杂交链式反应介导的发光银纳米簇系统用于miRNA-21的信号放大检测

MicroRNAs(miRNAs)是多种疾病的生物标志物,同时也能为疾病治疗提供潜在靶点,因此,发展简单、快速、灵敏的miRNAs分析方法具有十分重要的意义。本研究结合杂交链式反应(HCR)高的信号放大能力和以DNA为模板合成的银纳米簇(DNA-AgNCs)优异的发光性能,构建了一种免标记的通用型荧光传感器,实现了miRNA-21的快速灵敏检测。将合成银纳米簇(AgNCs)的DNA模板封闭在HCR的反应物(发夹DNA)中,当存在靶标DNA时,发夹DNA的杂交链式组装反应被引发,释放出大量自由的AgNCs模板序列,进而引发近红外荧光DNA-AgNCs的合成,AgNCs的近红外荧光信号强度与引发链DNA的浓度成正相关。进一步通过在检测系统中引入一个封闭有HCR引发链序列的辅助发卡序列,建立通用型HCR-AgNCs传感分析系统,用于靶核酸分子检测。以miRNA-21为模型分析物,只在miRNA-21存在时,此辅助发卡才能被打开,并生成自由的HCR引发链,进而引发HCR反应和AgNCs的合成。本方法检测miRNA-21的线性范围为250 pmol/L～8 nmol/L,线性方程为(F-F     

无标记电化学生物传感平台用于癌胚抗原的检测

基于目标物诱导DNA杂交链式反应(HCR)及银纳米颗粒(Ag NPs)自组装过程构建了无标记型电化学生物传感平台,并将其应用于癌胚抗原(CEA)的检测.在目标物存在的情况下,适配体对CEA进行特异性识别并结合,释放出与之互补的触发DNA链(t DNA).该t DNA能够被金电极上的捕获探针(c DNA)捕获,并启动HCR过程,使得两条发夹DNA链被相继打开并串联成长的DNA双链结构,带正电的Ag NPs通过与该DNA结构之间的静电作用大量自组装到电极表面,并产生强的电化学信号.在优化的实验条件下,该电化学生物传感平台能够在0.5 ng·L~(-1)到50μg·L~(-1)的浓度范围内实现对CEA的良好响应.     

基于链置换循环无标记检测端立酶RNA的荧光法

以氧化石墨烯(GO)作为DNA载体和荧光猝灭剂,SYBRGreen Ⅰ(SGⅠ)为荧光信号探针,发夹核酸探针为分子识别探针,基于目标物启动的发夹核酸探针链置换循环反应,建立了一种利用荧光共振能量转移和链置换循环放大技术检测端粒酶RNA (hTR)的荧光新方法.发夹核酸探针hpDNA1和hpDNA2吸附在GO表面,嵌插在发夹DNA探针茎部的SG Ⅰ的荧光信号被GO猝灭.当人工合成的目标物(T1)存在时,T1与hpDNA1杂交打开hpDNA1的茎-环结构而引发hpDNA2与T1之间的链置换循环反应,由此累积产生大量的hpDNA1/hpDNA2杂交双链.刚性的双链DNA脱离GO表面,导致所嵌插的SG Ⅰ产生较强的荧光信号.基于荧光信号的变化,可定量检测0.2～50 nmoL/L的T1,检出限为90 pmol/L.该方法为端粒酶RNA检测提供了一种高灵敏、高特异性且无需标记的荧光新途径.     

基于链置换循环无标记检测端粒酶RNA的荧光法

以氧化石墨烯(GO)作为DNA载体和荧光猝灭剂, SYBR Green Ⅰ(SGⅠ)为荧光信号探针, 发夹核酸探针为分子识别探针, 基于目标物启动的发夹核酸探针链置换循环反应, 建立了一种利用荧光共振能量转移和链置换循环放大技术检测端粒酶RNA(hTR)的荧光新方法. 发夹核酸探针hpDNA1和hpDNA2吸附在GO表面, 嵌插在发夹DNA探针茎部的SGⅠ的荧光信号被GO猝灭. 当人工合成的目标物(T1)存在时, T1与hpDNA1杂交打开hpDNA1的茎-环结构而引发hpDNA2与T1之间的链置换循环反应, 由此累积产生大量的hpDNA1/hpDNA2杂交双链. 刚性的双链DNA脱离GO表面, 导致所嵌插的SGⅠ产生较强的荧光信号. 基于荧光信号的变化, 可定量检测0.2~50 nmol/L的T1, 检出限为90 pmol/L. 该方法为端粒酶RNA检测提供了一种高灵敏、 高特异性且无需标记的荧光新途径.     

