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Long Oligonucleotide DNA Microarrays :

Long Oligonucleotide arrays are created using either ink-jet printing or robotic printing.

Algorithms are used in order to design long oligos of the same size of around 60 nucleotides (60-mers). However, these longer oligos are more difficult to pick as they need to have little homology to each other.

Ink-jet pump printing produces the 60-mer arrays. 100 picoliter droplets of reagents are printed onto a a hydrophobic surface containing chemically active hyrdoxyl- OH groups. The phosphoramidite DNA monomers in the droplets react with the OH groups, resulting in covalent bonding.

The slide can then be hybridized with labeled cDNA probes. Similar to other DNA microarrays, you wash after hybridization, scan and analyze the resulting data.

Companies regularly produce Long oligonucleotide arrays with greater than 25,000 different probes.

 

Differences and Advantages of Long Oligonucleotide DNA Microarrays:

- Long oligos can distinguish between alternatively spliced mRNAs (this is quite important as most genes have alternative isoforms!)

- Long oligos (60-mers) are single stranded which makes usual DNA microarray denaturation steps un-necessary

- Long oligos (60-mers) permit better specificity in DNA microarray hybridization

- Easily Modified

- Adaptable