title: CAT-3x20K-Pseudomonas_aeruginosa_PAO1-gene-layout-C3
status: Public on Sep 30 2014
contact.city: Kermanshah
contact.first: Hossein
contact.last: Fallahi
contact.email: Fallahi.raziuni@gmail.com
contact.state: Kermanshah
contact.address: Bagh-e-Abrisham
contact.department: Biology
contact.country: Iran
contact.institute: Razi University
contact.phone: +98 9127177784
organism: Pseudomonas aeruginosa PAO1
manufacture_protocol: As indicated on the manufacturer's website, array format 3x20K, number of unique probes per arry 5545, number of replicates per probe 3, The manufacturer do not spot presynthesized oligonucleotides. They directly synthesize them on a microscope slide. Their 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 they have introduced in their 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,they can synthesize tens of thousands oligonucleotides in parallel on the same microarray substrate. The advantage of using the phosphoramidite chemistry is that they can synthesize oligonucleotides at a reduced cost compared to other chemistries while maintainingtheir stepwise yield well above 99%. The probe lengths were between 45 and 47 nucleotides and the spacer has a length equivalent to a 15-mer sequence.