Oligonucleotide Arrays

The basic idea in these chips is similar. The difference is that these chips contain the oligos, and not the targets. The length of the oligos used depends on the application, but they are usually no longer than 25 bases. Since oligos are usually shorter, the density is much higher in these chips. For instance, a chip that is 1cm by 1cm can easily contain 100,000 oligos. The chips are used in a similar manner. They are exposed to a solution containing many copies of the target DNA. Hybridization occurs between oligos and matching DNA and then the chip can be heated in order to repeat the experiment. Figure 11.1 shows a schematic description of such an experiment. While the basic idea is the same, the chips are obviously intended for different experiments. This kind of chips is most useful in situations where we have relatively few targets, but a large number of oligos we wish to test. Another advantage is that we may want to hybridize targets against a ``standard'' oligo library. The oligo chips can thus be manufactured in large quantities, and their cost decreases.

  

Figure 11.1: A typical experiment with an oligonucleotide chip. Labeled RNA molecules are applied to the probes on the chip, creating a fluorescent spot where hybridization has occurred