DNA Micro Arrays

• A DNA Micro Array or DNA Chip is prepared by spotting DNA samples to a glass slide. Each spot represents a different DNA molecule.
• Micro Arrays are very powerful for assessing differences in gene expression between two different tissues or between the same tissue in different physiological states.
• For example, if we prepare mRNA from a tissue in two different states (A and B), then we can make cDNA from each sample and combine them. After cloning, we might end up with 10,000 DNA clones, each representing a specific gene expressed in either only in state A or state B or in both.
• We can now ask what genes are expressed in state A but not state B?
• To answer this question, we take the mRNA from state A and synthesize cDNA using a base that has a red fluorescent molecule attached to it. Thus, all cDNAs from state A will be red fluorescent.
• We repeat the experiment with mRNA from state B except this time the base is green fluorescent and all cDNAs from state B will be green fluorescent.
• We then mix these two samples and hybridize them to the DNA Micro Array.
  • If a gene is expressed in both states A and B, then the spot on the Micro Array corresponding to that gene will bind both Red and Green probes and will appear yellow.
  • If a gene is expressed only in state A, then the spot on the Micro Array corresponding to that gene will only bind the Red probe.
  • If a gene is only expressed in state B, then the spot on the Micro Array corresponding to that gene it will only bind the Green probe.

  Here we see a typical result. Some spots are yellow, no difference; some are green and some are red.

• Of course each spot corresponds to a clone that you have in your freezer, so you can go back and sequence the clone and identify it.