Jundishapur Journal of Microbiology

Published by: Kowsar

Potential siRNA Molecules for Nucleoprotein and M2/L Overlapping Region of Respiratory Syncytial Virus: In Silico Design

Somayeh Shatizadeh Malekshahi 1 , Ehsan Arefian 2 , Vahid Salimi 1 , Talat Mokhtari Azad 1 and Jila Yavarian 1 , *
Authors Information
1 Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
2 Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, IR Iran
Article information
  • Jundishapur Journal of Microbiology: April 2016, 9 (4); e60047
  • Published Online: April 23, 2016
  • Article Type: Research Article
  • Received: November 3, 2015
  • Revised: December 5, 2015
  • Accepted: February 16, 2016
  • DOI: 10.5812/jjm.34304

To Cite: Shatizadeh Malekshahi S, Arefian E, Salimi V, Mokhtari Azad T, Yavarian J. Potential siRNA Molecules for Nucleoprotein and M2/L Overlapping Region of Respiratory Syncytial Virus: In Silico Design, Jundishapur J Microbiol. 2016 ; 9(4):e60047. doi: 10.5812/jjm.34304.

Abstract
Copyright © 2016, Ahvaz Jundishapur University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/) which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.
1. Background
2. Objectives
3. Materials and Methods
4. Results and Discussion
Acknowledgements
References
  • 1. Martinelli M, Frati ER, Zappa A, Ebranati E, Bianchi S, Pariani E, et al. Phylogeny and population dynamics of respiratory syncytial virus (Rsv) A and B. Virus Res. 2014; 189: 293-302[DOI][PubMed]
  • 2. Tapia LI, Shaw CA, Aideyan LO, Jewell AM, Dawson BC, Haq TR, et al. Gene sequence variability of the three surface proteins of human respiratory syncytial virus (HRSV) in Texas. PLoS One. 2014; 9(3)[DOI][PubMed]
  • 3. Malekshahi SS, Azad TM, Yavarian J, Shahmahmoodi S, Naseri M, Rezaei F. Molecular detection of respiratory viruses in clinical specimens from children with acute respiratory disease in Iran. Pediatr Infect Dis J. 2010; 29(10): 931-3[PubMed]
  • 4. Laganas VA, Dunn EF, McLaughlin RE, Tiong-Yip CL, Yuzhakov O, Isabella VM, et al. Characterization of novel respiratory syncytial virus inhibitors identified by high throughput screen. Antiviral Res. 2015; 115: 71-4[DOI][PubMed]
  • 5. O’Donnell R. Features of respiratory syncytial virus. Paediatr Child Health. 2009; 19(1): 43-7[DOI]
  • 6. Ramilo O. Evolution of prophylaxis: MoAb, siRNA, vaccine, and small molecules. Paediatr Respir Rev. 2009; 10 Suppl 1: 23-5[DOI][PubMed]
  • 7. Salimi V, Hennus MP, Mokhtari-Azad T, Shokri F, Janssen R, Hodemaekers HM, et al. Opioid receptors control viral replication in the airways. Crit Care Med. 2013; 41(1): 205-14[DOI][PubMed]
  • 8. Borchers AT, Chang C, Gershwin ME, Gershwin LJ. Respiratory syncytial virus--a comprehensive review. Clin Rev Allergy Immunol. 2013; 45(3): 331-79[DOI][PubMed]
  • 9. Hardy RW, Harmon SB, Wertz GW. Diverse gene junctions of respiratory syncytial virus modulate the efficiency of transcription termination and respond differently to M2-mediated antitermination. J Virol. 1999; 73(1): 170-6[PubMed]
  • 10. Empey KM, Peebles RJ, Kolls JK. Pharmacologic advances in the treatment and prevention of respiratory syncytial virus. Clin Infect Dis. 2010; 50(9): 1258-67[DOI][PubMed]
  • 11. Faghihloo E, Yavarian J, Jandaghi NZ, Shadab A, Azad TM. Genotype circulation pattern of human respiratory syncytial virus in Iran. Infect Genet Evol. 2014; 22: 130-3[DOI][PubMed]
  • 12. DeVincenzo JP. Harnessing RNA interference to develop neonatal therapies: from Nobel Prize winning discovery to proof of concept clinical trials. Early Hum Dev. 2009; 85(10 Suppl)-5[DOI][PubMed]
  • 13. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 2001; 411(6836): 494-8[DOI][PubMed]
  • 14. Kim DH, Rossi JJ. Strategies for silencing human disease using RNA interference. Nat Rev Genet. 2007; 8(3): 173-84[DOI][PubMed]
  • 15. DeVincenzo JP. The promise, pitfalls and progress of RNA-interference-based antiviral therapy for respiratory viruses. Antivir Ther. 2012; 17(1 Pt B): 213-25[DOI][PubMed]
  • 16. Bora RS, Gupta D, Mukkur TK, Saini KS. RNA interference therapeutics for cancer: challenges and opportunities (review). Mol Med Rep. 2012; 6(1): 9-15[DOI][PubMed]
  • 17. Xu C, Wang J. Delivery systems for siRNA drug development in cancer therapy. Asian J Pharm Sci. 2015; 10(1): 1-12[DOI]
  • 18. Hajeri PB, Singh SK. siRNAs: their potential as therapeutic agents--Part I. Designing of siRNAs. Drug Discov Today. 2009; 14(17-18): 851-8[DOI][PubMed]
