基于纳米金比色检测NOS1AP基因单碱基突变

基于单、双链DNA与纳米金颗粒间的不同静电作用, 建立了一种基于颜色反应检测NOS1AP基因单碱基突变的方法. 根据NOS1AP基因的单碱基多态位点设计检测探针、互补靶序列及带有单碱基突变序列寡核苷酸DNA. 室温下, 检测探针分别与互补序列、单碱基突变序列在缓冲液中进行杂交, 再分别加入纳米金溶液以及NaCl溶液. 用肉眼可以观察到纳米金溶液在两种不同杂交溶液中产生明显不同的颜色变化. 这种变化可通过紫外-可见分光光度计测定纳米金溶液的紫外吸收峰值的变化来证实. 实验结果表明, 纳米金溶液在一定浓度NaCl存在的条件下, 对互补双链NOS1AP DNA及单碱基突变NOS1AP DNA呈现出不同的颜色反应及紫外吸收光谱的改变. 此方法可望用于相关疾病的医学诊断及单碱基突变的检测.     

高灵敏纳米金比色芯片检测乙型肝炎病毒DNA及其变异

构建了新型纳米金比色芯片,利用Taq DNA连接酶的连接特异性,将其与乙型肝炎病毒DNA( HBV-DNA)靶序列完全互补杂交的捕获探针(固定在芯片上)和纳米金修饰的探针连接成一条链,从而将纳米金颗粒固定到芯片点阵上,再通过银染反应放大,形成裸眼可见的显色信息.通过点阵的位置及灰度,即可判断HBV-DNA靶序列的单碱基突变,并得出相对定量信息.本实验对不同浓度的HBV-DNA靶序列进行了检测.结果显示:此技术对单碱基突变有很强的特异性识别能力,并且具有较高的灵敏度(约10 pmol/L),在10～100 pmol/L浓度范围内表现出较好的线性关系.该技术检测时间短(＜1 h)、操作简单、不需要特殊的检测设备,具有很好的临床应用前景.     

Toehold链置换辅助智能手机比色法特异性检测废水中新冠病毒靶标RNA

基于Toehold介导的链置换反应（TSDR）与DNA酶,构建了一个强特异性及低成本检测废水中SARS-CoV-2靶标RNA单碱基突变的比色生物传感器。SARS-CoV-2靶标RNA与双链DNA(dsDNA)引发TSDR,释放出完整的G-四链体序列并与氯化血红素（Hemin）结合,形成G-四链体/Hemin DNA酶,进而催化双氧水氧化3,3’,5,5’-四甲基联苯胺,使溶液呈蓝色。当SARS-CoV-2靶标RNA存在单碱基突变时,TSDR被抑制,导致裸眼观察到的溶液颜色与未突变异的靶标相比更浅。同时采用智能手机摄像头捕捉溶液的RGB值变化（ΔRGB）,对裸眼观察结果的准确性进行验证。在最优条件下,构建的比色生物传感器能够特异性识别单个碱基突变的SARS-CoV-2靶标RNA,具有用于废水中SARS-CoV-2变异毒株检测的潜力。     

基于纳米金胶标记DNA探针的电化学DNA传感器研究

以纳米金胶为标记物,将其标记于人工合成的5-端巯基修饰的寡聚核苷酸片段上,制成了具有电化学活性的金胶标记DNA电化学探针;在一定条件下,使其与固定在玻碳电极表面的靶序列进行杂交反应,利用ssDNA与其互补链杂交的高度序列选择性和极强的分子识别能力,以及纳米金胶的电化学活性,实现对特定序列DNA片段的电化学检测以及对DNA碱基突变的识别.     

