title: HIV genotyping DNA microarray CAB-HIV-160-v4.0
status: Public on Nov 30 2016
contact.city: Torrejón de Ardoz
contact.first: Carlos
contact.last: Briones
contact.email: cbriones@cab.inta-csic.es
contact.state: Madrid
contact.address: Ctra de Torrejón a Ajalvir, km 4
contact.department: Department of Molecular Evolution
contact.country: Spain
contact.institute: Centro de Astrobiología (CAB, CSIC-INTA)
organism: Simian-Human immunodeficiency virus
manufacture_protocol: Each oligonucleotide (whose name corresponded to the queried HIV-1 codon) included a 'C6 amino linker' group [NH2(CH2)6] at its 5'-end, a 15-mer spacer region with either (T) 15 or (TCC)5 sequence and the specific, 13 to 17 nt-long sequence containing the queried codon at its central position.  A total of 160 different probes were synthesized and HPLC-purified (Sigma): 154 probes specific to the queried HIV-1 codons, 4 positive controls and 2 negative controls. Among the specific probes, 37 of them corresponded to different variants of 11 PR codons, while 117 covered variants of 31 RT codons including insertions and deletions in the region 67-70 as well as the multidrug complex associated to the mutation Q151M. All oligonucleotides were diluted in 1× spotting solution (Telechem-Arrayit) at 50 uM final concentration, and spotted onto super-epoxy-coated glass slides (Telechem-Arrayit). Spots containing spotting solution with no oligonucleotide were used as additional negative controls. Microarrays were printed using a GMS 417 Arrayer (Genetic Microsystems) and defined four grids or subarrays per slide. Each subarray contained 360 spots arranged in two regions (PR and RT), every oligonucleotide being printed in duplicate spots of 150 um in diameter, with a center-to- center distance of 250 um.