Table 3 Nucleic acid geometry of siRNAs targeting non-structural and accessory genes of SARS-CoV-2: The tertiary structural validation of siRNA molecules against NSP3, NSP4 NSP6, ORF3a, ORF7a, ORF8, and ORF10 genes of SARS-CoV-2 using the MolProbity server
Target gene | NSP3 | NSP4 | NSP6 | ORF3a | ORF7a | ORF8 | ORF10 | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
siRNA | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 |
Probably wrong sugar puckers | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2* | 2* | 0 | 0 | 0 | 0 | 0 |
Bad backbone conformations | 0 (0.00%) | 0 (0.00%) | 1 (4.76%) | 0 (0.00%) | 0 (0.00%) | 1 (4.76%) | 0 (0.00%) | 1 (4.76%) | 1 (4.76%) | 2* (9.52%) | 8* (38.10%) | 6* (28.57%) | 0 (0.00%) | 0 (0.00%) | 5* (23.81%) | 1 (4.76%) | 6* (28.57%) |
Bad bonds | 0/495 (0.00%) | 0/471 (0.00%) | 0/494 (0.00%) | 0/471 (0.00%) | 0/489 (0.00%) | 0/493 (0.00%) | 0/481 (0.00%) | 0/500 (0.00%) | 0/484 (0.00%) | 0/481 (0.00%) | 0/503 (0.00%) | 0/494 (0.00%) | 0/492 (0.00%) | 0/504 (0.00%) | 0/497 (0.00%) | 0/497 (0.00%) | 0/508 (0.00%) |
Bad angles | 0/769 (0.00%) | 0/728 (0.00%) | 0/768 (0.00%) | 0/728 (0.00%) | 0/758 (0.00%) | 0/765 (0.00%) | 0/745 (0.00%) | 0/777 (0.00%) | 0/750 (0.00%) | 0/745 (0.00%) | 0/782 (0.00%) | 0/767 (0.00%) | 0/764 (0.00%) | 0/785 (0.00%) | 0/773 (0.00%) | 0/772 (0.00%) | 0/791 (0.00%) |
Chiral volume outliers | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 | 0/104 |