基于NUPACK预测设计的Toehold诱导链置换反应及其在DNA酶催化微流控化学发光单核苷酸多态性分析中的应用

以阿尔兹海默症相关的基因片段rs242557为研究对象,通过NUPACK软件预测Toehold(黏性末端)长度对链置换反应的影响,设计具有高特异性的双链核苷酸探针;富G的核苷酸序列首先被掩蔽在WatsonCrick双链结构中,当体系加入目标基因后,通过引发链置换反应解开该双链结构,形成的DNA酶可催化氧化鲁米诺化学发光反应,最终采用微流控化学发光法实现单核苷酸多态性(SNP)分析.该方法不仅具有设计简单、免标记及检测通量高等优点,而且在仅消耗2μL试样的条件下实现了单碱基突变的rs242557目标基因的SNP分析(区分因子达56),正常目标基因的检出限为1.7 nmol/L.     

基于CRISPR-Cas12a与G-四链体构建免标记电化学生物传感器检测microRNA

CRISPR-Cas12a是一种功能强大且可编程的分子诊断技术。本文基于CRISPR-Cas12a的附属切割活性与G-四链体/氯化血红素（Hemin）复合物,设计了一个免标记电化学生物传感器,实现对miRNA的强特异性检测。靶标miRNA-21与双链DNA探针上的Toehold区域结合并发生链置换反应,置换出双链DNA探针中较短的DNA。置换下来的DNA可以有效地激活CRISPR-Cas12a的附属切割活性。随后,具有附属切割活性的Cas12a切割电极表面上形成G-四链体/Hemin的DNA序列,导致电流信号减弱。在最优条件下,电流信号强度变化与10～100 pmol/L范围内的miRNA-21浓度呈良好的线性关系,检出限为4.2 pmol/L。该电化学生物传感器能够实现对单个碱基突变的miRNA-21或其它miRNA序列特异性识别,并可用于人血清样本（10%）中miRNA-21的检测。     

基于荧光小分子2-氨基-7-甲基-1,8-萘啶对C碱基的识别检测DNA双链中的C/C错配

单碱基错配是单核苷酸多态性(SNPs)的一种,是导致突变的DNA损伤类型之一.单碱基错配的检测对于从分子水平上阐明多种疾病形成的原因,实现基因水平的治疗都是至关重要的前提条件.发展具有高灵敏度、高选择性的单碱基错配检测方法势在必行.常用的单碱基错配检测方法包括凝胶电泳、荧光检测、SPR和质谱检测等.本文采用2-氨基-7-甲基-1,8-萘啶(AMND)作为荧光探针,AMND能嵌入双链DNA(ds-DNA)中的错配位点,并通过氢键识别错配碱基,这一结合过程伴随探针小分子的荧光淬灭,通过检测荧光淬灭现象实现单碱基错配及错配碱基类型的识别,建立了SNPs荧光分型方法.     

DNA调节纳米金模拟酶活性的癌胚抗原比色检测

本文构建了一个DNA调节纳米金颗粒（AuNPs）过氧化物酶模拟酶活性的比色检测方法,用于癌胚抗原的检测。将癌胚抗原的核酸适配体及其互补链通过碱基互补配对构成双链DNA,修饰在磁性微球负载的纳米金颗粒上,制备出具有可调节过氧化物酶模拟酶活性的生物探针。癌胚抗原被生物探针上的核酸适配体捕获后,在AuNPs表面形成空间位阻效应屏蔽底物,从而抑制了AuNPs的酶活性。且为了指示纳米金颗粒的酶活性,用生物探针催化氧化色源底物3,3′,5,5′-四甲基联苯胺（TMB）显色。TMB颜色随着癌胚抗原浓度的增加而变浅,根据体系650nm处的吸光度与癌胚抗原浓度之间的反比关系实现了对癌胚抗原的测定,线性范围为2~18 ng/mL,检测限达0.375 ng/mL。此外,癌胚抗原浓度超过4.8 ng/mL时,颜色出现了可直接用肉眼判断的显著变化。为使检测更加便携,本文同时设计了倒置磁分离检测管,在管中就能完成纳米探针捕获癌胚抗原、磁分离、洗涤。最优条件下,比色检测体系回收率为99%~100%,与临床检验差异显著性分析表明,t检验低于3.182,无明显差异。     

