DNA microarrays cDNA and oligonucleotide microarrays

Compared with other methods, the DNA microarray technology has the following important advantages: (i) it can measure thousands of different mRNA transcripts in parallel, (ii) it provides semi-quantitative data, and (iii) it is sensitive enough to detect low-abundance transcripts that are represented on a given array. In several organisms whose complete genome sequence is available, DNA microarrays enable the monitoring of whole-genome gene expression in a single experiment.

cDNA microarrays and oligonucleotide microarrays each have several advantages and disadvantages. One advantage of cDNA microarrays is that they can be prepared directly from the isolated cDNA clones. Once a set of corresponding PCR products has been generated, microarrays can be created in multiple versions containing the entire set of cDNA sequences, resulting in large-scale arrays for identification of differentially expressed genes of interest or small-scale arrays suitable for specific research applications. The most important advantage is that the cDNA microarray is less expensive to make than a single oligonucleotide array. However, cross-hybridization between homologous sequences is problematic for cDNA microarrays.

One advantage of oligonucleotide arrays is that oligonucleotides can be synthesized either in plates or directly on solid surfaces (in situ synthesis), making it easier to prepare the DNA probes than for cDNA microarrays. Also, the probes in an oligonucleotide array can be designed to represent unique gene sequences such that cross-hybridization between related gene sequences is minimized to a degree dependent upon the completeness of available sequence information. One primary disadvantage of oligo-based analysis is that oligonucleotide microarrays are expensive.

There are two types of oligonucleotide microarrays: one is the direct synthesis of oligonucleotides on a solid (34). Microarrays of this sort are produced by Affymetrix and Nimble Gen. The other is the immobilization of pre-synthesized oligonucleotides, for example produced by Agilent Technologies (Palo Alto, CA) and other companies. The spotted oligo micro-arrays are typically comprised of a single 50- to 70-mer oligonucleotide for each gene.

0 0

Post a comment