title: Optimized in situ construction of oligomers on an array surface.
abstract: 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.
authors.affiliation: Department of Biology, MIT/WHOI Joint Program, Cambridge, MA 02139, USA. tolonen@mit.edu
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Tolonen
authors.forename: Dinu F
authors.initials: DF
authors.lastname: Albeanu
authors.forename: Julia F
authors.initials: JF
authors.lastname: Corbett
authors.forename: Heather
authors.initials: H
authors.lastname: Handley
authors.forename: Charlotte
authors.initials: C
authors.lastname: Henson
authors.forename: Pratap
authors.initials: P
authors.lastname: Malik
mesh_terms: D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000138:chemical synthesis*
chemical_list: D009841:Oligonucleotides