基于金@二氧化锰纳米片超级纳米粒子从比色到单颗粒光谱检测谷胱甘肽

合成了由金纳米球和二氧化锰薄片组成的金@二氧化锰纳米片超级纳米粒子(AMNS-SPs), 将其作为探针, 利用比色和单颗粒光谱2种分析方法进行了谷胱甘肽的传感检测. 该传感检测基于选择性刻蚀探针AMNS-SPs中的二氧化锰纳米片, 使得该探针的局域表面等离子共振波长蓝移. 实验结果表明, 比色法和单颗粒光谱法检测谷胱甘肽的检出限分别为0.018 μmol/L和23.2 fmol/L, 且后者是目前检测谷胱甘肽灵敏度最高的传感方法之一. 该传感方法的优异性能主要源于非常薄的二氧化锰纳米片.     

基于等离子激元耦合效应的高灵敏汞离子传感器

提出了一种基于单颗粒光谱技术,能够高灵敏检测汞离子的新方法,原理是基于汞离子诱导的纳米金自组装过程.在两种不同大小的纳米金表面分别修饰两段富含T碱基的DNA序列,当Hg²⁺存在时,两段DNA序列自发形成双链结构,导致小金球能够在大金球表面自组装成核-卫星纳米金结构,这一过程伴随着纳米颗粒散射光颜色和散射峰位置的变化,变化的程度与Hg²⁺浓度具有相关性,依托单颗粒光谱技术极高的检测灵敏度,该方法可以实现pmol/L级的检测.     

A one-step highly sensitive method for DNA detection using dynamic light scattering

A one-step homogeneous DNA detection method with high sensitivity was developed using gold nanoparticles (AuNPs) coupled with dynamic light scattering (DLS) measurement. Citrate-protected AuNPs with a diameter of 30 nm were first functionalized with two sets of single-stranded DNA probes and then used as optical probes for DNA detection. In the presence of target DNA, the hybridization between target DNA and the two nanoparticle probes caused the formation of nanoparticle dimers, trimers, and oligomers. As a result, the nanoparticle aggregation increased the average diameter of the whole nanoparticle population, which can be monitored simply by DLS measurement. A quantitative correlation can be established between the average diameter of the nanoparticles and the target DNA concentration. This DLS-based assay is extremely easy to conduct and requires no additional separation and amplification steps. The detection limit is around 1 pM, which is 4 orders of magnitude better than that of light-absorption-based methods. Single base pair mismatched DNAs can be readily discriminated from perfectly matched target DNAs using this assay.     

Homogeneous DNA Detection Based on Fluorescence Quenching by Nanoparticles in Single-step Format :Target-Induced Configuration Transform

A new strategy for homogeneous detection of DNA hybridization in single-step format was developed based on fluorescence quenching by gold nanoparticles. The gold nanoparticle is functionalized with 5’-thiolated 48-base oligonucleotide (probe sequence), whose 3’-terminus is labeled with fluorescein (FAM), a negatively charged fluorescence dye. The oligonucleotide adopts an extended configuration due to the electrostatic repulsion between negatively charged gold nanoparticle and the FAM-attached probe sequence. After addition of the complementary target sequence, specific DNA hybridization induces a conformation change of the probe from an extended structure to an arch-like configuration, which brings the fluorophore and the gold nanoparticle in close proximity. The fluorescence is efficiently quenched by gold nanoparticles. The fluorescence quenching efficiency is related to the target concentration, which allows the quantitative detection for target sequence in a sample. A linear detection range from 1.6 to 209.4 nmol/L was obtained under the optimized experimental conditions with a detection limit of 0.1 nmol/L. In the assay system, the gold nanoparticles act as both nanoscaffolds and nanoquenchers. Furthermore, the proposed strategy, in which only two DNA sequences are involved, is not only different from the traditional molecular beacons or reverse molecular beacons but also different from the commonly used sandwich hybridization methods. In addition, the DNA hybridization detection was achieved in homogenous solution in a single-step format, which allows real-time detection and quantification with other advantages such as easy operation and elimination of washing steps.     

