Cartoons showing the pilin loci and the basis for the SQ-PCR assay

<p><b>Copyright information:</b></p><p>Taken from "A real-time semi-quantitative RT–PCR assay demonstrates that the sequence dictates the frequency and characteristics of pilin antigenic variation in "</p><p>Nucleic Acids Research 2005;33(10):3363-3371.</p><p>Published online 9 Jun 2005</p><p>PMCID:PMC1148172.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> () Pilin loci of gonococcal strain FA1090. The strain FA1090 chromosome contains one pilin expression locus, , and five silent pilin loci, . The locus contains the pilin expression gene (light blue rectangle) and the upstream silent pilin copy (white rectangle). The wavy line indicates the transcript. Each of the five loci contain between one and six silent pilin gene copies (colored rectangles). The silent copies are shown using an abbreviated nomenclature. Silent pilin locus 1 () gene copy 2 is shown as , copy 3 is , etc. () The SQ-PCR Av assay to measure recombination at pilE. Five general portions of the gene are shown: the 5′ constant region, a central SV region, the conserved and regions that flank the HV, which is followed by the hypervariable tail (HV) (). The wavy line indicates the transcript encoded by the gene and the rectangles indicate coding regions of DNA. Primers are shown as arrows, and the sequence targeted by the pairs of hybridization probes is starred. The 5′ primers are used with the constant region hybridization probes, LC-HybCONS 1 and 2, and detect total transcript levels. The 3′ primers are used with the 17 pairs of HV hybridization probes and detect individual to recombination at the HV of .