Advertisement

High throughput prediction and analysis of small interfering RNA from the 5′UTR and capsid genes of flavivirus through in silico strategies

  • Pallavi SomvanshiEmail author
  • Vijai Singh
  • P. K. Seth
Article

Abstract

The genus flavivirus in the family Flaviviridae consists of many arthropod transmitted human pathogens. siRNA is a novel strategy used for controlling the gene expression of flavivirus. These are 20–25 nucleotide long dsRNA molecules that target genes at expression level. Nine flavivirus genomes were used to in silico identify the siRNA. Twenty three siRNAs were identified in the 5′ UTR and capsid protein encoding gene from flavivirus. These siRNA can be useful to knockdown the flavivirus and it might also be helpful for constructing live attenuated vaccine.

Key words

siRNA pathogenesis knockdown vaccine 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. [1]
    Chowers, M.Y., Lang, R., Nassar, F., Ben-David, D., Giladi, M., Rubinshtein, E., Itzhaki, A., Mishal, J., Siegman-Igra, Y., Kitzes, R., Pick, N., Landau, Z., Wolf, D., Bin, H., Mendelson, E., Pitlik, S.D., Weinberger, M. 2001. Clinical characteristics of the West Nile fever outbreak, Israel, 2000. Emerg Infect Dis 7, 675–678.CrossRefPubMedGoogle Scholar
  2. [2]
    Gould, E.A., Solomon, T. 2008. Pathogenic flaviviruses. Lancet 371, 500–509.CrossRefPubMedGoogle Scholar
  3. [3]
    Gubler, D.J. 2002. Epidemic dengue/dengue haemorrhagic fever as a public VOL. 78, 2004 Dengue virus NS2B cofactor 13715 Downloaded from jvi.asm.org by on December 15, 2007 health, social and economic problem in the 21st century. Trends Microbiol 10, 100–103.CrossRefPubMedGoogle Scholar
  4. [4]
    Halstead, S.B. 1988. Pathogenesis of dengue: challenges to molecular biology. Science 239, 476–481.CrossRefPubMedGoogle Scholar
  5. [5]
    Kumar, P., Lee, S.K., Shankar, P., Manjunath, N. 2006. A single siRNA suppresses fatal encephalitis induced by two different flaviviruses. PLoS Med 3, e96.CrossRefPubMedGoogle Scholar
  6. [6]
    Li, Z.X., Liu, R., Si, Y., Sun, M., Jin, M., Chen, H., Qian, P. 2007. Inhibition of expression of RNA polymerase with small interfering RNAs targeting a conserved motif in the respective viral genes in viruses of the family Flaviviridae. Acta Virol 51, 195–201.PubMedGoogle Scholar
  7. [7]
    Lindenbach, B., Rich, C.M. 2000. Flaviviridae: The viruses and their replication. In: Knipe, D.M., Howley, P.M. (eds) fields virology Volume 1, 4th edition. Wolters Kluwer Co., Lippincott Williams & Wilkins, 991–1003.Google Scholar
  8. [8]
    Liu, X., Cao, S., Zhou, R., Xu, G., Xiao, S., Yang, Y., Sun, M., Li, Y., Chen, H. 2006. Inhibition of Japanese encephalitis virus NS1 protein expression in cell by small interfering RNAs. Virus Genes 33, 69–75.CrossRefPubMedGoogle Scholar
  9. [9]
    Lum, L.C., Lam, S.K., Choy, Y.S., George, R., Harun, F. 1996. Dengue encephalitis: A true entity? Am J Trop Med & Hygiene 54, 256–259.Google Scholar
  10. [10]
    Marfin, A.A., Gubler, D.J. 2001. West Nile encephalitis; an emerging disease in the United States. Clin Infect Dis 33, 1713–1719.CrossRefPubMedGoogle Scholar
  11. [11]
    Ong, S.P., Choo, B.G., Chu, J.J., Ng, M.L. 2006. Expression of vector-based small interfering RNA against West Nile virus effectively inhibits virus replication. Antiviral Res 72, 216–223.CrossRefPubMedGoogle Scholar
  12. [12]
    Pitaluga, A.N., Mason, P.W., Traub-Cseko, Y.M. 2008. Non-specific antiviral response detected in RNAtreated cultured cells of the sandfly, Lutzomyia longipalpis. Dev Comp Immunol 32, 191–197.CrossRefPubMedGoogle Scholar
  13. [13]
    Singh, V., Somvanshi, P. 2009. In silico identification of small interfering RNA (siRNA) in the putative genes of White spot syndrome virus. Online J Bioinform 10, 93–97.Google Scholar
  14. [14]
    Spiegland, I., Jasinska-Klingberg, W., Hofshi, E., Goldblum, N. 1958. Clinical and laboratory observations in an outbreak of West Nile fever in Israel (English summary). Harefuah 54, 275–281.Google Scholar
  15. [15]
    Stein, D.A., Shi, P.Y. 2008. Nucleic acid-based inhibition of flavivirus infections. Front Biosci 13, 1385–1395.CrossRefPubMedGoogle Scholar
  16. [16]
    Umenai, T., Kruzysko, R., Bektimirov, T.A., Assaad, F.A. 1985. Japanese encephalitis-Current world status. WHO Bulletin OMS 63, 625–631.Google Scholar
  17. [17]
    Westenberg, M., Heinhuis, B., Zuidema, D., Vlak, J.M. 2005. siRNA injection induces sequence-independent protection in Penaeus monodon against white spot syndrome virus. Virus Res 114, 133–139.CrossRefPubMedGoogle Scholar
  18. [18]
    Xu, J., Han, F., Zhang, X. 2007. Silencing shrimp white spot syndrome virus (WSSV) genes by siRNA. Antiviral Res 73, 126–131.CrossRefPubMedGoogle Scholar
  19. [19]
    Zhang, W., Singam, R., Hellermann, G., Kong, X., Juan, H.S., Lockey, R.F., Wu, S.J., Porter, K., Mohapatra, S.S. 2004. Attenuation of dengue virus infection by adeno-associated virus-mediated siRNA delivery. Genet Vaccines Ther 2, 8.CrossRefPubMedGoogle Scholar

Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer Berlin Heidelberg 2009

Authors and Affiliations

  1. 1.Bioinformatics centreJankipuram, LucknowIndia

Personalised recommendations