A sensitive fluorescence anisotropy method for point mutation detection by using core-shell fluorescent nanoparticles and high-fidelity DNA ligase

The present study reports a proof-of-principle for a sensitive genotyping assay approach that can detect single nucleotide polymorphisms (SNPs) based on fluorescence anisotropy measurements through a core-shell fluorescent nanoparticles assembly and ligase reaction. By incorporating the core-shell fluorescent nanoparticles into fluorescence anisotropy measurements, this assay provided a convenient and sensitive detection assay that enabled straightforward single-base discrimination without the need of complicated operational steps. The assay was implemented via two steps: first, the hybridization reaction that allowed two nanoparticle-tagged probes to hybridize with the target DNA strand and the ligase reaction that generated the ligation between perfectly matched probes while no ligation occurred between mismatched ones were implemented synchronously in the same solution. Then, a thermal treatment at a relatively high temperature discriminated the ligation of probes. When the reaction mixture was heated to denature the duplex formed, the fluorescence anisotropy value of the perfect-match solution does not revert to the initial value, while that of the mismatch again comes back as the assembled fluorescent nanoparticles dispart. The present approach has been demonstrated with the discrimination of a single base mutation in codon 12 of a K-ras oncogene that is of significant value for colorectal cancers diagnosis, and the wild type and mutant type were successfully scored. Due to its ease of operation and high sensitivity, it was expected that the proposed detection approach might hold great promise in practical clinical diagnosis.     

A one-step homogeneous immunoassay for cancer biomarker detection using gold nanoparticle probes coupled with dynamic light scattering

A one-step homogeneous immunoassay for the detection of a prostate cancer biomarker, free-PSA (prostate specific antigen), was developed using gold nanoparticle probes coupled with dynamic light scattering (DLS) measurements. A spherical gold nanoparticle with a core diameter around 37 nm and a gold nanorod with a dimension of 40 by 10 nm were first conjugated with two different primary anti-PSA antibodies and then used as optical probes for the immunoassay. In the presence of antigen f-PSA in solution, the nanoparticles and nanorods aggregate together into pairs and oligomers through the formation of a sandwich type antibody-antigen-antibody linkage. The relative ratio of nanoparticle-nanorod pairs and oligomers versus individual nanoparticles was quantitatively monitored by DLS measurement. A correlation can be established between this relative ratio and the amount of antigen in solution. The light scattering intensity of nanoparticles and nanoparticle oligomers is several orders of magnitude higher than proteins and other typical molecules, making it possible to detect nanoparticle probes in the low picomolar concentration range. f-PSA in the concentration range from 0.1 to 10 ng/mL was detected by this one-step and washing-free homogeneous immunoassay.     

Surface-grafted hybrid material consisting of gold nanoparticles and dextran exhibits mobility and reversible aggregation on a surface

Gold nanoparticles linked to linear carboxylated dextran chains were attached to 3-aminopropyltriethoxysilane-functionalized glass surfaces. This method provides novel hybrid nanostructures on a surface with the unique optical properties of gold nanoparticles. The particles attached to the surface retain the capability to aggregate and disaggregate in response to their environment. This procedure presents an alternative method to the immobilization of gold nanoparticles onto planar substrates. Compared to gold nanoparticle monolayers, larger particle surface densities were obtained. Exposure to hydrophobic environments changes the conformation of the hydrophilic dextran chains, causing the gold nanoparticles to aggregate and inducing changes in the absorption spectrum such as red-shifting and broadening of the plasmon absorption peaks. These changes, characteristic of particle aggregation, are reversible. When the substrates are dried and then immersed in an aqueous environment, these changes can be visually observed in a reversible fashion and the sample changes color from the red color of colloidal gold to a bluish-purple color of aggregated nanoparticles. Surface-bound nanoparticles that retain their mobility when attached to a surface by means of a flexible polymer chain could expand the use of aggregation-based assays to solid substrates.     

