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Volumn 9, Issue 1, 2017, Pages 23-30

A computational approach to design potential antiviral RNA for 3'utr post transcriptional gene silencing of different strains of zika virus

Author keywords

3' UTR region; Antiviral RNA; RNAi technology; SiRNA; Zika virus

Indexed keywords

SMALL INTERFERING RNA; VIRUS RNA;

EID: 85010644650     PISSN: 09751483     EISSN: 09751505     Source Type: Journal    
DOI: 10.5530/jyp.2017.9.5     Document Type: Article
Times cited : (5)

References (45)
  • 1
    • 49749225192 scopus 로고
    • Zika virus. I. Isolations and serological specificity
    • Dick GW, Kitchen SF, Haddow AJ. Zika virus. I. Isolations and serological specificity. Trans R Soc Trop Med Hyg. 1952;46(5):509-20.
    • (1952) Trans R Soc Trop Med Hyg , vol.46 , Issue.5 , pp. 509-520
    • Dick, G.W.1    Kitchen, S.F.2    Haddow, A.J.3
  • 3
    • 0014508499 scopus 로고
    • Isolation of Zika Virus from Aedes aegypti mosquitoes in Malaysia
    • Marchette NJ, Garcia R, Rudnick A. Isolation of Zika Virus from Aedes aegypti mosquitoes in Malaysia. Am J Trop Med Hyg. 1969;18(3):411-5.
    • (1969) Am J Trop Med Hyg , vol.18 , Issue.3 , pp. 411-415
    • Marchette, N.J.1    Garcia, R.2    Rudnick, A.3
  • 4
    • 0019740135 scopus 로고
    • Zika virus, a cause of fever in Central Java, Indonesia
    • Olson JG, Ksiazek TG, Suhandiman, Triwibowo. Zika virus, a cause of fever in Central Java, Indonesia. Trans R Soc Trop Med Hyg. 1981;75(3):389-93.
    • (1981) Trans R Soc Trop Med Hyg , vol.75 , Issue.3 , pp. 389-393
    • Olson, J.G.1    Ksiazek, T.G.2    Suhandiman, T.3
  • 6
    • 48749093929 scopus 로고    scopus 로고
    • Genetic and serologic properties of Zika virus associated with an epidemic, Yep State, Micronesia, 2007
    • Lanciotti RS, Kosoy OL, Laven JJ, Velez JO, Lambert AJ, Johnson AJ, et al. Genetic and serologic properties of Zika virus associated with an epidemic, Yep State, Micronesia, 2007. Emerg Infect Dis. 2008;14(8):1232-9.
    • (2008) Emerg Infect Dis , vol.14 , Issue.8 , pp. 1232-1239
    • Lanciotti, R.S.1    Kosoy, O.L.2    Laven, J.J.3    Velez, J.O.4    Lambert, A.J.5    Johnson, A.J.6
  • 8
    • 85010637106 scopus 로고    scopus 로고
    • Zika reaches Bangladesh. The Times of India [cited 2016 Mar 22
    • Zika reaches Bangladesh. The Times of India [cited 2016 Mar 22]. Available from: http://timesofindia.indiatimes.com/life-style/health-fitness/health-news/Zika-reaches-Bangladesh/articleshow/51511450.cms?.
  • 9
    • 70249130933 scopus 로고    scopus 로고
    • Zika virus outside Africa
    • Hayes EB. Zika virus outside Africa. Emerg Infect Dis. 2009;15(9):1347-50.
    • (2009) Emerg Infect Dis , vol.15 , Issue.9 , pp. 1347-1350
    • Hayes, E.B.1
  • 12
    • 84964276686 scopus 로고    scopus 로고
    • Zika virus and birth defects-reviewing the evidence for causality
    • Rasmussen SA, Jamieson DJ, Honein MA, Petersen LR. Zika Virus and Birth Defects-Reviewing the Evidence for Causality. N Engl J Med. 2016;374(20):1981-7.
    • (2016) N Engl J Med , vol.374 , Issue.20 , pp. 1981-1987
    • Rasmussen, S.A.1    Jamieson, D.J.2    Honein, M.A.3    Petersen, L.R.4
  • 13
    • 85010636596 scopus 로고    scopus 로고
    • CDC Concludes Zika Causes Microcephaly and Other Birth Defects. Centers for Disease Control and Prevention. [updated 2016 Apr 13; cited 2016 Apr 13
