基于磁性颗粒微阵列与双色荧光杂交的单核苷酸多态性分型方法研究

基于磁性颗粒微阵列与双色荧光杂交,建立了单核苷酸多态性(Single nucleoitide polymorphism,SNP)分型方法。将利用不对称扩增得到的含有待检测位点生物素标记的单链PCR产物固定在链亲和素修饰的金磁纳米颗粒(Gold magnetic nanoparticles,GMNPs)表面;将ssDNA-GMNPs混合物点样在底部固定有磁铁的载玻片上构建磁性颗粒微阵列,然后在基因框中与双色荧光探针杂交;杂交完全后,充分洗涤,通过扫描获得分型结果。通过优化不对称PCR的扩增条件,直接扩增出产量较高的单链DNA作为靶序列用于分型。利用本方法对24个样本MTHFR基因的C677T位点多态性进行了检测。实验证明,本方法步骤简单,易实现自动化操作、非常适用于分子诊断与法医鉴定。     

电化学发光-聚合酶链式反应方法检测胰腺癌中K-ras基因点突变

发展了一种可用于快速检测胰腺癌中K-ras癌基因点突变的电化学发光-聚合酶链式反应(ECL-PCR)分析方法。该法采用三联吡啶钌标记的上游引物和生物素标记的下游引物对目的片段进行PCR扩增;再采用限制性内切酶MvaI对扩增产物进行酶切。由于野生型样品和突变型样品间存在酶切位点的变化,其中只有野生型样品能被切断;通过生物素与链霉亲和素包被的磁珠连接,将生物素标记的DNA片段收集到检测池中,进行电化学发光检测。采用该法对13例胰腺癌组织中的K-ras癌基因第12位密码子进行点突变分析,只需要10μL样品、20min孵育时间和30s采集时间,就可得出其中有12例存在点突变,点突变率为92.3%。本方法操作简便、安全、快速、灵敏,可用于检测任何一种导致限制性内切酶位点改变的基因点突变。     

微流控芯片电泳-多重聚合酶链反应法同时测定多个单碱基多态性位点

以微流控芯片电泳为检测平台,建立了多重PCR扩增法同时测定多个单碱基多态性(SNP)位点的方法。先通过PCR扩增得一段含所有待测SNP位点的长片段;用限制性内切酶消化成短片段,再将酶切反应产物与脱氧核糖核酸适配器(DNAadapter)相连;以连接产物为模板,分成两管,分别用n条等位基因特异性引物和一条通用引物进行n重PCR扩增;最后用微流控芯片电泳法分离PCR扩增产物,根据两管扩增产物的芯片电泳图谱中扩增片段的大小判断SNP的类型。以细胞色素P4502D6(CYP2D6)基因中的5个SNP位点(100C>T、1661G>C、1758G>T、2470T>C和2850C>T)为检测对象,考察了各等位基因特异性引物之间的相互影响和扩增反应的特异性,采用微流控芯片电泳法成功测定了20名健康中国人的CYP2D6基因中5个SNP位点的基因多态性,与聚合酶链反应-限制性片段长度多态性法(PCR-RFLP)测定结果完全一致。     

一种基于磁性纳米粒子PCR的高通量SNP分型方法

利用磁性纳米粒子PCR扩增(MNPs-PCR)和等位基因特异性双色荧光探针(Cy3, Cy5)杂交, 建立了一种单核苷酸多态性(SNP)分型的新方法. 应用该方法对9个样本MTHFR基因的C677T多态进行检测, 野生和突变型样本正错配信号比大于9.0, 杂合型正错配信号比接近1.0, 分型结果经测序验证. 此方法无须产物纯化、浓缩, 扫描分型结果快速、直观, 是一种操作简单、快速、高通量、高灵敏度的分型方法.     

