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Nucleic Acids Research, 2002, Vol. 30, No. 20 e107
© 2002 Oxford University Press

Optimized in situ construction of oligomers on an array surface

Andrew C. Tolonen*, Dinu F. Albeanu1, Julia F. Corbett2, Heather Handley, Charlotte Henson3 and Pratap Malik2

Department of Biology, MIT/WHOI Joint Program, Cambridge, MA 02139, USA, 1 Department of Biology, MIT, Cambridge, MA 02139, USA, 2 Harvard University, Cambridge, MA 02115, USA and 3 Whitehead Institute/MIT Center for Genome Research, Cambridge, MA 02139, USA

*To whom correspondence should be addressed. Tel: +1 617 253 8686; Fax: +1 617 253 7475; Email: tolonen{at}mit.edu

Oligonucleotide arrays are powerful tools to study changes in gene expression for whole genomes. These arrays can be synthesized by adapting photolithographic techniques used in microelectronics. Using this method, oligonucleotides are built base by base directly on the array surface by numerous cycles of photodeprotection and nucleotide addition. In this paper we examine strategies to reduce the number of synthesis cycles required to construct oligonucleotide arrays. By computer modeling oligonucleotide synthesis, we found that the number of required synthesis cycles could be significantly reduced by focusing upon how oligonucleotides are chosen from within genes and upon the order in which nucleotides are deposited on the array. The methods described here could provide a more efficient strategy to produce oligonucleotide arrays.


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