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. 2012 Jun 12;1(3):79–90. doi: 10.5501/wjv.v1.i3.79

Table 1.

Selection of short hairpin RNAs against human immunodeficiency virus type 1

shRNA name HIV-1 target
 HIV-1 inhibition
 Target conservation (%)5
 Viral escape6 Lentiviral vector
 Cell toxicity9
 Drug resistance mutation10
Position1 Gene Transient3 Stable4 Subtype B All subtypes Vector targeting7 Titer reduction8 In vitro In vivo
LDR2 327 Leader 95 ++ 66 61 ND + ND ND ND -
LDR3 3282 Leader 94 ++ 68 61 ND + ND ND ND -
LDR4 3292 Leader 99 +++ 68 61 ND + ND ND ND -
LDR5 3302 Leader 94 ++ 68 61 ND + ND ND ND -
LDR7 3322 Leader 84 - 69 61 ND + ND ND ND -
LDR8 3332 Leader 79 ++ 69 61 ND + ND ND ND -
LDR9 3342 Leader 91 +++ 70 63 ND + ND ND ND -
CA 1032 CA-p24 97 - 87 67 ND - - - ND -
Gag5 1365 CA-p24 86 ++ 81 80 + - + + + -
Pol111 19102 Prot11 9711 +++11 8911 8511 +11 -11 -11 -11 -11 D30N, V32I11
Pol2 19112 Prot 86 - 89 85 ND - ND ND ND D30N, V32I
Pro 1 19122 Prot 99 +++ 85 81 ND - - - ND D30N, V32I
Pro 2 19132 Prot 99 ND 80 79 ND - ND ND ND D30N, V32I
Pro 3 19142 Prot 99 ND 80 79 ND - ND ND ND D30N, V32I
Pro 4 19152 Prot 98 ND 77 76 ND - ND ND ND D30N, V32I, L33F
Pro 5 19162 Prot 97 ND 79 78 ND - ND ND ND D30N, V32I, L33F
Pro 6 19182 Prot 98 ND 78 77 ND - ND ND ND D30N, V32I, L33F
Pro 7 19192 Prot 98 ND 77 76 ND - ND ND ND D30N, V32I, L33F
Pro 8 2026 RT 87 ND 58 17 ND - ND ND ND D30N, V32I, L33F
Pol6 37552 RT 97 - 72 75 ND - ND ND ND -
RT 1 (A) 37572 RT 95 ++ 71 74 ND - - - ND -
RT 2 (B) 37582 RT 98 ++ 73 75 ND - - + ND -
RT 3 (C) 37592 RT 95 ++ 73 75 ND - - - ND -
RT 4 (F) 37602 RT 85 ++ 69 69 ND - ND ND ND -
RT 5 (G) 37622 RT 94 - 72 72 ND - - - ND -
Int 1 4310 Int 91 ND 71 19 ND - ND ND ND -
Int 2 4344 Int 96 +++ 67 25 ND + + - ND -
Pol29 4393 Int 82 - 80 80 ND + ND ND ND -
Int 3 44202 Int 95 +++ 68 61 ND + + + ND -
Int 4 44222 Int 99 ND 71 64 ND + ND ND ND -
Int 5 4491 Int 81 ND 70 33 ND - ND ND ND -
Pol45 45432 Int 92 ++ 91 75 ND - ND ND ND -
Pol4711 45452 Int11 9211 +++11 9111 7311 +11 -11 -11 -11 -11 -11
Vif 4646 Int/Vif 96 - 82 31 ND - - - ND -
R/T511 5551 Rev/Tat11 9311 +++11 8711 7311 +11 -11 -11 -11 -11 -11
Env 1 7250 gp120 81 ND 83 76 ND + ND ND ND -
Env 2 78752 gp41 83 ND 49 33 ND - ND ND ND -
Env 3 78812 gp41 89 ND 19 6 ND + ND ND ND -
Env 4 78842 gp41 85 ND 21 6 ND + ND ND ND -
Env 5 8026 gp41 96 +++ 53 14 ND + + + ND -
Env 6 82772 gp41 98 ++ 53 18 ND - - + ND -
Env 7 82782 gp41 98 ++ 56 18 ND - - - ND -
Env 8 8359 gp41 97 +++ 3 1 ND - - - ND -
LTR 9072 3’LTR 95 ++ 53 1 ND - - - ND -
1

Position in human immunodeficiency virus type 1 (HIV-1) LAI mRNA;

2

Overlapping short hairpin RNA (shRNA) clusters;

3

Percentage of inhibition of HIV-1 production in co-transfected cells;

4

Inhibition of HIV-1 replication in stably transduced cells: +++ = strong, ++ = medium, + = low, - = no inhibition;

5

Percentage of sequences in Los Alamos database identical to shRNA target sequence;

6

Detection of escape mutations after prolonged culturing;

7

100% complementarity of the shRNA to JS1 lentiviral vector;

8

Titers compared to JS1 lentiviral vector; + = reduction > 1 log, - = reduction < 1 log;

9

Effects on cell growth; + = negative effect, - = no effect;

10

Drug resistance mutations in the shRNA target region;

11

Selected for the combinatorial gene therapy. ND: Not determined.