JGV Papers in Press. Published May 14, 2014 as doi:10.1099/vir.0.066084-0
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Delivery of anti-viral siRNA with gold-nanoparticles inhibits dengue virus infection in vitro
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Running title: AuNPs deliver anti-dengue siRNA
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Amber M. Paul1, Yongliang Shi2, Dhiraj Acharya1, Jessica R. Douglas1, Amanda Cooley1, John
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F. Anderson3, Faqing Huang2 and Fengwei Bai1*
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Department of Biological Sciences, 2Department of Chemistry and Biochemistry, University of
Southern Mississippi, Hattiesburg, MS 39406, USA.
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06504, USA
Department of Entomology, Connecticut Agricultural Experiment Station, New Haven, CT
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Word count (Summary): 162 words
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Word count (Main Text): 4330 words
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Journal’s Content’s Category: Human and Animal virus- Positive-stranded RNA
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Number of figure: 5 and number of table: 0.
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Corresponding Author: Fengwei Bai, Ph.D., Department of Biological Sciences, The University of Southern Mississippi, 118 College Drive # 5018, Hattiesburg, MS 39406, USA. Email:
[email protected]; Telephone 601-266-4748; Fax: 601-266-5797
AuNPs deliver anti-Dengue siRNA
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Summary
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Dengue virus (DENV) infection in humans can cause flu-like illness, life threatening
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hemorrhagic fever, or even death. There is no specific anti-DENV therapeutic or approved
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vaccine currently available, partially due to the possibility of antibody-dependent enhancement
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reaction. Small interfering RNAs (siRNAs) that target specific viral genes are considered a
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promising therapeutic alternative against DENV infection. However, in vivo, siRNAs are
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vulnerable to degradation by serum-nucleases and rapid renal excretion due to their small size
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and anionic character. To enhance siRNA delivery and stability, we complexed anti-DENV
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siRNAs with biocompatible gold nanoparticles (AuNPs) and tested them in vitro. We found that
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cationic AuNP-siRNA complexes can enter Vero cells and significantly reduce DENV-serotype
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2 replication and infectious virion release at both pre- and post-infection conditions. In addition,
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RNase-treated AuNP-siRNA complexes can still inhibit DENV replication, suggesting that
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AuNPs maintain siRNA stability. Collectively, these results demonstrate that AuNPs are able to
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efficiently deliver siRNAs and control infection in vitro, indicating a novel anti-DENV strategy.
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Keywords: dengue virus, siRNA delivery, gold nanoparticle
AuNPs deliver anti-Dengue siRNA
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Introduction
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Dengue virus (DENV) is a single-stranded, positive-sense RNA virus belonging to the
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family Flaviviridae. DENV is transmitted to humans primarily by the mosquito vectors, Aedes
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aegypti and Aedes albopictus (Xi et al., 2008). After DENV binds to host cellular receptors, it is
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endocytosed and uncoated within the endosome to release its RNA genome into the cytoplasm,
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where replication of the viral genome and assembly of virions occur (van der Schaar et al.,
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2008). The common symptoms of DENV infection in humans are characterized by fever,
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headache, joint and muscle pain and measle-like rashes (Halstead, 2007; Wilder-Smith et al.,
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2010). Although asymptomatic in most cases, DENV infection can lead to serious disease, such
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as hemorrhagic fever and systemic shock syndrome that can potentially be fatal. There are four
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serotypes of DENV (DENV-1, DENV-2, DENV-3 and DENV-4) and illness can be produced by
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any serotype (Tomashek & Margolis, 2011). Although recovery from infection to one serotype
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provides lifelong immunity against that particular serotype, subsequent infection by other co-
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circulating serotypes may cause an antibody-dependent enhancement reaction, which increases
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the risk of developing severe dengue hemorrhagic fever, shock and even death (Halstead, 1982;
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Kliks et al., 1989). DENV infection has been reported in more than 100 countries, including the
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United States (Gubler, 2002; Ramos et al., 2008; Tomashek & Margolis, 2011). A recent report
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has estimated that 390 million people are infected with DENV worldwide, with 96 million
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people manifesting clinical symptoms of disease (Bhatt et al., 2013).
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Since antibody-dependent enhancement hinders the development of an antibody-based
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vaccine, the development of therapeutics that target replication or expression of the viral genome
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may serve as promising alternatives to control DENV infection. Anti-host receptor (Alhoot et al.,
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2011) and anti-DENV (Stein et al., 2011; Subramanya et al., 2010) small interfering RNAs
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AuNPs deliver anti-Dengue siRNA
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(siRNAs) have considerably advanced both clinical- and laboratory-based applications as
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potential DENV therapeutic alternatives (Idrees et al., 2013). However, efficient delivery of
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siRNAs remains a great challenge for clinical applications. The most common siRNA delivery
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approach is with a lipid-based transfection reagent, whereby the negatively charged siRNA
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duplex binds to the cationic liposome transfection reagent, which allows for cell membrane
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endocytosis, micelle formation and intracellular release of the siRNA into the cytosol (Zuhorn et
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al., 2002). Although this method is successful for siRNA delivery in vitro, it is not an ideal
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candidate to use in vivo, as these chemically-based transfection reagents are physiologically toxic
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and could induce cellular stress or aberrant transcriptional profiles (Torchilin, 2005; Zhong et al.,
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2008).
