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研究生: 黃彥翔
Huang, Yen-Hsiang
論文名稱: 探討登革病毒NS5蛋白特異性DNA適體在登革病毒診斷和/或治療中的潛在應用
Exploration of dengue virus NS5 protein interacting DNA aptamers for the diagnosis use and/or treatment of dengue virus infection
指導教授: 王憲威
Wang, Shainn-Wei
學位類別: 碩士
Master
系所名稱: 醫學院 - 分子醫學研究所
Institute of Molecular Medicine
論文出版年: 2021
畢業學年度: 109
語文別: 英文
論文頁數: 60
中文關鍵詞: 登革病毒去氧核酸適體NS5蛋白奈米金橫向流免疫色譜分析
外文關鍵詞: Dengue virus, DNA aptamer, NS5 protein, gold nanoparticles, lateral flow assay
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  • 登革病毒(DENV)屬於黃熱病毒科,是具有外套膜的正股RNA病毒。共有四種血清型的登革病毒在全球零散的流行,並有接近40%人口處於被感染風險。感染登革病毒患者大多數是屬於無症狀或是出現輕微發燒類似感冒症狀,少數嚴重者則會出現登革出血熱(DHF)甚至引起休克(DSS)的症狀。迄今,通過世界衛生組織(WHO)認證的DENV疫苗,在使用上仍有安全疑慮,且目前亦無針對DENV的藥物可防治登革病毒感染。為了預防登革病毒的流行,開發高度敏感的登革病毒檢測工具以及找尋有效抑制登革病毒感染的藥物是迫切需要的。登革病毒中的非結構蛋白NS5為RNA聚合酶,對於登革病毒複製有著極重要的功能,並且此蛋白在四種血清型中是高度保守的,因此使用NS5為DENV偵測的評定目標或進行針對DENV的藥物開發應是極佳的選擇。許多研究已經證明,通過 SELEX 技術發現的蛋白質相互作用 DNA 適體(Aptamer),對於多種病毒的檢測和/或治療的會是具有潛力的標靶配體。此外,相較於抗體(Antibody),DNA適體對於側向流為基礎的抗原檢測平台(LFA)的應用,在成本、穩定性和通用化學修飾方面更具有優勢。這些平台通常是以紙張為基礎的生物傳感器並集成在一次性測試設備中,以進行快速側流免疫色譜分析。由於此類平台對輸入樣本量的要求極少,並且可在一步過程中實現經濟高效且高度靈敏的檢測,而後得以透過肉眼觀察結果,這些優勢使側向流條(LFS)成為現場護理(Point-Of-Care)應用的理想選擇。本實驗室在先前的研究中,已篩選出3個能與NS5重組蛋白高親和力結合並具有類似於常規抗體的低解離常數(Kd)的候選適體。在本篇研究中,旨在探索這些適體於治療和/或診斷 DENV 感染中的潛在應用。遺憾的是,我們的結果顯示三個能與NS5結合的適體無法抑制DENV複製。這些適體也被截短以保留預測的結構元素並進行硫代磷酸酯修飾以防止核酸內切酶的攻擊。然而,修飾的適體仍然未能減弱DENV複製。由於全長適體 A3具有最高的親和力能夠在聚合沉澱下拉實驗抓住NS5,我們進一步探索了它在 LFS 中作為檢測配體的可能性用途。為了了解NS5作為檢測抗原的特性,我們測試了病毒NS5蛋白是否可以分泌到上清液或包裝進病毒顆粒以利適體檢測。結果顯示作為病毒非結構蛋白的NS5是細胞內抗原,而不是DENV病毒的可分泌或可包裝至病毒顆粒的蛋白。這表明使用適體 A3開發的檢測工具只能用於檢測受DENV感染細胞中的NS5。因此,我們進一步測試了A3與來自細胞裂解物的變性或非變性NS5的結合關係。我們的結果顯示,通過基於西方墨點法的免疫檢測測定法確定適體A3不能用作檢測變性細胞裂解物中NS5蛋白的一抗配體。然而,適體A3能夠在非變性條件下下拉DENV感染細胞內的NS5蛋白。這與實驗室先前的數據一致,即A3能以高親和力與重組 NS5 蛋白結合,並且可以在酵素連結寡核甘酸試驗(ELONA)測定中專一性檢測40-1000 ng範圍內的細胞內DENV NS5蛋白。由於ELONA分析需要至少3小時以上的樣品處理和檢測,因此也開發了一種基於 LFS以及適體的檢測方法,旨在提高ELONA的檢測時間和靈敏度。對於LFS的設計,使用了生物素化適體A3(A3-AuNPs)偶聯的奈米金顆粒作為檢測配體,而抗NS5多克隆抗體用作測試線上的捕獲抗體,並使用鏈黴親和素(streptavidin)做為控制線,以捕獲側向流動中的A3-AuNPs 複合物。然而,我們的結果顯示即使此LFS對FPLC純化的NS5重組蛋白具有檢測能力,卻未能證明其對來自感染細胞裂解物中NS5的檢測能力。由於我們於聚合物下拉沉澱實驗發現,適體A3 可能與細胞裂解物中的未知成蛋白質發生非特異性相互作用,因此A3的這種非特異性結合活性可能會干擾檢測結果。本研究探討了使用DNA適體檢測或抑制DENV感染的可能性。然而,適體的特異性和半衰期顯示了它們的直接應用需要克服的兩個主要障礙。

    Dengue virus (DENV) is an enveloped, positive sense single-stranded RNA virus belonging to the Flaviviridae family. Four serotypes of DENV have sporadically caused a worldwide epidemic, and nearly 40% of people in the world are at risk of infection. Infected patients may be asymptomatic or experience mild flu symptoms to life-threatening dengue hemorrhagic fever (DHF) with or without shock (DSS). To date, DENV vaccines approved by the World Health Organization (WHO) remain to have safety concerns, and there is no specific medicine for the treatment of infection. To prevent DENV epidemics, highly sensitive virus detection tools and effective drugs are urgently required. The DENV NS5, which is the viral RNA polymerase critical for DENV replication, is highly conserved among 4 serotypes and thus an effective target for diagnosis and/or antiviral therapeutics. Many studies have proven that protein-interacting DNA aptamers, which can be identified by SELEX technology, are potential detecting and/or therapeutic ligands for several viruses. In addition, DNA aptamers in comparison to antibodies have advantages in cost, stability, and versatile chemical modifications to the applications in lateral flow-based antigen detection