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In-Silico Design of a Potent siRNA Molecule for Gene Silencing in Zaire Ebolavirus

by Gopaluni Sai Akash, Jayasree Ganugapati
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 113 - Number 4
Year of Publication: 2015
Authors: Gopaluni Sai Akash, Jayasree Ganugapati
10.5120/19815-1627

Gopaluni Sai Akash, Jayasree Ganugapati . In-Silico Design of a Potent siRNA Molecule for Gene Silencing in Zaire Ebolavirus. International Journal of Computer Applications. 113, 4 ( March 2015), 23-27. DOI=10.5120/19815-1627

@article{ 10.5120/19815-1627,
author = { Gopaluni Sai Akash, Jayasree Ganugapati },
title = { In-Silico Design of a Potent siRNA Molecule for Gene Silencing in Zaire Ebolavirus },
journal = { International Journal of Computer Applications },
issue_date = { March 2015 },
volume = { 113 },
number = { 4 },
month = { March },
year = { 2015 },
issn = { 0975-8887 },
pages = { 23-27 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume113/number4/19815-1627/ },
doi = { 10.5120/19815-1627 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T22:50:06.558107+05:30
%A Gopaluni Sai Akash
%A Jayasree Ganugapati
%T In-Silico Design of a Potent siRNA Molecule for Gene Silencing in Zaire Ebolavirus
%J International Journal of Computer Applications
%@ 0975-8887
%V 113
%N 4
%P 23-27
%D 2015
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Zaire ebolavirus (EBOV) is one of the most dangerous and the unknown to humans. This is a filamentous virus of the family Filoviridae. Genetic studies of EBOV have shown that it has a negative-stranded RNA as genetic material and seven genes in its genome. One among these genes is the gene 'L', that code for a protein L (Large structural protein), this protein functions as an RNA dependent RNA polymerase. RNAi (RNA interference) is an influential method for post-transcriptional gene slicing in a specific sequence. This is done with the help of a dsRNA called siRNA. Slicing a target mRNA would mean that the mRNA will not be able to produce any protein and the viral activity can be restrained. This mechanism is observed naturally in the organism to regulate the protein production and also as a defense mechanism against some viruses. In-silico construction of siRNA is possible using computational methods in biology. Construction of siRNA is guided by many parameters and the efficiency of the cleavage of mRNA with siRNA is determined by hybridization thermodynamics. The constructed siRNA is potent of knocking down the activity of the virus. This can lead to the discovery of an effective antiviral drug against EBOV.

References
  1. Goeijenbier M et al. 2014 72: 442. Ebola virus disease: a review on epidemiology, symptoms, treatment and pathogenesis. [PMID:25387613]
  2. Hoenen T et al. 2012 12: 859. Current Ebola vaccines. [PMCID: PMC3422127]
  3. Lroy EM et al. 2005 438: 575. Fruit bats as reservoirs of Ebola virus. [PMID:16319873]
  4. No authors listed. 1978 56: 247. Ebola hemorrhagic fever in Sudan, 1976. Report of a WHO/International Study Team. [PMID: 307455]
  5. WHO Ebola response team. The New England journal of medicine. 2014 371:1481 [PMID:25244186]
  6. Bukreyev A et al. 1993 322: 41. The VP35 and VP40 proteins of filoviruses. Homology between Marburg and Ebola viruses. [PMID: 8482365]
  7. http://www. ncbi. nlm. nih. gov/gene/?term=zaire+ebolavirus
  8. Elke M et al. 1999 73: 2333. Comparison of the Transcription and Replication Strategies of Marburg Virus and Ebola Virus by Using Artificial Replication Systems. [PMCID:PMC104478]
  9. Silva LP et al. 2012 7: e39978. Assembly of Ebola virus matrix protein VP40 is regulated by latch-like properties of N and C terminal tails. [PMID:22792204]
  10. Sinu P John et al. 2007 81: 8967. Ebola Virus VP30 Is an RNA Binding Protein. [PMCID: PMC1951390]
  11. Cardenas WB et al. 2006 80: 5168. Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling. [PMID:16698997]
  12. Ziying Han et al. 2003 77: 1793. Biochemical and Functional Characterization of the Ebola Virus VP24 Protein: Implications for a Role in Virus Assembly and Budding. [PMCID:PMC140957]
  13. Basler CF et al. 2009 29: 511. Evasion of interferon responses by Ebola and Marburg viruses. [PMID:19694547]
  14. Watanabe S et al. 2006 80: 3743. Functional mapping of the nucleoprotein of Ebola virus. [PMID:16571791]
  15. Fire A et al. 1998 391:806. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. [PMID:9486653]
  16. Lu R et al. 2005 436: 1040. Animal virus replication and RNAi-mediated antiviral silencing in C elegans. [PMCID:1388260]
  17. Ahlquist P et al. 2002 296: 1270. RNA-dependent RNA polymerases, viruses, and RNA silencing. [ PMID:12016304]
  18. Carette JE et al. 2011 477: 340. Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. [PMID:21866103]
  19. Zamore PD et al. 2000 101: 25. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. [PMID:10778853]
  20. Hammond SM et al. 2000 404:293. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. [PMID: 10749213]
  21. Ahn J et al. 2012 56: 3516. Antiviral effects of small interfering RNA simultaneously inducing RNA interference and type 1 interferon in coxsackievirus myocarditis. [PMID:22508300]
  22. Prechtel AT et al. 2006 311:139. Small interfering RNA (siRNA) delivery into monocyte-derived dendritic cells by electroporation. [PMID:16556448]
  23. Mykhayiyk O et al. 2008 10: 493. siRNA delivery by magnetofection. [PMID:18830925]
  24. Kleinhammer A et al. 2010 477:387. Gene knockdown in the mouse through RNAi. [PMID:20699152]
  25. Gupta et al. 2010 10: 4. A Novel Algorithm to Design an Efficient siRNA by Combining the Pre Proposed Rules of siRNA Designing.
  26. Lu ZJ et al. 2008 36: 640. Efficient siRNA selection using hybridization thermodynamics. [PMID:18073195]
  27. Y Seong et al. 2014 42: 12806. Global identification of target recognition and cleavage by the Microprocessor in human ES cells. [PMCID: PMC4227787]
  28. Tafer H et al. 2008 26: 578. The impact of target site accessibility on the design of effective siRNAs. [PMID:18438400]
  29. Reynolds A et al. 2004 22:326. Rational siRNA design for RNA interference. [PMID:14758366]
  30. Chi Y C et al. 2009 10: S33. A structural interpretation of the effect of GC-content on efficiency of RNA interference.
  31. Van Rii RP et al. 2006 20: 2985. The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. [PMID: 17079687]
  32. S Singh et al. 2012 8: 749. Design of potential siRNA molecules for hepatitis delta virus gene silencing. [PMCID:PMC3449391]
  33. Khalili MA et al. 2006 13:636. Gene therapy for carcinoma of the breast. [PMID: 16410823]
  34. Thi EP et al. 2014 20: 250. Marburg virus infection in nonhuman primates: Therapeutic treatment by lipid-encapsulated siRNA. [PMID:25143366]
  35. Krotz F et al. 2003 7:700. Magnetofection--a highly efficient tool for antisense oligonucleotide delivery in vitro and in vivo. [PMID:12718913]
Index Terms

Computer Science
Information Sciences

Keywords

RNAi siRNA EBOV Zaire Ebola

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