An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes

Table 2 List of potential siRNA molecules targeting accessory genes and validation filters: The gene, target positions, target sequences, RNA oligo sequence of the finally selected predicted siRNA molecules targeting ORF3a, ORF6, ORF7a, ORF8, and ORF10 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	∆MFE^a	∆MFE^b	T_mC_p	T_m (conc)	Binary score	s-Biopredsi Score	i-Score
					31.6–57.9*	< −30*	> 1.5*	< 100*	< 100*	> 0.7*	< 1*	≥65*
					%	kcal /mol	kcal /mol	°C	°C	> 0.7*	< 1*	≥65*
1	ORF3a	240–262	TTGCAACTTGCTGTTGTTGTTTG	AACAACAACAGCAAGUUGCAA GCAACUUGCUGUUGUUGUUUG	40.47	−32.9	1.5	84.5	83.4	0.980	0.840	69.7
2		550–572	TACCAGATTGGTGGTTATACTGA	AGUAUAACCACCAAUCUGGUA CCAGAUUGGUGGUUAUACUGA	40.47	−35.7	1.7	84.1	84.4	1.020	0.853	70.3
3		770–792	ATCCAGTAATGGAACCAATTTAT	AAAUUGGUUCCAUUACUGGAU CCAGUAAUGGAACCAAUUUAU	33.33	−32.2	1.9	81.6	83.4	0.992	0.869	78.0
4	ORF6	164–186	AGCAACCAATGGAGATTGATTAA	AAUCAAUCUCCAUUGGUUGCU CAACCAAUGGAGAUUGAUUAA	35.71	−29.9^c	1.6	82.3	81.0	0.963	0.855	72.0
5	ORF7a	332–354	CACTTTGCTTCACACTCAAAAGA	UUUUGAGUGUGAAGCAAAGUG CUUUGCUUCACACUCAAAAGA	38.09	−33.2	1.5	86.2	84.6	0.921	0.830	75.9
6	ORF8	41–63	CTGCATTTCACCAAGAATGTAGT	UACAUUCUUGGUGAAAUGCAG GCAUUUCACCAAGAAUGUAGU	38.09	−34.0	1.4^c	81.3	80.3	0.955	0.842	73.3
7		67–89	CAGTCATGTACTCAACATCAACC	UUGAUGUUGAGUACAUGACUG GUCAUGUACUCAACAUCAACC	40.47	−33.9	1.8	82.7	81.4	0.949	0.834	74.5
8		298–320	GTGCGTTGTTCGTTCTATGAAGA	UUCAUAGAACGAACAACGCAC GCGUUGUUCGUUCUAUGAAGA	42.85	−32.2	1.8	84.0	82.8	0.940	0.845	71.5
9	ORF10	20–42	TCGCTTTTCCGTTTACGATATAT	AUAUCGUAAACGGAAAAGCGA GCUUUUCCGUUUACGAUAUAU	35.71	−32.5	1.7	81.4	80.2	0.924	0.794	71.4

ISSN: 1471-2334