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AmiRzyn: PERL Centered Artificial MicroRNA Designing Aid

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Author Affiliations

  • 1nterdisciplinary Research Centre, Malankara Catholic College, Mariagiri, Kaliakkavilai- 629 153, Tamil Nadu, INDIA
  • 2Department of Bioinformatics, Malankara Catholic College, Mariagiri, Kaliakkavilai- 629 153, Tamil Nadu, INDIA

Int. Res. J. Biological Sci., Volume 1, Issue (5), Pages 18-23, September,10 (2012)

Abstract

RNA interference, a gene knock down tool has become a promising technology for researchers. Gene silencing, can be fastened by the process of designing small non- coding RNAs through computational tools. One of the current advancement in this field is artificial microRNA. It exploits the backbone of a miRNA for designing siRNA. The endogenous nature of the miRNA provides more success to this technology. In the current study, a tool named Amirzyn was developed for designing artificial microRNA using PERL language, which is very powerful in string manipulations. The tool facilitates the user to input their DNA sequences and by means of pre- defined parameters, the possible siRNA sequences are predicted as output. Possibilities of occurrence of off- target effects are verified by performing BLAST comparison. For amiRNA designing, AmiRzyn permits the specification of restriction site and miRNA backbone of user’s requirement, in addition to the predicted siRNA sequence as the input. AmiRzyn serves as a promising aid for researchers, in the field of gene silencing, to design artificial microRNAs.

References

  1. Du G., Yonekubo J., Zeng Y., Osisami M. and FrohmanM.A., Design of expression vectors for RNA interference based on miRNAs and RNA splicing, FEBS J., 273, 5421-5427 (2006)
  2. Fire A., Xu S., Montgomery M., Kostas S., Driver S. and Mello C., Potent and specific gene interference by double-stranded RNA in Caenorhabditis elegans, Nature,391, 806-811 (1998)
  3. Alvarez J.P., Pekker I., Goldshmidt A., Blum E., Amsellem Z. and Eshed Y., Endogenous and synthetic microRNAs stimulate simultaneous, efficient and localized regulation of multiple targets in diverse species, Plant Cell,18, 1134-1151 (2006)
  4. Schwab R., Ossowski S., Riester M., Warthmann N. and Weigel D., Highly specific gene silencing by artificial microRNAs in Arabidopsis, Plant Cell, 18, 1121–1133 (2006)
  5. Bartel D.P., MicroRNAs: Genomics, biogenesis, mechanism and function, Cell, 116, 281-297 (2004)
  6. Chapman J.E and C.J. Carrington, Specialization and evolution of endogenous smallRNA pathways, Nat. Rev., Genet., , 884-896 (2007)
  7. Filipowicz W., RNAi: The nuts and bolts of the RISC machine, Cell, 122, 17-20 (2005)
  8. Martinez J., Patkaniowska A., Urlaub H., Luhrmann R.and Tuschl T., Single stranded antisense siRNA guide target RNA cleavage in RNAi, Cell,110, 563- 574 (2002)
  9. Sijen T., Fleenor J., Simmer F., Thijssen K.L. and Parish S. et al., On the role of RNA amplification in dsRNA triggered gene silencing, Cell., 107, 465- 476 (2001)
  10. Baulcombe D., RNA silencing, Trends Biochem., 30, 290-293 (2005)
  11. Meister G. and T. Tuschl, Mechanisms of gene silencing by double-stranded RNA, Nature, 431, 343-349 (2004)
  12. Zhang J. and Hattori T., Small RNA molecules as Therapeutic Agents for Viral Infectious Diseases, Journal of Pharmacology and Toxicology,2(2), 103-113 (2007)
  13. Zeng Y., Wagner E.J. and Cullen B.R., Both natural and designed microRNAs can inhibit the expression of cognate mRNAs when expressed in human cells, Mol. Cell, 9, 1327-1333 (2002)
  14. Chung K.H., Hart C.H., Al-Bassam S., Avery A. and Taylor J. et al., Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155, Nucleic Acids Res., 34, e53 (2006)
  15. Wall L., Christiansen T. and Orwant J., Programming Perl. Third Edn., O'Reilly Media, USA (2000)
  16. Schwartz R., Christiansen T. and Wall L., Learning perl. Second Edn., O’Rielly and Associates, USA (1997)
  17. Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K. and Tuschi T., Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells, Nature 411, 494-498 (2001)
  18. Reynolds A., Leake D., Boese Q., Scaringe S., Marshall W.S. and Khvorova A., Rational siRNA design for RNA interference, Nat Biotechnol., 3, 326-330 (2004)
  19. Altschul S.F., Gish W., Miller W., Myers E.W. and Lipman D.J., Basic local alignment search tool, J. Mol. Biol., 215, 403–410 (1990)
  20. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W. and Lipman D.J., Gapped BLAST and PSI- BLAST: A new generation of protein database search programs, Nucleic Acids Res., 25, 3389-3402 (1997)
  21. Griffiths-Jones S., The microRNA Registry, Nucleic Acids Res., 32, D109-D111 (2004)
  22. Griffiths-Jones S., Saini H.K., van Dongen S. and Enright A.J., miRBase: Tools for microRNA genomics, Nucleic Acids Res., 36, D154-D158 (2008)
  23. Jeffrey R., Applied Microsoft: NET Framework Programming, Microsoft Press, Washington, 21-34 (2002)
  24. Naito Y., Yamada T., Ui-Tei K., Morishita S. and Saigo K., siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference, Nucleic Acids Res, 32(2), W124-W129 (2004)
  25. Park Y., Park S.M., Choi Y.C., Lee D., Won M. and Kim Y.J., AsiDesigner: exon-based siRNA design server considering alternative splicing, Nucleic Acids Research,36, W97–W103 (2008)
  26. Yiu S.M., Wong P.W.H., Lam T.W., Mui Y.C., Kung H.F., Lin M. and Cheung Y.T., Filtering of Ineffective siRNAs and improved siRNA Design Tool, Bioinformatics, 21 (2), 144-151(2005)