Change Color Effect and Spectral Properties of Gold Nanoparticle-cationic Surfactants System

The change color effect of gold nanoparticle solutions was studied by means of resonance scattering and absorption spectrometry and scan electron microscopy. The red Au nanoparticles with a size of 10 nm exhibit a resonance absorption peak and a resonance scattering peak all at 525 nm. After some inorganic electrolyte was added to a red Au nanoparticles solution, the color of the solution became blue and the absorbance at 600-700 nm was significantly increased. The ratio of the concentration of rnonovalent cations, at which the resonance scattering of the system at 525 nm is maximal to that of divalent cations, is in the range of 100 : 1--100 ; 1. 8. It is in good agreement with the Schulze-Hardy rule of the coagulation value of electrolyte. After adding some cationic surfactants to the above solution, the color of the solution is in deep blue, with two resonance absorption peaks at 550 and 680 nm, and a greatly enhanced resonance scattering peak at 525 nm. The experiments demonstrate that the stronger the hydrophobicity of the cationic surfactant is, the stronger the change color effect of the Au nanoparticle solution promoted by cationic surfactant is. The change color effect of Au nanoparticle solution is resulted from the increased diameter of Au nanoparticles, and the changes of resonance absorotion DeaR and resonance scattering.     

Effect of oligonucleotide probes substituted by deoxyinosines on the specificity of SNP detection on the DNA microarray

One of the main factors that can affect the quality of microarray results is the microarray hybridization specificity. The key factor that affects hybridization specificity is the design of the probes. In this paper, we described a novel oligonucleotide probe containing deoxyinosines aimed at improving DNA hybridization specificity. We compared different probes to determine the distance between deoxyinosine base and SNPs site and the number of deoxyinosine bases. The new probe sequences contained two set of deoxyinosines (each set had two deoxyinosines), in which the interval between SNP site and each set of deoxyinosines was two bases. The new probes could obtain the highest hybridization specificity. The experimental results showed that probes containing deoxyinosines hybridized effectively to the perfectly matched target and improved the hybridization specificity of DNA microarray. By including a simple washing step after hybridization, these probes could distinguish matched targets from single‐base‐mismatched sequences perfectly. For the probes containing deoxyinosines, the fluorescence intensity of a match sequence was more than eight times stronger than that of a mismatch. However, the intensity ratio was only 1.3 times or less for the probes without deoxyinosines. Finally, using hybridization of the PCR product microarrays, we successfully genotyped SNP of 140 samples using these new labeled probes. Our results show that this is a useful new strategy for modifying oligonucleotide probes for use in DNA microarray analysis.     

Simultaneous identification of point mutations via DNA ligase-mediated gold nanoparticle assembly

Multiplex single nucleotide polymorphisms analysis has found a great demand in human genetics and pharmacogenetics. The present study reports a novel approach for a genotyping assay that could achieve simultaneous identification of multiple point mutations via a ligase-mediated gold nanoparticle assembly. Based on the allelic specificity of DNA ligase, gold nanoparticles modified by oligonucleotide probes perfectly matched to the DNA targets were assembled into a thermally-stable aggregate, while a single-base mismatch would result in the dissociation of the gold nanoparticle assembly at high temperature. Then, DNA targets and their point mutations could be differentiated using a multi-step temperature elevation analysis monitored by ultraviolet-visible measurements. This approach offered a direct colorimetric discrimination of multiple point mutations without stringent temperature control. The proposed approach is demonstrated using a model system for the identification of single-base mutations in codon 17 and position -28 of the beta-thalassemia gene. The results reveal that the wild and the mutant types could be simultaneously determined successfully. Owing to its ease of operation and high specificity, it was expected that the proposed procedure might hold great promise in both research-oriented and clinical genomic assays.     

DNA Dangling‐End‐Induced Colloidal Stabilization of Gold Nanoparticles for Colorimetric Single‐Nucleotide Polymorphism Genotyping

A single‐nucleotide polymorphism (SNP) detection method was developed by combining single‐base primer extension and salt‐induced aggregation of gold nanoparticles densely functionalized with double‐stranded DNA (dsDNA‐AuNP). The dsDNA‐AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single‐base protrusion at the outermost surface disperse stably, allowing detection of a single‐base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single‐stranded DNA on the AuNP surface, the resulting dsDNA‐AuNP works as a visual indicator of single‐base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single‐base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.