Table 1 List of potential siRNA molecules targeting non-structural genes of SARS-CoV-2 and validation filters: The gene, target positions, target sequences, RNA oligo sequence of the finally selected siRNA molecules targeting NSP3, NSP4, and NSP6 genes of SARS-CoV-2 along with their GC content, minimum free energies of binding and folding, melting temperatures, binary validity scores, s-Biopredsi scores, and i-Scores
No. | Gene | Target position | Target sequence 21 nt target + 2 nt overhang | RNA oligo sequences 21 nt guide (5′ → 3′) 21 nt passenger (5′ → 3′) | GC content | ∆MFEa | ∆MFEb | TmCp | Tm (conc) | Binary score | s-Biopredsi Score | i-Score |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
31.6–57.9* | < − 30* | > 1.5* | 0–100* | 0–100* | >  0.7* | < 1* | ≥65* | |||||
% | kcal /mol | kcal /mol | °C | °C | ||||||||
1 | NSP3 | 597–619 | ACCAGTTGTTCAGACTATTGAAG | UCAAUAGUCUGAACAACUGGU CAGUUGUUCAGACUAUUGAAG | 38.1 | −34.8 | 1.5 | 81.2 | 80.0 | 1.008 | 0.830 | 66.9 |
2 | 682–704 | GTGGAAGAAGCTAAAAAGGTAAA | UACCUUUUUAGCUUCUUCCAC GGAAGAAGCUAAAAAGGUAAA | 35.71 | −33.9 | 1.8 | 82.5 | 81.2 | 1.062 | 0.863 | 84.4 | |
3 | 864–886 | CGGACACAATCTTGCTAAACACT | UGUUUAGCAAGAUUGUGUCCG GACACAAUCUUGCUAAACACU | 40.5 | −35.0 | 1.5 | 81.1 | 79.9 | 1.072 | 0.807 | 67.3 | |
4 | 1126–1148 | AAGAGTGAAAAGCAAGTTGAACA | UUCAACUUGCUUUUCACUCUU GAGUGAAAAGCAAGUUGAACA | 35.7 | −31.4 | 1.8 | 82.3 | 80.8 | 1.030 | 0.874 | 78.6 | |
5 | 1415–1437 | TTGTTCAAGAGGGTGTTTTAACT | UUAAAACACCCUCUUGAACAA GUUCAAGAGGGUGUUUUAACU | 35.7 | −31.5 | 1.8 | 85.1 | 83.6 | 1.031 | 0.781 | 66.8 | |
6 | 3917–3939 | ATGGTTTAGCTGCTGTTAATAGT | UAUUAACAGCAGCUAAACCAU GGUUUAGCUGCUGUUAAUAGU | 35.7 | −32.5 | 1.8 | 84.1 | 82.8 | 1.064 | 0.837 | 70.9 | |
7 | 5057–5079 | TTGATAAAGCTGGTCAAAAGACT | UCUUUUGACCAGCUUUAUCAA GAUAAAGCUGGUCAAAAGACU | 35.7 | −31.9 | 1.7 | 82.7 | 81.6 | 1.064 | 0.814 | 67.5 | |
8 | NSP4 | 692–714 | CTGGTGTTTGTGTATCTACTAGT | UAGUAGAUACACAAACACCAG GGUGUUUGUGUAUCUACUAGU | 38.1 | −34.2 | 1.8 | 82.2 | 80.9 | 1.001 | 0.873 | 78.8 |
9 | 713–735 | GTGGTAGATGGGTACTTAACAAT | UGUUAAGUACCCAUCUACCAC GGUAGAUGGGUACUUAACAAU | 40.5 | −36.8 | 1.7 | 85.8 | 84.5 | 1.024 | 0.762 | 69.7 | |
10 | NSP6 | 372–394 | AGCAAGAACTGTGTATGATGATG | UCAUCAUACACAGUUCUUGCU CAAGAACUGUGUAUGAUGAUG | 38.1 | −34.8 | 1.8 | 81.0 | 79.6 | 0.979 | 0.808 | 68.8 |