基于DNA纳米结构的传感界面调控及生物检测应用

生物传感技术在环境、安全和医学诊断等应用中具有重要意义。如何精确调控自组装界面上生物识别探针与界面的相互作用来提高生物传感的性能则是其中的关键问题。常规界面组装过程中,DNA等生物分子往往在界面形成非均一的自组装层,分子结合能量壁垒高,识别效率低。我们通过构建有序DNA纳米结构,发展了纳米尺度精确调控界面性质的方法。通过在界面上形成以熵驱动主导的均匀自组装层,增加探针分子间的有效距离,并通过精确调控界面上DNA纳米结构的尺寸,显著提高界面DNA杂交效率与速率。我们在DNA四面体上修饰不同的生物识别分子(DNA、抗体、核酸适配体等),可构建通用检测平台,实现对核酸、蛋白、小分子及细胞的高灵敏检测,并且在复杂样本中同样保持了优异的检测性能。在此基础上,我们将四面体三维结构探针应用于细胞内以及活体检测,研究了DNA四面体在细胞内的运输途径及靶向定位方式,并实现对细胞内ATP分布的传感成像及小鼠体内肿瘤组织的靶向成像,有望发展活体生物传感的新探针。     

基于链替代信号放大灵敏检测端粒酶活性的电化学方法

利用标记二茂铁基团的DNA(T-DNA)分子作为信号探针, 基于端粒酶特异性延长其底物链(TS)所引发的链替代反应, 建立了一种检测端粒酶活性的电化学信号放大法. 将巯基化的发夹型DNA分子(H-DNA)通过金-硫键自组装于金电极表面, 辅助DNA(A-DNA)与二茂铁修饰的T-DNA部分互补杂交形成双链AT-DNA; 当端粒酶存在时, 可在TS的3′末端合成TTAGGG的重复序列; A-DNA与TS延长链杂交置换出T-DNA; T-DNA与发夹H-DNA杂交使得二茂铁靠近电极表面; 一条TS延长链可以释放出多条T-DNA, 将二茂铁富集到金电极表面, 从而实现信号放大检测端粒酶活性. HeLa细胞个数在5~100范围内与电流值成正比, 最低可检测5个HeLa细胞中端粒酶的活性. 因此, 本文建立了一种简单灵敏检测端粒酶活性的电化学方法.     

基于DNAzyme和杂交链式反应用于检测铅离子的荧光生物传感器研究

通过将GR-5 DNAzyme的序列设计进发生杂交链式反应的发夹DNA中,在引发DNA的触发下,发夹DNA H1与H2反应生成具有重复双螺旋结构的纳米线T-H1-H2-H1-H2…。在H1与H2结合部分存在碱基不配对区域,此处将形成GR-5 DNAzyme结构,在铅离子的存在下,该部分GR-5 DNAzyme的底物链被裂解,HCR产物即被裂解成许多DNA双链小分子从而实现信号扩增,以此构建了简便灵敏的荧光生物传感器。该生物传感器可在30min完成对Pb²⁺的检测,线性范围为0.1μM～7μM,检测限为23.2nM。对实际水样进行检测,加标回收率在96.7%～106.6%之间,相对标准偏差均小于2%。     

基于DNA杂交链式反应和杂交空位的无标记荧光检测DNA研究

基于DNA杂交链式反应(Hybridization chain reaction,HCR)的信号放大策略,通过在参与HCR反应的发夹型DNA中设计一个特殊碱基,HCR反应后,该碱基对位出现杂交空位,利用杂交空位与荧光小分子(2-Amino-5,6,7-trimethyl-1,8-naphthyridine,ATMND)特异性结合产生的荧光淬灭效应,构建了一种无标记、无酶、灵敏的DNA检测体系。利用凝胶电泳和原子力显微镜等对目标DNA引发两个发夹型DNA交替自组装形成的超级长链进行了表征。通过对杂交盐浓度和ATMND浓度等条件的优化,获得了满意结果。相比于未利用此放大信号策略的分析方法,灵敏度提高了两个数量级,目标DNA浓度在5.0~72.7 nmol/L浓度范围内与荧光比值(F/F0)呈现良好的线性关系,检出限为2.0 nmol/L。     

