title: WSU_Salmonella Enteritidis_11977_v1
status: Public on Mar 01 2012
contact.city: Pullman
contact.first: Devendra
contact.middle: H
contact.last: Shah
contact.email: dshah@vetmed.wsu.edu
contact.state: WA
contact.address: 100 Dairy Rd
contact.department: Veterinary Microbiology and Pathology
contact.country: USA
contact.institute: Washington State University
contact.phone: 509-335-6071
organism: Salmonella enterica subsp. enterica serovar Enteritidis
manufacture_protocol: Proprietary Light Directed Oligonucleotide Synthesis
  We do not spot presynthesized oligonucleotides. We directly synthesize them on a microscope slide. Our synthesis is using the robust phosphoramidite chemistry refined since the 1970's for commercial oligonucleotide synthesis. In standard oligonucleotide synthesis, the terminal acid-labile protective group of a growing oligomer is removed by a treatment with a strong acid.
  The only modification we have introduced in our process is the usage of a photo-generated acid. At a given synthesis cycle, each spot that needs to be deprotected is exposed to light in the presence of a photogenerated acid precursor, leading to local acid production and cleavage of the terminal protective group. Only the deprotected spots will be able to react with a new monomer. By so doing, we can synthesize tens of thousands oligonucleotides in parallel on the same microarray substrate.
  The advantage of using the phosphoramidite chemistry is that we can synthesize oligonucleotides at a reduced cost compared to other chemistries while maintaining our stepwise yield well above 99%.
  To expose the oligonucleotide spots to light during the deprotection step of the synthesis cycle, we do not use any physical mask but instead we use a digital micromirror device (DMD) made of several hundred of thousands individually addressable mirrors. At each deprotection step, a computer simply generates an image to be projected on the microarray surface. Using this digital photolithography approach, we can synthesize any custom microarray with no upfront design cost or minimal order size.
  High Quality Glass Substrates
  We synthesize our microarrays on high quality microscope slides. For uniform synthesis and hybridization and enhanced scanner image quality, we use only low-background glass slides polished to atomic flatness (±20 angstroms). Their precise physical dimension (25 ± 0.2 mm x 76 ± 0.3 mm x 0.940 mm ± 0.025 mm) is compatible with all major brands of slide microarray scanners.