基于核酸适体构象变化的荧光钾离子检测

噻唑橙(Thiazole orange,TO)在游离状态下几乎没有荧光,但当其与富G的DNA结合后,会产生很强的荧光增强效应。据此,利用TO识别有无钾离子存在时富G序列的构象变化,建立了一种基于核酸适体(Aptamer)构象效应进行钾离子检测的无标记荧光检测方法。在优化实验条件下,钾离子浓度在(1～60)×10-6mol/L和(4～9)×10-4mol/L范围内与荧光强度呈良好的线性关系,检出限(S/N=3)为2.2×10-7mol/L。对Li+、Na+、Ca2+、Mg2+、NH4+5种离子进行对照试验的结果表明,该方法不仅具有较好的灵敏度还具有较好的选择性,且无需对DNA进行标记,成本低,分析速度快。     

核酸适配体功能化近红外量子点结合流式细胞术快速检测白血病细胞

利用作为肿瘤细胞识别分子的核酸适配体(Aptamer)的高特异性和高亲和力以及作为信号报告单元的近红外量子点(QDs)的高荧光发射强度和低生物背景干扰特性,构建了一种基于Aptamer功能化近红外QDs的新型纳米荧光探针,并进一步结合流式细胞术在单细胞荧光分析方面的高通量、简便和快速等优势,建立了一种检测白血病细胞的新方法.以基于Cell-SELEX(Cell-based systematic evolution of ligands by exponential enrichment)技术针对CCRF-CEM人急性白血病细胞筛选的特异性Aptamer Sgc8c为模型,构建了Sgc8c-QDs探针,其仅需与细胞样品培育30 min即可实现对缓冲液和血清中靶细胞的简单、快速和高特异性检测.与传统荧光染料标记技术相比,该方法不仅大大提高了分析灵敏度,还显示出对血清等复杂生物样品的高适用性和优良检测性能.鉴于Cell-SELEX技术在其它白血病细胞Aptamer筛选领域的应用潜力,该方法有望作为一种通用技术在白血病诊断及预后监测等方面发挥重要作用.     

双链荧光核酸适体探针用于蛋白质的简便快速检测

发展了一种基于双链荧光核酸适体(F-Aptamer)探针的简单快速检测蛋白质的分析方法.该双链荧光Aptamer探针由一条带荧光标记的Aptamer探针和带猝灭标记的互补DNA组成,当靶蛋白存在时,能形成比双链荧光Aptamer探针更稳定的F-Aptamer/蛋白质复合物,并发出荧光,从而实现对蛋白质的简便快速检测,检测线性范围为6~100 nmol/L,检出限为6 nmol/L.该方法设计简单,对核酸适体分子的大小和空间结构没有要求,可作为一种通用的基于F-Aptamer识别机理的蛋白质检测方法.     

比率型荧光纸芯片快速检测赭曲霉毒素A

采用双荧光染料构建了一种新型比率型荧光纸芯片,将荧光染料Cy3和Cy5分别作为荧光供体和荧光受体,以二者间荧光共振能量转移(FRET)引起的荧光变化实现对赭曲霉毒素A(OTA)的一步法快速灵敏检测。将标记Cy3基团的核酸适配体(Aptamer)和标记Cy5基团的辅助DNA(aDNA)同时与纸芯片表面的互补DNA(CDNA)形成特定双链结构而发生FRET,导致Cy3荧光减弱而Cy5荧光增强。当存在OTA时,Aptamer与OTA结合后脱离双链结构,Cy3和Cy5两个荧光团远离,Cy3荧光增强而Cy5荧光减弱。实验结果表明,此系统的比率信号F₅₆₇/F₆₆₉(F₅₆₇/F₆₆₉为Cy3在567 nm处的荧光强度值与Cy5在669 nm处荧光强度值的比值)与OTA浓度在10～300 nmol/L范围内呈良好的线性响应,检出限(S/N=3)为5.6 nmol/L,花生和红酒样品中OTA的加标回收率为92.7%～107.6%。此传感器为食品中OTA等霉菌毒素污染检测提供了一种高效便捷的新方法。     