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Recently, gold nanoparticles (AuNPs) have been suggested as promising vehicles to
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deliver siRNA both in vitro and in vivo (Conde et al., 2012; Conde et al., 2013; Mitra et al.,
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2013; Yang et al., 2013). Several advantages make them well suited for safe and efficient
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protection and transport of siRNA: a) biocompatibility (Chithrani & Chan, 2007; Lewinski et
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al., 2008); b) ease of preparation and facile surface modification (Elbakry et al., 2009; Lee et al.,
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2011; Song et al., 2010); and c) high siRNA loading capacity. In this study, we constructed novel
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anti-DENV AuNP-siRNA nanoplexes and found that AuNPs are able to promote siRNA stability
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and efficiently deliver anti-DENV siRNAs in vitro.
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AuNPs deliver anti-Dengue siRNA
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Results
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Antiviral siRNAs efficiently inhibit DENV replication
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Two antiviral siRNAs (si-1 and si-3) were designed to target the most prevalent dengue
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serotype, DENV-2. Vero cells were transfected with siRNA (20 nM) using a lipofectamine-based
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transfection reagent (TR) and subsequently infected with DENV-2 (multiplicity of infection,
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MOI = 0.1). Sequence scrambled siRNA (siSCRM) was used as a negative control and a
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previously described anti-DENV siRNA (DC-3) was used as a positive control (Stein et al.,
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2011). At 48 hr post-infection, the cells were harvested for total RNA extraction, cDNA
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synthesis and subjected to real-time quantitative polymerase chain reaction (Q-PCR) for the
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measurement of DENV capsid gene and cellular β-actin gene expression. The Q-PCR results
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showed that si-1, si-3 and DC-3 significantly reduced DENV-2 capsid gene expression compared
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to the control, in which cells were treated with TR only (p < 0.001, Fig. 1a). In contrast, siSCRM
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did not show any inhibitory effect (p = ns, Fig. 1a), suggesting that siRNA inhibition is
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sequence-specific. To test if infectious viral particles released from the infected cells were
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reduced with siRNA transfection, the media were quantified by a plaque forming assay (plaque
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forming unit, PFU) and an immunostaining assay (focus forming unit, FFU), with the latter
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detecting viral envelope (E) protein expression. Since the DENV-2 genome shares some
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homology with other DENV-serotypes, the antiviral effect of si-1 and si-3 (20 nM) was also
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evaluated against the replication of DENV-1, DENV-3 and DENV-4 (MOI = 0.1). Q-PCR
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analysis showed that si-1 and si-3 were able to inhibit DENV-3 and DENV-4 replication, but
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showed no inhibitory activity for DENV-1, compared to the control in which cells were treated
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with TR, without siRNA (p < 0.001 and p = ns, Fig. 1d-f). RNA sequence alignment analysis
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suggested that the lack of inhibition of si-1 and si-3 against DENV-1 replication might be due to
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AuNPs deliver anti-Dengue siRNA
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lower homology between their targeting sequences (approximately 50% and 70% respectively,
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data not shown). In summary, these results demonstrated that both si-1 and si-3 were able to
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significantly inhibit replication of DENV serotypes 2, 3 and 4.
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Design and optimization of AuNP complexes for anti-DENV siRNA delivery in vitro
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Recently, AuNPs have been designed and optimized as delivery vehicles for siRNA both
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in vitro and in vivo (Conde et al., 2013; Gilleron et al., 2013; Mitra et al., 2013; Yang et al.,
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2013; Zheng et al., 2012). Optimization of AuNPs has been focused on certain properties that
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enhance siRNA delivery and reduce possible cytotoxicity. Such properties include surface
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charge, surface complexity and size of the AuNPs (De Jong & Borm, 2008). In this study, three
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AuNP-siRNA complexes (anionic, neutral and cationic) were prepared by a novel layer-by-layer
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(LbL) approach to deliver anti-DENV siRNA into Vero cells. To confirm each layer was
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successfully coated on the AuNPs, the AuNP complexes were characterized by UV-Vis spectra,
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DLS and Zeta potential. AuNPs and AuNP-PEI-siRNAs (PEI: polyethylenimine) were measured
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by UV-Vis, which disclosed a shift in the Surface Plasmon Resonance (SPR) peaks with the
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addition of siRNA (Fig. 2a). DLS measured the hydrodynamic diameters of the different
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complexes: AuNPs (12.92 nm), AuNP-PEI (24.97 nm), AuNP-PEI-siRNA (41.79 nm), and
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AuNP-PEI-siRNA-PEI (43.25 nm), which indicated that the diameters increased with the
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addition of each layer (Fig. 2b). AuNPs were first coated with an inner layer of HS-PEI (thiol-
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labeled PEI) via Au-S bonds, rendering the particles cationic. The negatively charged siRNAs
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were then coated on the AuNP-PEIs through electrostatic interactions, rendering the complexes
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anionic. Adjusting the concentration of the outer layer PEI with the AuNP-PEI-siRNA
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complexes (Fig. 2c) altered the overall charge from negative to positive. Zeta potential
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AuNPs deliver anti-Dengue siRNA
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determined the surface charges of the complexes: AuNPs (-34.9 mV), AuNP-PEI (46.9 mV),
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AuNP-PEI-siRNA (-38.8 mV) and AuNP-PEI-siRNA-PEI (53.3 mV) (Fig. 2d, neutral charge
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data not shown). These results demonstrated the optimization of AuNPs and successful synthesis
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of AuNP-siRNA complexes.
