Table 2.
EGFP-targeting siRNA sequences selected for this study, sorted by algorithm rank.
| 5'Target Position | siRNA Sequence | End 5' Nucleotides | Thermodynamic ΔΔG (kcal/mol) | Algorithm Rank | Testing Rationale | |
|---|---|---|---|---|---|---|
| Anti:Sense | Rank | |||||
| 415 | UGUACUCCAGCUUGUGCCC | U:G | 1 | 4.2 | 1 | Highest algorithm ranking |
| 416 | UUGUACUCCAGCUUGUGCC | U:G | 1 | 2.1 | 17 | Highest Dharm. rank (91) |
| 274 | UGCGCUCCUGGACGUAGCC | U:G | 1 | 0.8 | 38 | On Ambion list |
| 757 | UGGGCAGCGUGCCAUCAUC | U:G | 1 | −2.6 | 177 | High end, low ΔΔG |
| 306 | CUUGUAGUUGCCGUCGUCC | C:G | 7 | 2.9 | 239 | On Ambion list |
| 396 | CAGGAUGUUGCCGUCCUCC | C:G | 7 | 0.5 | 389 | On Ambion list |
| 126 | GAUGAACUUCAGGGUCAGC | G:G | 10 | 1.9 | 418 | On Ambion list |
| 711 | AUGGCUAAGCUUCUUGUAC | A:G | 2 | −3.7 | 551 | Low rank, high Dharm. (73) |
| 783 | CAUCCCGCUCUCCUGGGCA | C:U | 16 | 3.1 | 695 | Low end, high ΔΔG |
| 159 | GGGCCAGGGCACGGGCAGC | G:G | 10 | −2.3 | 700 | On Ambion list |
| 253 | CGGGCAUGGCGGACUUGAA | C:U | 16 | −5.2 | 824 | Lowest algorithm rank |