To select sequences that would target Igl1 and Igl2

both separately and simultaneously, those portions of their coding sequences which were identical or divergent were input separately, while the entire coding sequence of URE3-BP was used to select siRNA sequences. For EhC2A the portion of the gene sequence selected for targeting was the poly-proline region (bases 301–567) since this region is least similar BAY 63-2521 price to the other gene family members. From the pool of selected 21 mer sequences, those with runs of more than 4 As or Ts were eliminated, and those with GC content between 30% and 50% were lengthened to 29 bp by see more adding the next eight bases in the genomic sequence. The TIGR E. histolytica Genome Project database [52] was used to check that each 29-bp sequence was unique to its gene, PX-478 with non-unique ones eliminated. A minimum of four unique sequences were selected

per gene. To create a scrambled control sequence, one of the selected sequences was chosen, and the bases were scrambled (each began with the AA dinucleotide); these sequences were then checked to confirm they matched nothing in the E. histolytica genome. In addition, a sequence targeted to the green fluorescent protein (GFP) was included as a control [30]. The chosen sequences, those ultimately transfected into E. histolytica HM1:IMSS trophozoites, are Staurosporine solubility dmso shown in Table 1. Constructs that did not successfully transfect are not shown. shRNA primer design Primers were designed based

on the method used by Gou et al (2003) [30] to yield PCR-generated shRNA constructs in a 2-step PCR process diagrammed in Figure 1. The final PCR product contained the E. histolytica U6 promoter followed by the sense strand of the hairpin, the 9 bp loop (TTCAAGAGA) [28], the antisense strand of the hairpin, and the U6 terminator sequence [30]. An ApaI restriction site (GGGCCC) was included between the 3′ end of the U6 promoter and the beginning of the shRNA sequence [30]. To facilitate cloning of the PCR product into the expression vector, a HindIII site was added to the 5′ end of the U6 promoter sequence, and a NotI site was added following the terminator sequence. The selected siRNA sequences, shown in Table 1, were used to design oligos to create shRNAs. Two rounds of PCR were employed to generate the final shRNA constructs, using one forward primer and two reverse primers, whose sequences are listed in Table 2. In the first round of PCR, the E. histolytica U6 promoter followed by the sense strand and the loop were generated using a forward primer amplifying the 5′ end of the U6 promoter and a first reverse primer containing the sequence of the sense strand of the shRNA and the future loop (Figure 1A, Table 2).