Oligo-Fingerprinting

This type of chips was the first to be used. These chips consist of a matrix, with each cell of the matrix containing target DNA. The chip is exposed to a solution containing many identical oligos, and hybridization occurs between matching DNA and oligos. Again, if the oligos are tagged, either with fluorescent dye or radioactive label, we can then see at each point of the matrix whether the hybridization occurred (i.e., which of the DNAs hybridized to the oligo we tested). The chip can then be heated, separating the oligos from the DNA, and the experiment can be repeated with a different type of oligo. Finally, we get a matrix M, with each row representing a specific target DNA from the matrix, and each column representing an oligo:

$$M_{i,j} = \begin{array}{ll} 1 & \mbox{if hybridization oc... ...j$ } \\ 0 & \mbox{no hybridization occurred} \end{array}$$

The chips contain some 50,000 cells of target DNA sequences and the experiment can be repeated with 100 to 500 oligos. The advantage of using a DNA chip is obvious: each experiment tests an oligo against 50,000 targets at once. In 1989, six patent applications were issued for this kind of DNA chips, and the issue is still debated in court. However, nowadays most people use different chips.