discovery and toxicological research, will certainly benefit from the use of DNA microarray technology. View an example of the microarray image (38K).



For a very well-written introduction on the steps involved in a microarray experiment, visit Jeremy Buhler's Anatomy of a Comparative Gene Expression Study



An excellent collection of Genomics Glossaries (including a Microarrays Glossary) is being maintained by Mary Chitty of Cambridge Healthtech Institute.


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