    • CDC Concludes Zika Causes Microcephaly and Other Birth Defects. Centers for Disease Control and Prevention. [updated 2016 Apr 13; cited 2016 Apr 13]. Available from: http://www.cdc.gov/media/releases/2016/s0413-zika-microcephaly. html.
  • 14
    • 85010681161 scopus 로고    scopus 로고
    • Zika Virus, Microcephaly and Guillain-Barré Syndrome. World Health Organization. [cited 2016 Apr 7
    • Zika Virus, Microcephaly and Guillain-Barré Syndrome. World Health Organization. [cited 2016 Apr 7]. Available from: http://www.who.int/emergencies/zika-virus/situation-report/7-april-2016/en/.
  • 15
    • 85010633596 scopus 로고    scopus 로고
    • Bangladesh still free from Zika virus. The daily observer [updated 2016 Jan 31; cited 2016 May 4
    • Bangladesh still free from Zika virus. The daily observer [updated 2016 Jan 31; cited 2016 May 4]. Available from: http://www.observerbd.com/2016/01/31/133894.php.
  • 17
    • 80053317134 scopus 로고    scopus 로고
    • Functional RNA elements in the dengue virus genome
    • Gebhard LG, Filomatori CV, Gamarnik AV. Functional RNA elements in the dengue virus genome. Viruses, 2011;3(9):1739-56.
    • (2011) Viruses , vol.3 , Issue.9 , pp. 1739-1756
    • Gebhard, L.G.1    Filomatori, C.V.2    Gamarnik, A.V.3
  • 18
    • 20744431725 scopus 로고    scopus 로고
    • Control of Translation by the 5'-and 3'-terminal regions of the dengue virus genome
    • Chiu WW, Kinney RM, Dreher TW. Control of Translation by the 5'-and 3'-terminal regions of the dengue virus genome. J Virol. 2005;79(13):8303-15.
    • (2005) J Virol , vol.79 , Issue.13 , pp. 8303-8315
    • Chiu, W.W.1    Kinney, R.M.2    Dreher, T.W.3
  • 19
    • 33947379655 scopus 로고    scopus 로고
    • Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses
    • Kuno G, Chang GJ. Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses. Arch Virol, 2007;152(4):687-96.
    • (2007) Arch Virol , vol.152 , Issue.4 , pp. 687-696
    • Kuno, G.1    Chang, G.J.2
  • 20
    • 33747344212 scopus 로고    scopus 로고
    • A 5' RNA element promotes dengue virus RNA synthesis on a circular genome
    • Filomatori CV, Lodeiro MF, Alvarez De, Samsa MM, Pietrasanta L, Gamarnik AV. A 5' RNA element promotes dengue virus RNA synthesis on a circular genome. Genes Dev. 2006;20(16):2238-49.
    • (2006) Genes Dev , vol.20 , Issue.16 , pp. 2238-2249
    • Filomatori, C.V.1    Lodeiro, M.F.2    Samsa, M.M.3    Pietrasanta, L.4    Gamarnik, A.V.5
  • 22
    • 57049096375 scopus 로고    scopus 로고
    • A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity
    • Pijlmam GP, Funk A, Kondratieva N, Leung J, Torres S, van der Aa L, Liu WJ, et al. A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity. Cell Host Microbe. 2008;4(6):579-91.
    • (2008) Cell Host Microbe , vol.4 , Issue.6 , pp. 579-591
    • Pijlmam, G.P.1    Funk, A.2    Kondratieva, N.3    Leung, J.4    Torres, S.5    Van Der Aa, L.6    Liu, W.J.7
  • 23
    • 0031849664 scopus 로고    scopus 로고
    • Identification of specific nucleotide Sequences within the conserved 3'-SL in the dengue type-2 virus genome required for replication
    • Zeng L, Falgout B, Markoff L. Identification of specific nucleotide Sequences within the conserved 3'-SL in the dengue type-2 virus genome required for replication. J Virol. 1998;72(9):7510-22.
    • (1998) J Virol , vol.72 , Issue.9 , pp. 7510-7522
    • Zeng, L.1    Falgout, B.2    Markoff, L.3
  • 24
    • 85010656235 scopus 로고    scopus 로고
    • The Nobel Prize in Physiology or Medicine 2006. Nobelprize.org [cited 2016 Apr 4]