platforms. These platforms usually integrate a paper-based biosensor in a disposable device for a speedy lateral flow immunochromatographic assay. As such platforms allow cost-effective and highly sensitive detection in one-step process with minimum requirement of input sample volume for visual detection with naked eyes, these advantages make the lateral flow strip (LFS) an ideal choice for point-of-care testing. We have previously identified 3 aptamer candidates that can bind with high affinity to the recombinant NS5 with low Kd similar to regular antibodies. In this study, the potential applications of these aptamers for treatment and/or diagnosis of DENV infection were explored. Unfortunately, our results indicated that the three NS5-interacting aptamers cannot inhibit DENV replication. These aptamers were also truncated to retain predicted structural elements and phosphorothioate modified to prevent endonucleases attack. However, the modified aptamer still failed to attenuate DENV replication. Since the full-length aptamer A3 was capable of pulling down NS5 with the highest affinity, we explored further its use in LFS as a detection ligand. To understand the characteristics of NS5 as a detection antigen, we test whether the NS5 can be secreted to supernatant or packaged into viral particles for aptamers detection. The result indicated that the NS5 is an intracellular antigen, which as a nonstructural viral protein is not a secretable nor packable element of the DENV virus. This pinpointed that the detection tool developed with the aptamer A3 can only be used to target NS5 from infected cells. Consequently, the binding relationship of A3 to denatured or nondenatured NS5 from cell lysates were tested further. our results indicated that the aptamer A3 cannot be used as a primary antibody to detect NS5 protein from denatured cell lysates as determined by Western blotting based immunodetection assay. However, aptamer A3 was capable of pulldown intracellular NS5 of DENV infected cells in a non-denaturing condition. This is consistent to our previous data that A3 binds to a recombinant NS5 with high affinity and could detect intracellular DENV NS5 within the range of 40–1000 ng with specificity in an Enzyme-linked oligonucleotide assay (ELONA). As the ELONA assay required at least 3 hours for sample processing and detection, an aptamer-based LFS detection method was therefore developed with aims to improve the detection time and sensitivity of ELONA. For the design of LFS, the gold-nanoparticles that are conjugated with biotinylated aptamer A3 (A3-AuNPs) were used as the detection ligand, while an anti-NS5 polyclonal antibody was used as the capturing antibody in the test zone and the streptavidin was coated in the control zone to capture the A3-AuNPs complex from the lateral flow. However, our results failed to demonstrate the detection ability of A3 to the NS5 from infected cell lysates but not to the FPLC-purified NS5 recombinant protein. As indicated by a pulldown experiment that aptamer A3 may non-specifically interact with unknown proteins in the cell lysates, it is possible that such a non-specific binding activity of A3 may interfere with the detection outcome. This study explores the possibility of using DNA aptamers to the detection or inhibition of DENV infection. However, the specificity and half-life of aptamers represent two major obstacles to be overcame for their immediate application.