结晶紫光谱探针法无标记检测Pb~(2+)的DNA生物传感器

基于Pb~(2+)与凝血酶适配体(Thrombin Aptamer,TBA)特异性结合,以及结晶紫(CV)与凝血酶适配体、G-四链体结合后荧光信号的差异,建立了一种简单、灵敏、无需标记检测Pb2+的DNA生物传感器。实验研究了不同浓度的Pb~(2+)引起CV/TBA体系荧光强度变化的规律,考察了DNA序列、TBA与CV浓度比,以及稳定时间等因素对检测灵敏度的影响。实验结果表明:大多数金属离子无明显干扰,在最优实验条件下,Pb~(2+)浓度在5~50nmol/L范围内与体系荧光强度的变化呈良好的线性关系(r=0.9984),检测限(S/N=3)为2.0×10~(-9) mol/L。     

基于聚合酶反应和发夹型核酸适体的蛋白质荧光检测新方法

设计合成了一种发夹型核酸适体(Aptamer), 结合聚合酶反应建立了蛋白质荧光分析新方法. 该核酸适体同时作为蛋白质配体和聚合反应模板, 与靶蛋白特异结合后, 其构象发生了变化, 启动聚合反应, 从而在未直接标记核酸适体的情况下, 通过监测聚合反应进程来检测蛋白质的浓度. 采用该方法检测凝血酶的线性范围为0.5~8 nmol/L, 检测下限为0.5 nmol/L, 为蛋白质检测提供了一种简便快速的非直接标记的荧光分析方法, 有望在蛋白质组学的研究中得到广泛的应用.     

钾离子掺杂对石墨型氮化碳光催化剂能带结构及光催化性能的影响

以双氰胺和氢氧化钾为原料制备了能带可控的钾离子掺杂石墨型氮化碳(g-C3N4)光催化剂,并与碱处理的g-C3N4及g-C3N4/KOH复合催化剂进行了对比。采用X射线衍射(XRD)光谱、紫外-可见(UV-Vis)光谱、傅里叶变换红外(FTIR)光谱、N2吸附、电感耦合等离子体-原子发射光谱(ICP-AES)、荧光(PL)光谱、X 光电子能谱(XPS)等分析手段对制备的催化剂进行了表征。结果表明,钾离子含量对氮化碳催化剂的价带及导带位置有显著影响。此外,钾离子的引入抑制了氮化碳晶粒的生长,提高了氮化碳的比表面积以及对可见光的吸收,降低了光生电子-空穴对的复合几率。以染料罗丹明B的降解为探针反应系统研究了钾离子掺杂对g-C3N4在可见光下催化性能的影响,研究了光催化反应机理。结果表明,钾离子掺杂后氮化碳的光催化性能显著提高。制备的钾离子掺杂氮化碳催化剂表现出良好的结构及催化稳定性。     

基于核酸适配体荧光标记及荧光共振能量转移检测赭曲霉毒素A

本研究基于荧光共振能量转移(Fluorescence Resonance Energy Transfer, FRET)原理,以荧光素(Fluorescein, FAM)标记的核酸适配体(Aptamer)及猝灭基团(Dabycl)标记的互补链(cDNA)为主体,构建了赭曲霉毒素A(Ochratoxin A,OTA)的荧光标记检测方法。该方法对OTA的检测限为0.01μg/mL,OTA浓度在0.01～0.25μg/mL范围内与荧光强度线性关系良好(R²=0.9991),回收率在86.40%～97.50%之间,可用于实际样品的检测。与传统检测方法酶联免疫吸附剂分析相比,本方法具有检测快速、灵敏度高、特异性强等优点,为食品中对人体有害物质的检测提供了一种新思路。     

基于金纳米粒子的动态光散射法检测溶液中的汞离子

发展了种基于汞离子(Hg2+)适配体(Aptamer)免标记金纳米粒子的动态光散射(DLS)法,用于灵敏、选择性的检测溶液中的Hg2+。Aptamer 5’-TTTCTTCTTTCTTCCCCCCTTGTTTGTTGTTT-3’与Hg2+的特异性结合使金纳米粒子失去保护,在含有100 mmol/L NaCl的缓冲溶液中发生聚集,金纳米粒子的平均水合粒径变大。在pH=7.43,110 nmol/L Aptamer,100 mmol/L NaCl,Hg2+与Probe DNA孵育时间为30 min的实验条件下,金纳米粒子水合粒径的变化值("D)与Hg2+的浓度成正比。检出Hg2+的线性范围为0.1 nmol/L~5μmol/L,检出限达0.1 nmol/L。湖水及矿泉水两种水样加标实验表明本方法能够用于实际水样中Hg2+的检测。     