基于免标记发夹型探针和核酸外切酶Ⅲ的荧光信号放大DNA检测

设计合成了一种长臂发夹型核酸探针,结合核酸外切酶Ⅲ水解反应建立了一种免标记荧光信号放大高灵敏检测DNA的新方法.当不存在靶DNA时,SYBR GreenⅠ荧光染料能够嵌入发夹型探针的茎部而发出很强的荧光,而当存在靶DNA并与发夹型探针杂交后,核酸外切酶Ⅲ从杂交产物的3'端开始水解发夹型探针,释放出靶DNA,并触发下一个酶水解反应,同时SYBR GreenⅠ染料也随发夹型探针水解而释放,导致荧光信号降低,从而实现了对DNA的免标记荧光信号放大高灵敏检测.该方法的检出限低至320 fmol/L,比传统双标的分子信标的方法降低了4~5个数量级,且该方法还具有免标记、简单、快速的特点.     

基于杂交链式反应和共价有机框架的新型荧光传感器用于ctDNA的高灵敏和选择性检测

共价有机框架是近年来发展起来的一种高度结晶的多孔聚合物,由有机单元连接形成。由于其优异的孔隙率,模块性,结晶性和生物相容性,在传感领域显示出良好的应用前景。本文开发了一种基于杂交链式反应 (HCR) 和共价有机框架的新型荧光传感平台,用于高灵敏的检测循环肿瘤DNA (ctDNA)。ctDNA可以作为HCR的激活剂,通过触发发夹1 (H1) 和发夹2 (H2) 的自主交叉打开,激活HCR形成延伸的有缺口的双链DNA,导致荧光信号的变化,从而实现ctDNA的定量检测。HCR产物和荧光信号分别采用琼脂糖凝胶电泳和荧光光谱进行表征。ctDNA浓度在0-10 nM范围内,ctDNA的浓度与荧光信号呈良好的线性关系,检测限为1.3 nM。该方法对ctDNA具有满意的选择性,并在人类血清样品中显示出良好的性能。该荧光传感平台为ctDNA的检测提供了新思路,在癌症早期诊断中显示出潜在的应用前景。     

Fluorescence Signal Amplification Strategies Based on DNA Nanotechnology for miRNA Detection

In this review,the most recent progresses in the field of fluorescence signal amplification strategies based on DNA nanotechnology for miRNA are summarized.The types of signal amplification are given and the principles of amplification strategies are explained,including rolling circle amplification(RCA),catalytic hairpin assembly(CHA),hybridization chain reaction(HCR)and DNA walker.Subsequently,the application of these signal amplification methods in biosensing and bioimaging are covered and described.Finally,the challenges and the outlook of fluorescence signal amplification methods for miRNA detection are briefly commented.     

Aptamer‐Based SERS Assay of ATP and Lysozyme by Using Primer Self‐Generation

A simple bifunctional surface‐enhanced Raman scattering (SERS) assay based on primer self‐generation strand‐displacement polymerization (PS‐SDP) is developed to detect small molecules or proteins in parallel. Triphosphate (ATP) and lysozyme are used as the models of small molecules and proteins. Compared to traditional bifunctional methods, the method possesses some remarkable features as follows: 1) by virtue of the simple PS‐SDP reaction, a bifunctional aptamer assembly binding of trigger 1 and trigger 2 was used as a functional structure for the simultaneous sensing of ATP or lysozyme. 2) The concept of isothermal amplification bifunctional detection has been first introduced into SERS biosensing applications as a signal‐amplification tool. 3) The problem of high background induced by excess bio‐barcodes is circumvented by using magnetic beads (MBs) as the carrier of signal‐output products and massive of hairpin DNA binding with SERS active bio‐barcodes relied on Au nanoparticles (Au NPs), SERS signal is significantly enhanced. Overall, with multiple amplification steps and one magnetic‐separation procedure, this flexible biosensing system exhibited not only high sensitivity and specificity, with the detection limits of ATP and lysozyme of 0.05 nM and 10 fM , respectively.     

Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits

Catalyzed hairpin assembly (CHA) is a robust enzyme-free signal-amplification reaction that has a wide range of potential applications, especially in biosensing. Although most studies of the analytical applications of CHA have focused on the measurement of concentrations of biomolecules, we show here that CHA can also be used to probe the spatial organization of biomolecules such as single-stranded DNA. The basis of such detection is the fact that a DNA structure that brings a toehold and a branch-migration domain into close proximity can catalyze the CHA reaction. We quantitatively studied this phenomenon and applied it to the detection of domain reorganization that occurs during DNA self-assembly processes such as the hybridization chain reaction (HCR). We also show that CHA circuits can be designed to detect certain types of hybridization defects. This principle allowed us to develop a "signal on" assay that can simultaneously respond to multiple types of mutations in a DNA strand in one simple reaction, which is of great interest in genotyping and molecular diagnostics. These findings highlight the potential impacts of DNA circuitry on DNA nanotechnology and provide new tools for further development of these fields.     

Coupling hybridization chain reaction with DNAzyme recycling for enzyme-free and dual amplified sensitive fluorescent detection of methyltransferase activity

Aberrant DNA methylation originated from changes in DNA methyltransferase activity can lead to many genetic diseases and tumor types, and the monitoring of methyltransferase activity is thus of great importance in disease diagnosis and drug screening. In this work, by combing hybridization chain reaction (HCR) and metal ion-dependent DNAzyme recycling, we have developed a convenient enzyme-free signal amplification strategy for highly sensitive detection of DNA adenine methyltransferase (Dam MTase) activity and its inhibitors. The Dam MTase-induced methylation and subsequent cleavage of the methylated hairpin DNA probes by DpnI endonuclease lead to the release of ssDNA triggers for HCR formation of many Mg²⁺-dependent DNAzymes, in which the fluorescently quenched substrate sequences are catalytically and cyclically cleaved by Mg²⁺ to generate remarkably amplified fluorescent signals for highly sensitive detection of Dam MTase at 7.23 × 10⁻⁴ U/mL. In addition, the inhibition of different drugs to Dam MTase activity can also be evaluated with the developed method. With the advantages of simplicity and significant signal amplification over other common methods, the demonstrated biosensing approach thus offers great potential for highly sensitive detection of various methyltransferases and provides a convenient platform for drug screening for therapeutic applications.     

Amplified Self‐Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA‐Minimal Architectures

Triggering the release of small molecules in response to unique biomarkers is important for applications in drug delivery and biodetection. Due to low quantities of biomarker, amplifying release is necessary to gain appreciable responses. Nucleic acids have been used for both their biomarker‐recognition properties and as stimuli, notably in amplified small‐molecule release by nucleic‐acid‐templated catalysis (NATC). The multiple components and reversibility of NATC, however, make it difficult to apply in vivo. Herein, we report the use of the hybridization chain reaction (HCR) for the amplified, conditional release of small molecules from standalone nanodevices. We couple HCR with a DNA‐templated reaction resulting in the amplified, immolative release of small molecules. We integrate the HCR components into single nanodevices as DNA tracks and spherical nucleic acids, spatially isolating reactive groups until triggering. This could be applied to biosensing, imaging, and drug delivery.     

DNA hybridization chain reaction and DNA supersandwich self-assembly for ultrasensitive detection

The fabrication of sensitive sensors with high selectivity is highly desirable for the detection of some important biomarkers,such as nucleic acids,proteins,small molecules and ions.DNA hybridization chain reaction(HCR) and DNA supersandwich self-assembly(SSA) are two prevalent enzyme-free signal amplification strategies to improve sensitivity of the sensors.In this review,we firstly describe the characteristics about DNA HCR and DNA SSA,and then summarize the advances in the one-dimensional DNA nanostructures assisted by HCR and SSA.This review has been divided into three parts according to the two signal amplification methods and highlights recent progress in these two strategies to improve the detection sensitivity of proteins,nucleic acids,small molecules and ions.     