  • 19. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, et al. Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol. 2003; 21(6): 635-7[DOI][PubMed]
  • 20. Scacheri PC, Rozenblatt-Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, et al. Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. Proc Natl Acad Sci U S A. 2004; 101(7): 1892-7[DOI][PubMed]
  • 21. Cejka D, Losert D, Wacheck V. Short interfering RNA (siRNA): tool or therapeutic? Clin Sci (Lond). 2006; 110(1): 47-58[DOI][PubMed]
  • 22. Nolte A, Ott K, Rohayem J, Walker T, Schlensak C, Wendel HP. Modification of small interfering RNAs to prevent off-target effects by the sense strand. N Biotechnol. 2013; 30(2): 159-65[DOI][PubMed]
  • 23. Yuan B, Latek R, Hossbach M, Tuschl T, Lewitter F. siRNA Selection Server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res. 2004; 32-4[DOI][PubMed]
  • 24. Lagana A, Shasha D, Croce CM. Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools. Front Bioeng Biotechnol. 2014; 2: 65[DOI][PubMed]
  • 25. Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 2004; 32(3): 936-48[DOI][PubMed]
  • 26. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A. Rational siRNA design for RNA interference. Nat Biotechnol. 2004; 22(3): 326-30[DOI][PubMed]
  • 27. Jagla B, Aulner N, Kelly PD, Song D, Volchuk A, Zatorski A, et al. Sequence characteristics of functional siRNAs. RNA. 2005; 11(6): 864-72[DOI][PubMed]
  • 28. Amarzguioui M, Prydz H. An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun. 2004; 316(4): 1050-8[DOI][PubMed]
  • 29. Bernhart SH, Tafer H, Muckstein U, Flamm C, Stadler PF, Hofacker IL. Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol. 2006; 1(1): 3[DOI][PubMed]
  • 30. Fearns R, Peeples ME, Collins PL. Increased expression of the N protein of respiratory syncytial virus stimulates minigenome replication but does not alter the balance between the synthesis of mRNA and antigenome. Virology. 1997; 236(1): 188-201[DOI][PubMed]
  • 31. Collins PL, Hill MG, Cristina J, Grosfeld H. Transcription elongation factor of respiratory syncytial virus, a nonsegmented negative-strand RNA virus. Proc Natl Acad Sci U S A. 1996; 93(1): 81-5[PubMed]
  • 32. Cowton VM, McGivern DR, Fearns R. Unravelling the complexities of respiratory syncytial virus RNA synthesis. J Gen Virol. 2006; 87: 1805-21[DOI][PubMed]
  • 33. Kanasty RL, Whitehead KA, Vegas AJ, Anderson DG. Action and reaction: the biological response to siRNA and its delivery vehicles. Mol Ther. 2012; 20(3): 513-24[DOI][PubMed]
  • 34. Schneider WL, Roossinck MJ. Genetic diversity in RNA virus quasispecies is controlled by host-virus interactions. J Virol. 2001; 75(14): 6566-71[DOI][PubMed]
  • 35. Villegas-Rosales PM, Mendez-Tenorio A, Ortega-Soto E, Barron BL. Bioinformatics prediction of siRNAs as potential antiviral agents against dengue viruses. Bioinformation. 2012; 8(11): 519-22[DOI][PubMed]
  • 36. Raza A, Shareef H, Salim H, Khushal R, Bokhari H. Selection of predicted siRNA as potential antiviral therapeutic agent against influenza virus. Bioinformation. 2011; 6(9): 340-3[PubMed]
  • 37. Naito Y, Nohtomi K, Onogi T, Uenishi R, Ui-Tei K, Saigo K, et al. Optimal design and validation of antiviral siRNA for targeting HIV-1. Retrovirology. 2007; 4: 80[DOI][PubMed]
  • 38. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, et al. 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods. 2006; 3(3): 199-204[DOI][PubMed]
  • 39. Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, et al. Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA. 2006; 12(7): 1179-87[DOI][PubMed]
  • 40. Kirchner R, Vogtherr M, Limmer S, Sprinzl M. Secondary structure dimorphism and interconversion between hairpin and duplex form of oligoribonucleotides. Antisense Nucleic Acid Drug Dev. 1998; 8(6): 507-16[PubMed]
  • 41. Schroeder SJ. Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships. J Virol. 2009; 83(13): 6326-34[DOI][PubMed]
  • 42. Ameres SL, Martinez J, Schroeder R. Molecular basis for target RNA recognition and cleavage by human RISC. Cell. 2007; 130(1): 101-12[DOI][PubMed]
  • 43. Hu X, Hipolito S, Lynn R, Abraham V, Ramos S, Wong-Staal F. Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus. Nucleic Acids Res. 2004; 32(15): 4609-17[DOI][PubMed]
Creative Commons License Except where otherwise noted, this work is licensed under Creative Commons Attribution Non Commercial 4.0 International License .

Search Relations:

Author(s):

Article(s):

Create Citiation Alert
via Google Reader

Readers' Comments