# | Target | p-2,1 | Core 19 mer (p0) | p+1,2 * | Loop | T.sp. |
|---|
2
| Gag 533-20 | AG | GAGCCACCCCACAAGATTT | AA | TCTCGAGT | Â |
3
| Pol 248-20 | AG | GAGCAGATGATACAGTATT | AG | CCTCGAGC | Â |
6
| Vif 9-21 | AA | CAGATGGCAGGTGATGATT | GT | ACTCGAGA | Â |
7
| Tat (x1) 140-21 | CT | ATGGCAGGAAGAAGCGGAG | AC | ACTCGAGA | A |
8
| Vpu 143-20 | AA | GAGCAGAAGACAGTGGCAA | TG | CCTCGAGC | Â |
9
| Env 1428-21 | AA | TTGGAGAAGTGAATTATAT | AA | ACTCGAGA | Â |
- The 6 shRNAs came from our previous study of 96 highly conserved shRNAs for HIV-1. The shRNAs had either 20 or 21 bp stems (as indicated in the shRNA name) built around a 19 bp p0 core placed at the base terminus of the shRNA. Nineteen bp targets were selected using a conservation profile method, where the 2 bases immediately upstream (p-2,1) and downstream (p+1,2) of the 19 bp target were also taken into consideration when estimating conservations. The identity of the sequence external to the shRNA stem was adjusted, where possible, to correspond to the flanking sequence in the target. Each shRNA consisted of a stem made from the 19 mer p0 core (shown) plus the p+1 nucleotide for 20 bp stems, or both p+1, 2 nucleotides for 21 bp stems, connected by the indicated loop. shRNAs for which the last base of the anti-sense stem was 'T' also included a 'termination spacer' (T.sp.) so as to prevent premature termination via an early run of 'T's. This nucleotide was always the complement of the first nucleotide of the p-1 position (but never a 'T'), so that if included in the processed siRNA product(s) it was also matched to the target. * The bases shown in bold (the p+2 position) were not a part of the stem for these shRNAs as they only had 20 bp stems. The shRNAs with 21 bp stems included both p+1, 2 positions.