    • The Nobel Prize in Physiology or Medicine 2006. Nobelprize.org [cited 2016 Apr 4]. Available from: http://www.nobelprize.org/nobel-prizes/medicine/laureates/2006/.
  • 25
    • 84934435982 scopus 로고    scopus 로고
    • Swiss army knives: Non-canonical functions of nuclear Drosha and Dicer
    • Burger K, Gullerova M. Swiss army knives: non-canonical functions of nuclear Drosha and Dicer. Nat Rev Mol Cell Biol. 2015;16(7):417-30.
    • (2015) Nat Rev Mol Cell Biol , vol.16 , Issue.7 , pp. 417-430
    • Burger, K.1    Gullerova, M.2
  • 26
    • 84865639678 scopus 로고    scopus 로고
    • The PEI-introduced C S shell/PMMA core nanoparticle for silencing the expression of E6/E7 oncogenes in human cervical cells
    • Saengkrit N, Sanitrum P, Woramongkolchai N, Saesoo S, Pimpha N, Chalenwlert-Umpon S, et al. The PEI-introduced C S shell/PMMA core nanoparticle for silencing the expression of E6/E7 oncogenes in human cervical cells. Carbohydr Polym. 2012;90(3):1323-9.
    • (2012) Carbohydr Polym , vol.90 , Issue.3 , pp. 1323-1329
    • Saengkrit, N.1    Sanitrum, P.2    Woramongkolchai, N.3    Saesoo, S.4    Pimpha, N.5    Chalenwlert-Umpon, S.6
  • 28
    • 77952584927 scopus 로고    scopus 로고
    • RNAi therapeutics for CNS disorders
    • Boudreau RL, Davidson BL. RNAi therapeutics for CNS disorders. Brain Res. 2010;1338;112-21.
    • (2010) Brain Res , vol.1338 , pp. 112-121
    • Boudreau, R.L.1    Davidson, B.L.2
  • 29
    • 84883445125 scopus 로고    scopus 로고
    • An in silico approach to design potential siRNA molecules for ICP22 (US1) gene silencing of different strains of human herpes simplex 1
    • Nur SM, Amin MA, Alam R, Hasan MA, Hossain MA, Mannan A. An in silico approach to design potential siRNA molecules for ICP22 (US1) gene silencing of different strains of human herpes simplex 1. J Young Pharm. 2013;5(2):46-49.
    • (2013) J Young Pharm , vol.5 , Issue.2 , pp. 46-49
    • Nur, S.M.1    Amin, M.A.2    Alam, R.3    Hasan, M.A.4    Hossain, M.A.5    Mannan, A.6
  • 30
    • 85027933914 scopus 로고    scopus 로고
    • RNAi-based therapeutic strategies for metabolic disease
    • Czech MP, Aouadi M, Tesz GJ. RNAi-based therapeutic strategies for metabolic disease. Nat Rev Endocrinol. 2011;7:473-84.
    • (2011) Nat Rev Endocrinol , vol.7 , pp. 473-484
    • Czech, M.P.1    Aouadi, M.2    Tesz, G.J.3
  • 31
    • 38049161918 scopus 로고    scopus 로고
    • RNAi for treating hepatitis B viral infection
    • Chen Y, Cheng G, Mahato RI. RNAi for treating hepatitis B viral infection. Pharm Res. 2008;25(1):72-86.
    • (2008) Pharm Res , vol.25 , Issue.1 , pp. 72-86
    • Chen, Y.1    Cheng, G.2    Mahato, R.I.3
  • 32
    • 84867380325 scopus 로고    scopus 로고
    • Therapeutic potential of RNA interference: A new molecular approach to antiviral treatment for hepatitis C
    • Motavaf M, Safari S, Alavian SM. Therapeutic potential of RNA interference: a new molecular approach to antiviral treatment for hepatitis C. J Viral Hepat. 2012;19:757-65.
    • (2012) J Viral Hepat , vol.19 , pp. 757-765
    • Motavaf, M.1    Safari, S.2    Alavian, S.M.3
  • 33
    • 85010634957 scopus 로고    scopus 로고
    • National Center of Biotechnology Information (NCBI) [cited 2016 May 4
    • National Center of Biotechnology Information (NCBI) [cited 2016 May 4]. Available from: http://www.ncbi.nlm.nih.gov.
  • 34
    • 72549097028 scopus 로고    scopus 로고