基于离子通量的电位型传感器检测鱼精蛋白

体外循环后精确控制鱼精蛋白用量对抗肝素,是预防鱼精蛋白中毒性反应的关键环节.由于血液中存在高浓度的亲脂性钾离子(如血液中钾离子的浓度约为5mg/L,血细胞中钾离子的浓度高达150mg/L),而传统的聚阳离子选择性电极膜相中含有阳离子位点,在这种情况下,钾离子很容易进入聚合物膜相而干扰鱼精蛋白阳离子的测定.为了克服血液中钾离子的干扰,开发了肝素活化的聚阴离子选择性电极技术,成功实现了鱼精蛋白聚阳离子的检测,高浓度的钾离子不干扰测定.在最佳条件下,该电极对鱼精蛋白聚阳离子的检出限可达0.1mg·L-1,线性范围为0.5~10mg·L-1.     

A highly sensitive fluorescence resonance energy transfer aptasensor for staphylococcal enterotoxin B detection based on exonuclease-catalyzed target recycling strategy

An ultrasensitive fluorescence resonance energy transfer (FRET) bioassay was developed to detect staphylococcal enterotoxin B (SEB), a low molecular exotoxin, using an aptamer-affinity method coupled with upconversion nanoparticles (UCNPs)-sensing, and the fluorescence intensity was prominently enhanced using an exonuclease-catalyzed target recycling strategy. To construct this aptasensor, both fluorescence donor probes (complementary DNA₁–UCNPs) and fluorescence quencher probes (complementary DNA₂–Black Hole Quencher₃ (BHQ₃)) were hybridized to an SEB aptamer, and double-strand oligonucleotides were fabricated, which quenched the fluorescence of the UCNPs via FRET. The formation of an aptamer–SEB complex in the presence of the SEB analyte resulted in not only the dissociation of aptamer from the double-strand DNA but also both the disruption of the FRET system and the restoration of the UCNPs fluorescence. In addition, the SEB was liberated from the aptamer–SEB complex using exonuclease I, an exonuclease specific to single-stranded DNA, for analyte recycling by selectively digesting a particular DNA (SEB aptamer). Based on this exonuclease-catalyzed target recycling strategy, an amplified fluorescence intensity could be produced using different SEB concentrations. Using optimized experimental conditions produced an ultrasensitive aptasensor for the detection of SEB, with a wide linear range of 0.001–1 ng mL⁻¹ and a lower detection limit (LOD) of 0.3 pg mL⁻¹ SEB (at 3σ). The fabricated aptasensor was used to measure SEB in a real milk samples and validated using the ELISA method. Furthermore, a novel aptasensor FRET assay was established for the first time using 30 mol% Mn²⁺ ions doped NaYF₄:Yb/Er (20/2 mol%) UCNPs as the donor probes, which suggests that UCNPs are superior fluorescence labeling materials for food safety analysis.     

A fluorescent molecular switch for room temperature operation based on oligonucleotide hybridization without labeling of probes or targets

A molecular switch was prepared by self-assembly. Neutravidin served as a template that allowed for a biotinylated probe oligonucleotide to be placed adjacent to a biotinylated long-chain linker that was terminated with thiazole orange (TO). Hybridization of probe oligonucleotide with target to form double-stranded DNA resulted in intercalation of the adjacent TO probe. This was a reversible process that could be tracked by fluorescence intensity changes. Formamide was used as a denaturant for double-stranded DNA, and could be used to depress thermal denaturation temperatures. In this work formamide had a dual function, providing for control of hybridization selectivity at room temperature, while concurrently ameliorating non-specific adsorption to improve signal-to-noise when using thiazole orange as a fluorescence signalling agent to determine oligonucleotide hybridization. Room temperature single nucleotide polymorphism (SNP) discrimination for oligonucleotide targets was achieved both in solution and for molecular switches that were immobilized onto optical fibers. In solution, a concentration of 18.5% formamide provided greater than 40-fold signal difference between single-stranded DNA and double-stranded DNA, in contrast to only a 2-fold difference in the absence of formamide. Selectivity for SNP determination in solution was demonstrated using targets of varying lengths including a 141-base PCR amplicon. The improved signal-to-noise achieved by use of formamide is likely due to preferential displacement of dye molecules that are otherwise electrostatically bound to the polyanionic nucleic acid backbone.     

