DNA microarray


Staff member
Here is a paragraph from a white paper I was reading:

Identifying genes is important, but it is equally important to characterize the proteins they encode. Primarily through systematic characterization of extracellular proteins secreted by GAS, Musser and his team have already identified more than 40 new proteins, and they are working to understand which ones are relevant to infection. Using microarrays, Musser discovered that nearly half of these proteins are upregulated during infection and therefore are good candidates for study. One of the new proteins, homologous to the alpha subunit of human Mac-1, inhibits the normal function of human neutrophils, which attach to and break down foreign cells. Such a protein is likely to assist the bacteria in evading destruction by the immune cells.

My question is what information does a DNA microarray contain? Is it a subset or a specific set of DNA sequence? How can you find a specific external protein from the microarray since it is the DNA?
The microarray consists of thousands (up to 40K) of unique complimentary sequence "spots" covalently linked to a glass slide. Each spot consists of millions of identical, short DNA segments (DNA probes) that are complimentary to a specific messenger RNA (mRNA) sequence. A cellular broth is applied to the entire slide where, in theory, every mRNA will find it's complimentary probe and anneal. The slide is washed and a fluorescent tag is applied that binds to mRNA. The slide is again washed and then each spot has it's fluorescent intensity read. The fluorescence is proportional the amount of mRNA bound to the spot - and here is the leap of conjecture - the amount of mRNA bound is proportional to the amount of specific protein (the protein encoded by the specific mRNA in question) production.

So to answer your question, the microarray does not measure protein production or regulation directly, and is blind to the complex regulatory mechanisms taking place at the cellular level.
Thank you FlowerPower, and welcome to sciforums. Finally we have a member in the Genomics area.Due to the terrorist situation, we will call upon you to comment on security and biological activities soon....
BTW, we do not use mRNA for hybridization, instead, we use cDNA. Fluorescent labelling is done during cDNA synthesis (reverse transcript PCR). Basically each slide contains about 10k probes, so 3-5 slides could cover all the genes in Human.
dna microarrays

Dear flowerPower and unknown1024,

Thanks for the informative replies. I would appreciate some refs. to the theory behind DNA micro-array analyses and how it's used. I don't need anything too basic (I have a Ph.D. in Zoology) but my research expertise is in DNA extraction, PCR, sequencing and analysis and haven't used these new techniques yet. Thanks
It is a comparative assay, that means try to find out the gene expression difference between for example cancer and normal cell. Some oncogene may express higher in cancer than normal and you can discover those genes from this technique. However, the gene expression of human cell is much complicated, people try to use the large no. of gene experiment results from microarray (about 100-10000 gene per experiment) to explain such as relatioship between gene. They call it bioinformatics, some algorithm used in zoology such as hierarchical clustering has been used in this study. Of course, microarray is a technology and you are free to imagine any purpose on your own, such as genotyping and sequencing by hybridization.
reply to unknown

Thanks for your reply. I was actually requesting any published refs. you could pass on. Maybe something in the journal BioTechniques that you think would be useful? Thanks
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