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To test the effect of surface charge on siRNA delivery efficiency, we treated Vero cells
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with anionic (-40 mV), neutral (0 mV) and cationic (+40 mV) AuNP-siRNA complexes (20 nM)
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for 48 hrs and subsequently infected them with DENV-2 (MOI = 0.1) for an additional 48 hrs. Q-
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PCR analysis showed that cationic AuNP-si-1 and AuNP-si-3 complexes significantly reduced
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DENV-2 replication (p < 0.005, Fig. 2e). While anionic AuNP-si-3, but not AuNP-si-1
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complexes, also inhibited DENV-2 replication compared to the control, in which cells were
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infected with DENV-2 only (p < 0.05, Fig. 2e). In contrast, neither the neutrally charged AuNP-
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si-1 nor the AuNP-si-3 complex inhibited viral replication, suggesting inefficient delivery of
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siRNAs by neutral AuNP-siRNA complexes (Fig. 2e). In summary, these results showed that
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cationic AuNP-siRNA complexes could effectively deliver anti-DENV siRNAs into cells.
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To confirm cationic AuNP-siRNAs are able to enter cells, Vero cells were cultured with
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cationic AuNP-si-1 (80nM) for 48 hrs and subsequently infected with DENV-2 (MOI = 0.1) for
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an additional 72 hrs. Ultra-thin sections embedded in epoxy resin were imaged using a
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transmission electron microscope (TEM). The TEM images showed that AuNPs localized within
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the cytoplasm of Vero cells (Fig. 2f, g and inserts), which implied AuNP complexes were able to
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deliver siRNAs into the cells.
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Cationic AuNP-siRNA complexes are non-toxic to Vero cells
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AuNPs deliver anti-Dengue siRNA
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AuNPs have been noted as biocompatible vehicles for drug delivery (Connor et al., 2005;
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Shukla et al., 2005). However, they also have been suggested to have some cytotoxicity due to
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their cationic polarity and surface modifications (Gerber et al., 2013; Goodman et al., 2004). To
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exclude the possibility that inhibition of DENV-2 replication was due to the AuNP-siRNA
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complexes causing Vero cell death, we assessed the cytotoxicity of the AuNP-siRNA complexes
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when exposed to Vero cells. We incubated AuNP-siRNA complexes (+40 mV) with Vero cells
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at the same experimental conditions and concentrations that were used for the pre-treatment
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transfection assays, without DENV-2 infection. Cellular morphology was imaged and cell
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number was quantified by using DAPI-nuclear staining and examined under a confocal
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microscope. No morphological changes (Fig. 3a, i and ii) or cell number reduction (Fig. 3b) were
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observed with any AuNP-siRNA treated samples compared to the untreated control. To further
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confirm this, cellular lactate dehydrogenase (LDH) released from broken cell membrane was
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also measured. The LDH cytotoxicity assay results showed no significant toxicity (≤ 6.5%
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cytotoxicity), which was similar with the untreated cell control (2% cytotoxicity, Fig. 3c). These
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data suggested that Vero cells exposed to AuNP-siRNA complexes have negligible cytotoxicity,
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which indicated that inhibition of DENV-2 replication was due to siRNA mediated RNA
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interference.
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Cationic AuNP-siRNA complexes inhibit DENV-2 infection in both pre- and post-infection
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conditions
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To further confirm that cationic AuNP-siRNA complexes inhibit DENV-2 replication, we
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pre-treated Vero cells with cationic AuNP-siRNAs (+40 mV) at 20 nM and 80 nM for 48 hrs and
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subsequently infected them with DENV-2 (MOI = 0.1) for an additional 48 and 72 hrs, followed
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AuNPs deliver anti-Dengue siRNA
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by Q-PCR analysis. The results showed that compared to DENV-2 only infected controls,
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AuNP-si-1 (20 nM) reduced DENV replication approximately 2-fold at both 48 and 72 hrs (p