An Aptamer-Based Competitive Fluorescence Quenching Assay for IgE

A simple competitive fluorescence quenching assay based on aptamer was developed for IgE detection. Two DNA probes were used. One is 5′-end fluorescein-labeled IgE aptamer; the other is 3′-end DABCYL-labeled short DNA, which would hybridize with IgE aptamer to quench the fluorescence. In the presence of IgE, the aptamer-IgE complex formed is strong enough to prevent the short DNA probes hybridizing with the bounded aptamer probes, which results in the less decrease of fluorescence intensity. The signal change was found to be proportional to the concentration of IgE from 0.35 to 35 nM with a detection limit of 0.17 nM.     

Study of thiazole orange in aptamer-based dye-displacement assays

We screened a series of RNA and DNA aptamers for their ability to serve in the dye displacement assays in which analytes compete with TO dye. We conclude that, while the performance of the TO dye displacement approach is not always predictable, it is still a simple and sensitive assay to detect binding between RNA aptamers and small molecules. In particular, we describe efficient assays for tobramycin and theophylline, with up to 90% displacement of TO observed, and we describe the first aptameric assay for cAMP. Figure An RNA or DNA aptamer against a molecule (circle) binds TO dye, resulting in a fluorescent complex. Presence of free molecule in solution results in the displacement of TO from the complex and a reduction in fluorescence Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

单分子荧光成像研究凝血酶核酸适体的折叠

通过对固定在表面的TMR标记凝血酶核酸适体进行单分子荧光成像, 在单分子水平上研究了凝血酶核酸适体的折叠. 在有K+存在的条件下, 核酸适体分子与K+结合后发生折叠, 形成G四分体结构, 使得TMR靠近富含鸟嘌呤的G四分体, 并与鸟嘌呤发生电子转移, 从而导致TMR荧光强度降低. 根据TMR的单分子荧光强度观察到不同K+浓度下核酸适体在折叠和无规卷曲两种状态下的分布. 结果表明, 可利用电子转移引起的荧光强度变化在单分子水平上研究核酸适体构象变化, 这一新方法的建立是对常用的单分子荧光共振能量转移(FRET)法的重要补充.     

Target-Dependent Protection of DNA Aptamers against Nucleolytic Digestion Enables Signal-On Biosensing with Toehold-Mediated Rolling Circle Amplification

We report a generalizable strategy for biosensing that takes advantage of the resistance of DNA aptamers against nuclease digestion when bound with their targets, coupled with toehold mediated strand displacement (TMSD) and rolling circle amplification (RCA). A DNA aptamer containing a toehold extension at its 5′-end protects it from 3′-exonuclease digestion by phi29 DNA polymerase (phi29 DP) in a concentration-dependent manner. The protected aptamer can participate in RCA in the presence of a circular template that is designed to free the aptamer from its target via TMSD. The absence of the target leads to aptamer digestion, and thus no RCA product is produced, resulting in a turn-on sensor. Using two different DNA aptamers, we demonstrate rapid and quantitative real-time fluorescence detection of two human proteins: platelet-derived growth factor (PDGF) and thrombin. Sensitive detection of PDGF was also achieved in human serum and human plasma, demonstrating the selectivity of the assay.     

