In silico design of short hairpin RNA (shRNA)Molecules for DNA pol gene of Contagious Ecthyma virus (ORFV)

Abstract

Contagious ecthyma is an infectious skin disease of ruminants caused by the ORF virus (ORFV) that is a member of genus Parapoxvirus of the Poxviridae family. In addition to the significant effects on lambs and human, ORFVs have been recently shown to infect other hosts. The disease causes significant economic damages to the sheep industry, so attempts to eliminate it must be taken into.RNA interference (RNAi) is an evolutionarily conserved mechanism in which the expression of homologous target genesis is suppressed by means of double-stranded RNA molecules. Since RNAi can be considered as a therapeutic method for viral gene silencing, we tend to make the most of this capability. The present study aims to design potential shRNAs to knockdown the DNA-polymerase gene coded by ORF025.A significant number of computational methods such as clustal omega website to target alignment, BLAST-NCBI to similarity search, CLC software to secondary structure prediction, BLOCK-iTRNAi Designer and WI siRNA Selection Program and Software to design of shRNA molecules and scoring have been applied for shRNA molecules designing against the ORF025-DNA pol gene of ORFV. Then three shRNA molecules were logically designed against the ORF025-DNA pol gene. In conclusion the present study provides a strong and superior approach for achieving a validated strategy to design an antiviral shRNA molecule that meets many sequence features for efficient ORFV knockdown and treatment at the mRNA level. The efficiency of these anti ORFV shRNAs need to be tested