Microarray probes are nucleic acids immobilized on a solid glass substrate. Several strategies exist to obtain probes. These include PCR amplification of cloned cDNA libraries using vector specific primers or genomic DNA using gene specific primers. Oligonucleotides synthesized from sequence information also are used as probes. Both cDNA and oligonucleotide probes need to be purified to remove enzymes, nucleotides, buffer salts and detergents, all of which interfere with hybridization. The concentration of probes as denatured single strand DNA should be high enough to allow for printing.

Important aspects to take in consideration during the probe selection process include the following:

cDNA
	Optimal length for hybridization is between 300 – 800bp Probes should not contain repetitive sequences Probes should contain unique sequence to eliminate cross hybridization

Oligonucleotide

Length for optimal hybridization efficiency varies between 50 – 70bp Requires known sequence Sequence accuracy is crucial for hybridization efficiency Can be designed to distinguish between alternative splicing, different alleles, and different members of gene families Requires less time and effort to prepare for printing Repeat sequences should be avoided Chosen sequences should not be homologous to other genes Have to test oligonucleotide for hybridization efficiency before printing Probe sequences may not be accessible to target molecules near the attachment site, and in some cases mSpacers need to be added