Dna Array

Pat Brown developed a technique where cDNAs can be embedded onto lass slided.Using these DNA arrays,he could do large-scale expression studies

Growth stage-specific mRNA are isoloated,and then reverse transcribed to give inique cDNA populations.These are directly embedded onto specially cated gass slides.

These slides are coated with poly-lysine,which is positively charged.DNA is negatively charged,so that cDNA "sticks" to the slide through an ionic interaction.The cDNA can still interact with DNA probe.






Brown used srrays to obtain gene expression profiles of cancer.Diffuse large B-cell lymphoma(DLBCL) is a common lymphoma-cancer of the lymp nodes.He found sub-types of DLBCL that correlated with survival rates.

Brown made a chip with genes expressed by the lymph nodes and those importtant in cancer biology .a total of 17856 cDNA genes were printed onto what we called "lymphochip".Remember ,each square on teh chip corresponds to a differnt cDNA.

Then ,he made CDNAs from different DLBCL tumors.

He labelled one set of cDNA with a red florescent tag;the other with a green tag.

Brown incubated the arrays with the tagged cDNAs, which bound to the matching genes printed on the array.

Since he knew the positions of the genes on the DNA array,Brown could figure out the levels of gene expression based on the color signal.If the gene was only expressed in DLBCL1 cells,the square was red.similarly ,of the gene was only expressed in DLBCL2 cells,the square was green.If the gene was expressed equally in both cells,the square was yellow

Thus ,brown identified two sub-types of DLBCL-GC B-like and Activated B-like DLBCL.These sub-types have different responses to the therapy,and with this type of diagnosis,more tailored treatment can begin for patients.This type of tailored treatment is called "pharmacogenomics."

Brown can also analyse the differences in gene expression for these two very similar lymphomas.This may give better understanding of how cancers work, and hopeflly develop beter therapies and cures.














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Genechip Animation

Definition
An array of short DNA oligonucleotides (usually 20 nucleotides long) synthesized onto a solid support by photolithography, each of which corresponds to a single gene.

Stephen Fodor developed a technique called GeneChip probe arrays where he built the sequences he wanted. These GeneChip arrays are printed on special glass.DNA Sequence are built up using light directed chemical synthesis. First, a substrate with a nucleotide is fixed onto the chip at specific positions.The nucleotide has a protecting group(X) that blocks polymerization. This protector group is photolabile and is released on exposure to UV light. Without the protector, polymerization and chain build-up occur.A filter is added to the chip so that only some of the nucleotides are exposed to light. These deprotected groups are then free to add the next nucleotide to the chain.By alternating the position of the filter, Fodor can build a GeneChip with an array of different sequences about 20 nucleotides long.Fodor added a cDNA probe to the GeneChip.He could simultaneously assay tens of thousands of different sequences at the same time.

















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