Immunoinformatic and molecular docking approaches: siRNA prediction to silence cell surface binding protein of monkeypox virus

Beni-Suef University Journal of Basic and Applied Sciences

Table 1 siRNA’s with target sequences predicted by siDirect webserver

Alias	Target sequence (21nt target + 2nt overhang)	Target position in mRNA of cell surface binding protein	RNA oligo sequences 21nt guide (5′ → 3′) 21nt passenger (5′ → 3′)	Functional siRNA selection: Ui-Tei Reynolds Amarzguioui	Seed duplex stability (Tm) (°C)
Alias	Target sequence (21nt target + 2nt overhang)	Target position in mRNA of cell surface binding protein		Functional siRNA selection: Ui-Tei Reynolds Amarzguioui	Guide	Passenger
S1	GCGAATATCGTTGACTCATAAGA	18–40	UUAUGAGUCAACGAUAUUCGC GAAUAUCGUUGACUCAUAAGA	U R A	20.3	8.8
S2	GAGAATAGCGGTGAGTATAAATA	43–65	UUUAUACUCACCGCUAUUCUC GAAUAGCGGUGAGUAUAAAUA	U R A	6.3	20.4
S3	TACGAATACTATGGCAATAATTG	64–86	AUUAUUGCCAUAGUAUUCGUA CGAAUACUAUGGCAAUAAUUG	U R A	15.3	14.5
S4	GACGACAATAGTGTTCTGAATTT	302–324	AUUCAGAACACUAUUGUCGUC CGACAAUAGUGUUCUGAAUUU	U R A	20.4	16.1
S5	ATGTTTATTGGTGTTGGAAAAAT	344–366	UUUUCCAACACCAAUAAACAU GUUUAUUGGUGUUGGAAAAAU	U R A	20.1	− 1.4
S6	AGGTAGCAAATTGTCTAGATAAA	433–455	UAUCUAGACAAUUUGCUACCU GUAGCAAAUUGUCUAGAUAAA	U R A	20.2	19.7
S7	ATCCAATTGATTGACTATCTTTT	499–521	AAGAUAGUCAAUCAAUUGGAU CCAAUUGAUUGACUAUCUUUU	U R A	18.9	13.8
S8	ATCAAGTGATTGGATCCATAATC	671–693	UUAUGGAUCCAAUCACUUGAU CAAGUGAUUGGAUCCAUAAUC	U R A	21.2	19.2
S9	GTCTTCCTTTCCCCAATATATAT	694–716	AUAUAUUGGGGAAAGGAAGAC CUUCCUUUCCCCAAUAUAUAU	U R A	0.0	18.7
S10	TGGTTGGTTTCGACTCATTATAA	813–835	AUAAUGAGUCGAAACCAACCA GUUGGUUUCGACUCAUUAUAA	U R A	13.4	18.8

Here all these 10 siRNA’s follows the all three rules of siRNA selection e.g., Ui-Tei, Reynolds and Amarzguioui