    摘要 ii Abstract iv Acknowledgements vi Figure Index ix Table Index x Introduction 1 Epidemic of Dengue virus 1 Serotypes and Genome Organization of Dengue Virus 2 Therapies for Dengue Virus Infection 3 Detection Tools for Dengue Virus Diagnosis 4 Aptamer and Systematic Evolution of Ligands by Exponential Enrichment (SELEX) 5 Aptamer Applications in Biosensor 6 Aptamer Applications in Therapeutics 7 Lateral flow assay (LFA) 8 Goals and specific aims: 11 Materials and Methods 12 Reagents and Antibodies 12 Cells and virus 16 Aptamer transfection for functional assays 17 Functional inhibition of viral replication 17 Plaque assay 17 Western blot analysis 18 Pull-down assays 19 Preparation of gold nanoparticles (AuNPs) 19 Preparation of AuNPs-aptamer conjugate 20 Salting to optimize the binding conditions of aptamer and AuNPs 20 Preparation of the lateral flow strip and the detection procedure 21 Results 23 Time course evaluation of the DENV protein expression level in Huh7 cells 23 Attenuation of DV2 replication in Huh7 cells was not observed with the immediate presence of the 3 transfected aptamer candidates 23 The DENV2 NS5 protein is an intracellular viral protein, which is not a secretable nor an extracellular viral component 25 The aptamer A3 cannot bind to denatured NS5 protein on the blotting membrane 25 Aptamer A3 can bind to the natural form of NS5 but also interacts with other proteins in the cell lysate 26 Design of the later flow assay (LFA) strip for DENV NS5 detection 27 Characterization of gold nanoparticles (AuNPs) 27 Preparation and optimization of gold nanoparticles-aptamer conjugates (AuNPs-Apt) 28 Application of lateral flow strip for NS5 protein detection 29 Discussion 30 Full length aptamer candidates cannot inhibit DENV replication 30 Modified aptamer candidate cannot inhibit DENV replication 31 Three-dimensional structural simulation may be a better way to truncate aptamers 32 The NS5 protein expression level is low in FBS-free culture medium 32 The aptamer A3 cannot be used as a primary antibody in the Western blotting 33 Non-specific effect of the aptamer A3 34 The aptamer-based LFA strip cannot detect DENV infection 35 NS1 protein of DENV may be a better target for diagnosis 36 References 38 Figures 45 Tables 59 Curriculum Vitae 60 Fig. 1 Time course evaluation of the DENV protein expression levels in Huh7 cells 45 Fig. 2 Analyses of the inhibitory effects of aptamer candidates to DENV2 replication by Western blotting and plaque assay 46 Fig. 3 Analyses of the inhibitory effects of a phosphorothioated aptamer A1 to DENV2 replication by Western blotting and plaque assay 48 Fig. 4 Characterization of the DENV NS5 protein as the intracellular or extracellular viral component 50 Fig. 5 Inability of biotinylated aptamer A3 to bind the recombinant NS5 and the virus-derived NS5 in the denatured Western blotting condition 52 Fig. 6 Ability of aptamer A3 to bind native NS5 protein in the cell lysate 53 Fig. 7 Schematic diagram of the lateral flow assay (LFA) for DENV NS5 detection 54 Fig. 8 Ultraviolet-Visible (UV-Vis) spectroscopy of gold nanoparticles by Nanodrop spectrophotometer 55 Fig. 9 Preparation and optimization of gold nanoparticles-aptamer conjugates (AuNPs-Apt) 56 Fig. 10 Application of lateral flow strip for DENV2 NS5 detection 58 Table 1 Two-dimensional structure of full-length and truncated aptamers 59

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