Photolithographic synthesis oligonucleotide arrays

DNA arrays are fabricated by immobilizing the complementary DNA (cDNA) onto a solid substrate such as silicon, nylon or glass. This can be achieved by robotic printing of polymerase chain reaction (PCR) products (also known as direct-deposition approach), photolithographical synthesis of complementary oligonucleotides or piezoelectric inkjet printing of PCR products (also known as indirect-deposition approach). 

FIGURE 11.2 Photolithographic synthesis of oligonucleotide probe arrays. 

McGall, G. H. and J. A. Fidanza, 2001. Photolithographic synthesis of high-density oligonucleotide arrays. Methods Mol. Biol. 170 71-101. 

Micro-arrays can be manufactured in two different ways, by synthesis in situ or by delivery. In the in situ synthesis approach, nucleic acids are synthesized directly on a chip surface. This is made possible by a light-directed chemical synthesis technology developed by scientists at Affymetrix. By using different sets of photolithographic masks, scientitsts can define the chip exposure sites and, thereby, the sequence of the oligonucleotides. In this way, arrays can be synthesized with up to 400,000 different oligonucleotides in an area of 1.6 cm. Every spot contains about... 

Essentially two fabrication approaches exist, leading to microarrays with different properties. In one approach, customized cDNA probes are prepared separately and then mechanically spotted on the support, with a density of about 10,000 spots/cm [52,53]. Because of errors in the handling and printing of probes, this procedure is prone to erroneous arraying [54]. The second approach uses photolithographic techniques to carry out the parallel synthesis of the oligonucleotides directly on the surface [55,56]. The length of the probes is typically for only 14 to 25 bases, much shorter than for... 

Probe arrays and DNA target. The studies described here have been carried out with arrays of 10-, 12-, 14-, 16-, 18-, and 20-base oligonucleotide probe synthesis sites 200 jim X 200 jim in size. The probes are covalently attached to a siloxane derivatized 15 mm X 15 mm x 0.7 mm borosilicate glass substrate and were synthesized using photolithographic techniques that have been described elsewhere. U... 

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