Amplified Self-Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA-Minimal Architectures

Triggering the release of small molecules in response to unique biomarkers is important for applications in drug delivery and biodetection. Due to low quantities of biomarker, amplifying release is necessary to gain appreciable responses. Nucleic acids have been used for both their biomarker-recognition properties and as stimuli, notably in amplified small-molecule release by nucleic-acid-templated catalysis (NATC). The multiple components and reversibility of NATC, however, make it difficult to apply in vivo. Herein, we report the use of the hybridization chain reaction (HCR) for the amplified, conditional release of small molecules from standalone nanodevices. We couple HCR with a DNA-templated reaction resulting in the amplified, immolative release of small molecules. We integrate the HCR components into single nanodevices as DNA tracks and spherical nucleic acids, spatially isolating reactive groups until triggering. This could be applied to biosensing, imaging, and drug delivery.     

Label-free and non-enzymatic detection of DNA based on hybridization chain reaction amplification and dsDNA-templated copper nanoparticles

A label-free and non-enzymatic amplification fluorescent method for detection of DNA has been developed by using hybridization chain reaction (HCR) and dsDNA-templated copper nanoparticles (CuNPs). First, the biotinylated capture DNA probes were immobilized on the streptavidin-modified beads through the interaction of biotin and streptavidin. Then, target DNA hybridized with the capture DNA probes, which formed a hybridized DNA with sticky end. The sticky end triggered the HCR process and formation of dsDNA polymers while two hairpin probes coexisted. Subsequently, the dsDNA polymers were employed as template for synthesis of CuNPs with excellent fluorescent properties, which provided a label-free, non-enzymatic signal response. Meanwhile, the fluorescence sensing depended on the target DNA triggered HCR, which render this method a high selectivity against single-base mismatch sequences. The concept and methodology developed in this work show great promise in the quantitative detection of DNA in biological and medical applications.     

DNA-based hybridization chain reaction amplification for assaying the effect of environmental phenolic hormone on DNA methyltransferase activity

In this work, a novel electrochemical protocol with signal amplification for determination of DNA methylation and methyltransferase activity using DNA-based hybridization chain reaction (HCR) was proposed. After the gold electrode was modified with dsDNA, it was treated with M.SssI MTase, HpaII endonuclease, respectively. And then the HCR was initiated by the target DNA and two hairpin helper DNAs, which lead to the formation of extended dsDNA polymers on the electrode surface. The signal was amplified by the labeled biotin on the hairpin probes. As a result, the streptavidin-alkaline phosphatase (S-ALP) conjugated on the electrode surface through the specific interaction between biotin and S-ALP. ALP could convert 1-naphthyl phosphate into 1-naphthol and the latter could be electrochemically oxidized, which was used to monitor the methylation event and MTase activity. The HCR assay presents good electrochemical responses for the determination of M.SssI MTase at a concentration as low as 0.0067 unit mL⁻¹. Moreover, the effects of anti-cancer drug and environmental phenolic hormone on M.SssI MTase activity were also investigated. The results indicated that 5-fluorouracil and daunorubicin hydrochloride could inhibit the activity, and the opposite results were obtained with bisphenol A and nonylphenol. Therefore, this method can not only provide a platform to screen the inhibitors of DNA MTase and develop new anticancer drugs, but also offer a novel technique to investigate the possible carcinogenesis mechanism.     

Nucleic Acid-to-Small Molecule Converter through Amplified Hairpin DNA Circuits

Many microRNAs (miRNAs) are characteristically found in cancer cells, making miRNAs promising marker biomolecules for cancer diagnosis and therapeutics. However, it is challenging to use miRNA as a cancer signature because it is difficult to convert the nucleic acid sequence information into molecular functionality. To address this challenge, we realize nucleic acid-to-small molecule converters using hairpin DNA circuits. Harnessing a Staudinger reduction as a trigger for the conversion, we constructed hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) circuits that respond to oncogenic miR-21. Fluorophore and dye molecules were released in response to miR-21 through the HCR, providing fluorogenic and chromogenic readouts. Selective cytotoxicity in miR-21-abundant cells was realized by the CHA to release the anticancer drug SN-38. This would be the first example of selective activation of a small-molecule prodrug triggered by oncogenic miRNA in human living cells.