    • SiDirect 2.0: Update software for designing functional siRNA with reduced seed-dependent off-target effect
    • cited 2016 May 4
    • Naito Y, Yoshimura J, Morishita S, Ui-Tei K. siDirect 2.0: update software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics. 2009;10:392. [cited 2016 May 4]. Available from: http://sidirect2.rnai.jp/design.cgi.
    • (2009) BMC Bioinformatics , vol.10 , pp. 392
    • Naito, Y.1    Yoshimura, J.2    Morishita, S.3    Ui-Tei, K.4
  • 35
    • 1642346273 scopus 로고    scopus 로고
    • Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference
    • Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, OhkiHamazaki 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.
    • (2004) Nucleic Acids Res , vol.32 , Issue.3 , pp. 936-948
    • Ui-Tei, K.1    Naito, Y.2    Takahashi, F.3    Haraguchi, T.4    OhkiHamazaki, H.5    Juni, A.6
  • 36
    • 1642273831 scopus 로고    scopus 로고
    • An algorithm for selection of functional siRNA sequences
    • Amarzguioui M, Prydz H. An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun. 2004;316(4):1050-8.
    • (2004) Biochem Biophys Res Commun , vol.316 , Issue.4 , pp. 1050-1058
    • Amarzguioui, M.1    Prydz, H.2
  • 38
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • cited 2016 May 4
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res. 1994;22(22):4673-80. [cited 2016 May 4]. Available from: http://www.genome. jp/tools/ClustalW.
    • (1994) Nucleic Acid Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 39
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • cited 2016 May 4
    • Altschul SF., Gish W., Miller W., Myers EW., Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10. [cited 2016 May 4]. Available from: http://genome.ucsc.edu/cgi-bin/hgBlat.
    • (1990) J Mol Biol , vol.215 , Issue.3 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3    Myers, E.W.4    Lipman, D.J.5
  • 40
    • 85010699494 scopus 로고    scopus 로고
    • ENDMEMO. DNA/RNA GC content calculator [cited 2016 May 4
    • ENDMEMO. DNA/RNA GC content calculator [cited 2016 May 4]. Available from: http://www.endmemo.com/bio/gc.php.
  • 41
    • 85010692370 scopus 로고    scopus 로고
    • The RNA Institute. The mfold Web Server [cited 2016 May 4
    • The RNA Institute. The mfold Web Server [cited 2016 May 4]. Available from: http://unafold.rna.albany.edu/?q=mfold.
  • 42
    • 85010699481 scopus 로고    scopus 로고
    • RNAcofold WebServer [cited 2016 May 4
    • RNAcofold WebServer [cited 2016 May 4]. Available from: http://rna.tbi.univie. ac.at/cgi-bin/RNAcofold.cgi.
  • 43
    • 58749086586 scopus 로고    scopus 로고
    • Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect
    • Ui-Tei K, Naito Y, Nishi K, Juni A, Saigo K. Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect. Nucleic Acids Res. 2008;36(22):7100-9.
    • (2008) Nucleic Acids Res , vol.36 , Issue.22 , pp. 7100-7109
    • Ui-Tei, K.1    Naito, Y.2    Nishi, K.3    Juni, A.4    Saigo, K.5
  • 45
    • 84883448061 scopus 로고    scopus 로고
    • Design of potential siRNA molecules for hepatitis delta virus gene silencing
    • Singh S, Gupta SK, Nischal A, Khattri S, Pant KK, Seth PK. Design of potential siRNA molecules for hepatitis delta virus gene silencing. Bioinformation. 2012;8(16):749-57.
    • (2012) Bioinformation , vol.8 , Issue.16 , pp. 749-757
    • Singh, S.1    Gupta, S.K.2    Nischal, A.3    Khattri, S.4    Pant, K.K.5    Seth, P.K.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.