Abstract
Objectives
To develop an RNA aptamer specific for the methyltransferase (MTase) of dengue virus (DENV) which is essential for viral genome replication and translation acting directly on N-7 and 2′-O-methylation of the type-I cap structure of the viral RNA.
Results
We identified 2′-fluoro-modified RNA aptamers that can specifically bind DENV serotype 2 (DENV2) MTase using systematic evolution of ligands by exponential enrichment technology. We truncated the chosen aptamer into a 45-mer RNA sequence that can bind DENV2 MTase with K d ~ 28 nM and inhibit N-7 methylation activity of the protein. Moreover, the 45-mer truncated aptamer could not only bind with an K d ~ 15.6 nM but also inhibit methylation activity of DENV serotype 3 (DENV3) MTase. The 45-mer aptamer competitively impeded binding of both DENV2 and DENV3 genomic RNA to MTase of each serotype.
Conclusion
The selected 45-mer truncated RNA aptamer specifically and avidly bound DENV MTase and competitively inhibited its methylation activity, and thus could be useful for the development of anti-DENV agents.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Coleman TM, Wang G, Huang F (2004) Superior 5′ homogeneity of RNA from ATP-initiated transcription under the T7 φ2.5 promoter. Nucleic Acids Res 32:e14
Daffis S et al (2010) 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members. Nature 468:452–456
Diamond MS, Pierson TC (2015) Molecular insight into dengue virus pathogenesis and its implications for disease control. Cell 162:488–492
Dong H, Ray D, Ren S, Zhang B, Puig-Basagoiti F, Takagi Y, Ho CK, Li H, Shi PY (2007) Distinct RNA elements confer specificity to flavivirus RNA cap methylation events. J Virol 81:4412–4421
Dong H, Zhang B, Shi PY (2008) Flavivirus methyltransferase: a novel antiviral target. Antivir Res 80:1–10
Dong H, Chang DC, Xie X, Toh YX, Chung KY, Zou G, Lescar J, Lim SP, Shi PY (2010) Biochemical and genetic characterization of dengue virus methyltransferase. Virology 405:568–578
Durbin AP (2016) A dengue vaccine. Cell 166:1
García-Sastre A (2011) 2 Methylate or not 2 methylate: viral evasion of the type I interferon response. Nat Immunol 2:114–115
Han SR, Lee SW (2017) Inhibition of japanese encephalitis virus (JEV) replication by specific RNA aptamer against JEV methyltransferase. Biochem Biophys Res Commun 483:687–693
Iglesias NG, Filomatori CV, Gamarnik AV (2011) The F1 motif of dengue virus polymerase NS5 is involved in promoter-dependent RNA synthesis. J Virol 85:5745–5756
Jung SN, Kang SK, Yeo GH, Li HY, Jiang T, Nah JW, Bok JD, Cho CS, Choi YJ (2015) Targeted delivery of vaccine to dendritic cells by chitosan nanoparticles conjugated with a targeting peptide ligand selected by phage display technique. Macromol Biosci 15:395–404
Keefe AD, Pai S, Ellington A (2010) Aptamers as therapeutics. Nat Rev Drug Discov 9:537–550
Kim SH, Yang IY, Jang SH, Kim J, Truong TT, Van Pham T, Truong NU, Lee KY, Jang YS (2013) C5a receptor-targeting ligand-mediated delivery of dengue virus antigen to M cells evokes antigen-specific systemic and mucosal immune responses in oral immunization. Microbes Infect 15:895–902
Kroschewski H (2008) Mutagenesis of the dengue virus type 2 NS5 methyltransferase domain. J Biol Chem 283:19410–19421
Lee CH, Lee YJ, Kim JH, Lim JH, Kim JH, Han W, Lee SH, Noh GJ, Lee SW (2013) Inhibition of hepatitis C virus (HCV) replication by specific RNA aptamers against HCV NS5B RNA replicase. J Virol 87:7064–7074
Mukhopadhyay S, Kuhn RJ, Rossmann MG (2005) A structural perspective of the flavivirus life cycle. Nat Rev Microbiol 3:13–22
Potisopon S et al (2014) The methyltransferase domain of dengue virus protein NS5 ensures efficient RNA synthesis initiation and elongation by the polymerase domain. Nucleic Acids Res 42:11642–11656
Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510
Whitehead SS, Blaney JE, Durbin AP, Murphy BR (2007) Prospects for a dengue virus vaccine. Nat Rev Microbiol 5:518–528
Zhou Y, Ray D, Zhao Y, Dong H, Ren S, Li Z, Guo Y, Bernard KA, Shi PY, Li H (2007) Structure and function of flavivirus NS5 methyltransferase. J Virol 81:3891–3903
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
Züst R et al (2011) Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5. Nat Immunol 12:137–143
Acknowledgements
The present research was conducted by the research fund of Dankook University in Republic of Korea in 2015.
Supporting information
Supplementary Table 1—Sequence of primers.
Supplementary Fig. 1—Enrichment of selected RNA aptamer pool.
Supplementary Fig. 2—Aptamer truncation experiment.
Supplementary Fig. 3—Comparison of amino acid sequence of MTase protein of DENV 1-4 serotypes.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflicts of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Jung, J.I., Han, S.R. & Lee, SW. Development of RNA aptamer that inhibits methyltransferase activity of dengue virus. Biotechnol Lett 40, 315–324 (2018). https://doi.org/10.1007/s10529-017-2462-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10529-017-2462-7