Table 2.
siRNAs and BNAs targeting the ATXN3 CAG repeat region.
| siRNA | Sequence | Position of mismatch |
Tm (°C) |
mutIC50 (nM) |
wtIC50 (nM) |
Selectivity (fold) |
|---|---|---|---|---|---|---|
| siREP | GCUGCUGCUGCUGCUGCUGtt | 86.8 | 12 ± 4 | 24 ± 9 | 2 lit | |
| siP4 | GCUACUGCUGCUGCUGCUGtt | 4 | 84.0 | - | - | - |
| siP5 | GCUGAUGCUGCUGCUGCUGtt | 5 | 83.2 | - | - | - |
| siP6 | GCUGCAGCUGCUGCUGCUGtt | 6 | 85.1 | - | - | - |
| siP7 | GCUGCUACUGCUGCUGCUGtt | 7 | 82.7 | - | - | - |
| siP8 | GCUGCUGAUGCUGCUGCUGtt | 8 | 83.8 | - | - | - |
| siP9 | GCUGCUGCAGCUGCUGCUGtt | 9 | 86.7 | 4.6 | >50 | 11 |
| siP10 | GCUGCUGCUACUGCUGCUGtt | 10 | 83.5 | - | - | - |
| siP10R | GCUGCUGCUUCUGCUGCUGtt | 10 | 78.0 | - | - | - |
| siP11 | GCUGCUGCUGAUGCUGCUGtt | 11 | 83.7 | 5.4 ± 3.9 | >50 | 9 |
| siP12 | GCUGCUGCUGCAGCUGCUGtt | 12 | 85.6 | - | - | - |
| siP13 | GCUGCUGCUGCUACUGCUGtt | 13 | 82.8 | - | - | - |
| siP16 | GCUGCUGCUGCUGCUACUGtt | 16 | 76.4 | - | - | - |
| siP910 | GCUGCUGCAACUGCUGCUGtt | 9,10 | 83.5 | 3.1 ± 0.9 | >50 | 16 |
| siPM3 | GCUGCUGCAAAUGCUGCUGtt | 9,10,11 | 79.9 | 5.2 ± 1.1 | >50 | 10 |
| siPM4 | GCUGCUGAAAAUGCUGCUGtt | 8,9,10,11 | 76.4 | 6.5 ± 2.8 | >50 | 8 |
| siRM4 | GCAGCUGUUGCUACUGUUGtt | 3,8,13,17 | 78.0 | - | - | - |
| siCM | GCUAUACCAGCGUCGUCAUtt | - | 80.0 | - | - | - |
| BNAs | ||||||
| carba LNA |
gc[T]gc[T]gc[T]gc[T]gc[T]gc[T]g | 76.5 | 25 ± 6.0 | 55 ± 18 | 2.2 | |
| cET | gcUgcUgcUgcUgcUgcUg | 82.8 | 9.3 ± 0.8 | 25 ± 3.8 | 2.6 | |
All sequences are listed from 5’ to 3’. Only the guide strand of siRNA is shown. RNA bases are in capital letters. Mismatched bases are underlined and in bold letters. For BNA oligomers, carba-LNA modified bases are in square bracket, cEt bases are in italics. DNA bases are in lowercase. Selectivity is calculated by comparing the IC50 for inhibition of wild-type versus the IC50 for inhibition of mutant ataxin-3 protein. Error is standard deviation. siCM is a non-complementary negative control siRNA. The Tm value for BNAs was calculated using complementary DNA sequences. Tm values for siRNAs are values for the duplex The molecular weight (calculated/observed) is 6042/6037 for carba LNA and 5965/5969 for cET.