Figure 3

Detection and validation of EhSINE1 polymorphic loci 13, 17, 19 and 42. (A) Schematic representation of primers designed from different loci. The hollow box represents the EhSINE1 element; flanking genes have not been shown for simplicity. (B) PCR was performed using genomic DNA of HM-1:IMSS (H) and Rahman (R) strains as template, using primers from sequences flanking the EhSINE1 copy as shown in the schematic representation. The size of amplicons was determined by electrophoresis in 1% agarose gels (Top panel). Of 4 SINE1 unoccupied sites found computationally two were tested (13 and 42). Two more (17 and 19) were evaluated by PCR and Southern Blotting in Rahman. The sizes of amplicons obtained are indicated on the right, with arrows. The amplicon from strain Rahman was shorter by ~550 bp (the size of EhSINE1) at loci 13, 17 and 19, but was longer at locus 42 (explained in the text). The absence of EhSINE1 was further confirmed by Southern blotting with EhSINE1 probe, which failed to hybridize with the amplicons from strain Rahman (Bottom panel).