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Computational Approach to Design a Potential siRNA Molecule to Silence the Nucleocapsid Gene of Different Nipah Virus Strains of Bangladesh

Arafat Rahman Oany, Mohammad Uzzal Hossain and Shah Adil Ishtiyaq Ahmad*

Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Santosh, Tangail – 1902, Bangladesh.

ABSTRACT: Nipah virus (NiV) is a single stranded negative-strand RNA virus which was first identified in Malaysia and Singapore. It causes fatal respiratory illness and encephalitis in humans. The progression of this infection is very rapid and causes death within 18 days of infection in most of the cases. Scientists are yet to find out a successful therapeutic approach to treat the NiV affected people. In this study, we have tried to utilize different computational methods to design a siRNA molecule to silence the Nucleocapsid gene of Nipah virus. The nucleocapsid protein (N) gene is one of the most suitable targets for the diagnosis and treatment of NIVs. To find out a common siRNA molecule against five different Nipah virus strains, at first the complete nucleocapsid gene sequences of these five strains were collected from NCBI database. SiDirect 2.0 server was used to design a siRNA molecule against these strains. The siRNA molecule was checked for its secondary structure and GC content using Mfold and OligoCalc server respectively. Blast tool was used to identify any off-target similarity with the designed siRNA molecule. In this study we have proposed a duplex siRNA molecule for N gene silencing of five different strains of NiVs. The siRNA molecule was rationally designed and authenticated using different computational methods. It was also confirmed that the designed siRNA does not match with any off-target sequences. There is no effective therapy available at present to cure Nipah virus infections. The designed siRNA molecule might provide an alternative therapeutic approach against the five major Nipah virus strains in Bangladesh.

KEYWORDS: molecular therapy, therapeutic siRNA, siDirect, Reynolds rule.


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