Table 2.
Validation of siRNAs designed to distinguish between matched and mismatched SNP isoforms. IC50 values are given as the average ± standard deviation for at least three independent experiments. The IC50 is reported as > 20 nM for siRNAs that failed to achieve half-maximal inhibition at the highest concentration tested.
| Reference Number |
siRNA guide strand | SNP position |
primary mismatch |
secondary mismatch position |
secondary mismatch |
IC50 (nM) |
Discrimination ratio |
|
|---|---|---|---|---|---|---|---|---|
| Match | Mismatch | |||||||
| rs363125 | 5′-agcguugaaguacugucccca-3′ | 10 | G:A | none | none | 0.17 ± 0.11 | 0.27 ± 0.25 | 1.6 |
| rs363125 | 5′-agcguugaauuacugucccca-3′ | 10 | U:C | none | none | 0.18 ± 0.09 | 0.22 ± 0.07 | 1.2 |
| rs363125 | 5′-ucuucuagcguugaaguacug-3′ | 16 | G:A | none | none | 0.36 ± 0.24 | >20 | >55 |
| rs363125 | 5′-ucuucuagcguugaauuacug-3′ | 16 | U:C | none | none | 0.74 ± 0.40 | >20 | >27 |
| rs362307 | 5′-cacaagggcgcagacuuccaa-3′ | 10 | G:U | none | none | 0.36 ± 0.04 | 0.77 ± 0.16 | 2.1 |
| rs362307 | 5′-uacaagggcacagacuuccaa-3′ | 10 | A:C | none | none | 0.16 ± 0.09 | 0.14 ± 0.10 | 0.87 |
| rs362307 | 5′-gcagggcacaagggcgcagac-3′ | 16 | G:U | none | none | 0.73 ± 0.12 | 0.72 ± 0.12 | 0.99 |
| rs362307 | 5′-ucagggcacaagggcacagac-3′ | 16 | A:C | none | none | 0.19 ± 0.02 | 0.20 ± 0.06 | 1.1 |
| rs362307 | 5′-cgcaagggcacagacuuccaa-3′ | 10 | A:C | 2 | G:U | 1.0 ± 0.35 | 1.9 ± 0.27 | 1.9 |
| rs362307 | 5′-cauaagggcacagacuuccaa-3′ | 10 | A:C | 3 | U:G | 3.0 ± 1.8 | 3.5 ± 1.6 | 1.2 |
| rs362307 | 5′-caccagggcacagacuuccaa-3′ | 10 | A:C | 4 | C:U | 1.0 ± 0.22 | 1.6 ± 1.2 | 1.6 |
| rs362307 | 5′-cacacgggcacagacuuccaa-3′ | 10 | A:C | 5 | C:U | 0.62 ± 0.43 | >20 | >32 |
| rs362307 | 5′-cacaauggcacagacuuccaa-3′ | 10 | A:C | 6 | U:C | 1.5 ± 0.31 | >20 | >13 |
| rs362307 | 5′-cacaagugcacagacuuccaa-3′ | 10 | A:C | 7 | U:C | 1.3 ± 0.51 | 5.9 ± 1.9 | 4.5 |
| rs362307 | 5′-cacaauggcgcagacuuccaa-3′ | 10 | G:U | 6 | U:C | 3.2 ± 2.2 | >20 | >6 |
| rs362273 | 5′-guugaucuguagcagcagcuu-3′ | 10 | U:G | none | none | 0.09 ± 0.14 | 0.01 ± 0.006 | 0.11 |
| rs362273 | 5′-guugaucugcagcagcagcuu-3′ | 10 | C:A | none | none | 0.12 ± 0.06 | 0.44 ± 0.11 | 3.7 |
| rs362273 | 5′-cucgggguugaucuguagcag-3′ | 16 | U:G | none | none | 0.01 ± 0.002 | 0.007 ± 0.002 | 0.70 |
| rs362273 | 5′-cucgggguugaucugcagcag-3′ | 16 | C:A | none | none | 0.01 ± 0.003 | 0.004 ± 0.001 | 0.41 |
| rs362273 | 5′-ucugaucuguagcagcagcuu-3′ | 10 | U:G | 2 | C:A | 0.01 ± 0.002 | 0.06 ± 0.008 | 5.9 |
| rs362273 | 5′-uucgaucuguagcagcagcuu-3′ | 10 | U:G | 3 | C:A | 0.02 ± 0.003 | 0.29 ± 0.04 | 15 |
| rs362273 | 5′-uuuuaucuguagcagcagcuu-3′ | 10 | U:G | 4 | U:C | 0.03 ± 0.006 | 0.37 ± 0.11 | 11 |
| rs362273 | 5′-uuugcucuguagcagcagcuu-3′ | 10 | U:G | 5 | C:U | 0.02 ± 0.003 | 0.59 ± 0.08 | 31 |
| rs362273 | 5′-uuugaccuguagcagcagcuu-3′ | 10 | U:G | 6 | C:A | 0.02 ± 0.002 | 0.06 ± 0.015 | 2.7 |
| rs362273 | 5′-uuugauuuguagcagcagcuu-3′ | 10 | U:G | 7 | U:G | 0.006 ± 0.001 | 0.10 ± 0.02 | 17 |
| rs362273 | 5′-uuugcucugcagcagcagcuu-3′ | 10 | C:A | 5 | C:U | 0.15 ± 0.04 | 0.74 ± 0.11 | 4.9 |