Design and Prediction of Potential RNAi (siRNA) Molecules for 3' UTR PTGS of Different Strains of Zika Virus: A Computational Approach

Zika virus is an aedes mosquito borne pathogen belonging to the member of Flaviviridae subgroup causes an emerging disease called Zika fever, known as a benign infection usually presenting as influenza like illness with cutaneous rash. Nowadays epidemic outbreak caused by Zika virus is highly contagious and incurable with present technologies; thus considered as a major health risk which need enhanced surveillance. Genetic studies on Flavivirus have shown that, the 3' untranslated region (UTR) is consists of seven highly conserved stem loop structure and is important for viral replication and pathogenesis. Therefore, 3' UTR of Zika virus can be utilized as suitable target for controlling Zika virus mediated infection. Viral infection can be reduced by RNA interference (RNAi) technology in which double stranded RNA (siRNA and miRNA) molecules mediate the post transcriptional gene silencing (PTGS) of genes in a sequence specific manner. However genetic variability has been determined in different viral isolates; it is a great challenge to design potential siRNA (small interfering RNA) molecules to repress the expression of respective target gene rather than any other viral gene simultaneously. This work is done using various computational tools to design 21 nucleotides long siRNA sequence on the basis of rational siRNA designing method targeting CDS (coding sequence) of 3' UTR of Zika virus. In this study out of one hundred seventy eight computationally identified siRNAs only four most promising siRNA molecules for gene silencing of 3' UTR of Zika virus were verified using other computer aided tools which might lead to suppress the viral activity. Thus, this approach may provide an insight for chemically synthesized RNA molecules as antiviral agent for Zika virus mediated infection and acts as a foundation stone for an efficient therapeutics at genome level. (Shawan MMAK, Hossain MM, Hasan MA, Hasan MM, Parvin A, Akter S, Uddin KR, Banik S, Morshed M, Rahman MN and Rahman SMB. Design and Prediction of Potential RNAi (siRNA) Molecules for 3'UTR PTGS of Different Strains of Zika Virus: A Computational Approach. Nat Sci 2015;13(2):37-50). (ISSN: 1545-0740). http://www.sciencepub.net/nature. 7