Aptamer switch probe based on intramolecular displacement

A novel aptamer-based molecular probe design employing intramolecular signal transduction is demonstrated. The probe is composed of three elements: an aptamer, a short, partially cDNA sequence, and a PEG linker conjugating the aptamer with the short DNA strand. We have termed this aptamer probe an "aptamer switch probe", or ASP. The ASP design utilizes both a fluorophore and a quencher which are respectively modified at the two termini of the ASP. In the absence of the target molecule, the short DNA will hybridize with the aptamer, keeping the fluorophore and quencher in close proximity, thus switching off the fluorescence. However, when the ASP meets its target, the binding between the aptamer and the target molecule will disturb the intramolecular DNA hybridization, move the quencher away from the fluorophore, and, in effect, switch on the fluorescence. Both ATP and human alpha-thrombin aptamers were engineered to demonstrate this design, and both showed that fluorescence enhancement could be quantitatively mediated by the addition of various amounts of target molecules. Both of these ASPs presented excellent selectivity and prompt response toward their targets. With intrinsic advantages resulting from its intramolecular signal transduction architecture, the ASP design holds promising potential for future applications, such as biochip and in situ imaging, which require reusability, excellent stability, prompt response, and high sensitivity.     

Modified DNA aptamer that binds the (R)-isomer of a thalidomide derivative with high enantioselectivity

A thalidomide-binding aptamer was produced by systematic evolution of ligands by exponential enrichment from a library of non-natural DNA in which thymidine had been replaced with a modified deoxyuridine bearing a cationic functional group via a hydrophobic methylene linker at the C5 position. The additional functional group in the modified DNA aptamer could improve stability against nucleases and increase the binding affinity to thalidomide. The selected aptamer could recognize thalidomide enantioselectively, although a racemic thalidomide-attached gel was used for the selection. Surface plasmon resonance and fluorescence titration studies revealed that the selected modified DNA aptamer and a truncated version bound with an (R)-thalidomide derivative with high enantioselectivity, but not with the (S)-form. The modified group in the DNA aptamer is indispensable for the interaction with thalidomide, as the corresponding natural type DNA bearing the same base sequence showed no binding affinity with (R)- nor (S)-thalidomide. Computational sequence analysis suggested that the selected apatamer (108 mer) could fold into a three-way junction structure; however, truncation of this aptamer (31 mer) revealed that the thalidomide-binding site is a hairpin-bulge region that is a component of one of the arms of the three-way junction structure. The Kd value of the truncated 31 mer aptamer for binding with the (R)-thalidomide derivative was 1.0 microM estimated from fluorescence titration study. The aptamer that can recognize a single enantiomer of thalidomide will be useful as a biochemical tool for the analysis and study of the biological action of thalidomide enantiomers.     

KF polymerase-based fluorescence aptasensor for the label-free adenosine detection

We have developed a simple, inexpensive, and label-free method for the selective detection of adenosine. Klenow fragment polymerase (KF polymerase) is a commonly-used 5' to 3' DNA polymerase, it also has 3' to 5' exonuclease activity that can digest single-stranded DNA. An adenosine binding DNA aptamer was employed, the aptamer was split into two pieces of single-stranded DNA (aptamer-A1 + aptamer-A2). Without the addition of adenosine, aptamer-A1 and aptamer-A2 existed as single-stranded DNA which could be efficiently degraded by the exonuclease activity of KF polymerase. Much reduced background fluorescence was obtained when SYBR Green dye was added. However, in the presence of adenosine, aptamer-A1 and aptamer-A2 bound to adenosine, and hybridization of the complementary sequences resulted in the formation of a duplex DNA structure, which could initiate DNA polymerization. The addition of SYBR Green dye resulted in a very high fluorescence enhancement, which could be used for the quantification of adenosine.     

Structure-switching signaling aptamers

Aptamers are single-stranded nucleic acids with defined tertiary structures for selective binding to target molecules. Aptamers are also able to bind a complementary DNA sequence to form a duplex structure. In this report, we describe a strategy for designing aptamer-based fluorescent reporters that function by switching structures from DNA/DNA duplex to DNA/target complex. The duplex is formed between a fluorophore-labeled DNA aptamer and a small oligonucleotide modified with a quenching moiety (denoted QDNA). When the target is absent, the aptamer binds to QDNA, bringing the fluorophore and the quencher into close proximity for maximum fluorescence quenching. When the target is introduced, the aptamer prefers to form the aptamer-target complex. The switch of the binding partners for the aptamer occurs in conjunction with the generation of a strong fluorescence signal owing to the dissociation of QDNA. Herein, we report on the preparation of several structure-switching reporters from two existing DNA aptamers. Our design strategy is easy to generalize for any aptamer without prior knowledge of its secondary or tertiary structure, and should be suited for the development of aptamer-based reporters for real-time sensing applications.