基于磁性纳米颗粒和金纳米粒子构建DNA电化学生物传感技术

本文构建了一种基于纳米粒子、茎环DNA和丝网印刷电极(SPCE)的电化学生物传感技术用于乳腺癌基因的快速、灵敏检测。该传感技术中,探针DNA的两端分别标记了巯基和生物素,巯基用于与金纳米粒子(AuNPs)作用,生物素用于与磁性纳米颗粒(MNPs)表面修饰的链酶亲和素作用以达到富集的目的,之后利用SPCE进行电化学检测。无目标DNA存在时,双标记DNA保持茎环结构,使得生物素分子很难和MNPs上的亲和素接触。一旦加入目标DNA,茎环结构打开,生物素得以与MNPs上的链霉亲和素发生特异性结合,形成的复合物(MNPs-DNA-AuNPs)通过磁性富集到SPCE表面,从而获得AuNPs的电化学信号。该DNA电化学生物传感对单碱基错配有良好的分辨能力,完全互补DNA的检出限为8.0×10-13 mol/L。     

表面等离子体子共振传感器用于研究不同材质包裹的磁性纳米粒子性质

利用自行设计组装的以白色发光二极管为光源的表面等离子体子共振传感器实验装置, 检测了不同材质包裹的磁性纳米粒子连接靶向DNA与生物素化DNA探针的结合程度. 结果表明, 与聚苯乙烯磁性微球连接的靶向DNA相比, Fe3O4@SiO2核壳式纳米微球连接的靶向DNA与生物素化的DNA探针结合速率较快, 且其相对标准偏差较小.     

基于引物延伸反应进行SNP基因分型的电化学方法

引物延伸反应的高特异性使其成为单核苷酸多态性(SNP)基因分型的最常用方法. 本文利用引物延伸反应, 通过二茂铁标记的dUTP将二茂铁引入到延伸的产物中, 用一条捕获探针将延伸产物捕获到电极表面, 用差分脉冲伏安法对电极表面的二茂铁进行检测, 从而实现了SNP基因分型. 考察了延伸反应的退火温度、聚合酶用量以及DNA杂交温度等因素的影响. 应用该方法对β-地中海贫血基因密码子28位单碱基突变进行检测, 获得了满意的基因分型结果. 该方法检测限可达到0.86 fmol/L, 是一种简便、快速且灵敏的SNP分型方法.     

液相色谱-串联质谱法测定生物样本全基因组DNA甲基化

建立了基于液相色谱-电喷雾串联质谱的分析方法,对生物样本中全基因组DNA甲基化水平进行定量测定.首先将DNA从生物样本中提取出来,将DNA片段酶解为单核苷,利用液相色谱-串联质谱测定胞嘧啶核苷和5-甲基胞嘧啶核苷的含量,从而计算出其全基因组DNA甲基化率.利用该法研究了暴露于全氟辛烷磺酸的L-02细胞、10例原发性肝癌病例血浆样本和10例对照血浆样本的全基因组DNA甲基化水平,得出了它们的总甲基化率变化的初步结果.本方法操作简单,具有很高的灵敏度和稳定性,为研究生物样本,尤其是临床上易得但DNA含量极低的血浆样本的总甲基化水平提供了思路.     

基于克隆测序技术的人类白细胞抗原基因高分辨率分型方法的建立

运用优化的扩增和克隆测序技术,建立了人类白细胞抗原( HLA-B)基因的高分辨率分型方法。针对HLA-B基因保守区序列设计引物进行等位基因扩增,基于质粒不相容原理将杂合型等位基因有效克隆入质粒DNA中,经细菌培养后进行Sanger测序,根据测序结果经ClustalX2软件分析和IMTG/HLA数据库的BLAST比对即可完成HLA-B基因的高分辨率分型。利用建立的方法对7例临床样本进行了HLA-B基因分型,并且与第三方直接碱基序列分析基因分型技术( PCR-SBT)进行比对,结果完全一致。本方法无需专业分型软件,准确度高,成本低;采用通用引物进行等位基因的扩增和测序,无需传统方法中繁琐的引物设计和过程优化,实现了HLA-B基因的高分辨率分型。     

实时荧光聚合酶链式反应偶联高特异性核酸侵入反应检测单核苷酸多态性

建立了实时荧光聚合酶链式反应( PCR)偶联高特性核酸侵入反应检测单核苷酸多态性( SNP)的方法。优化了体系中flap核酸内切酶1(FEN1酶)和野生型检测探针等用量,确定了最佳反应条件,即FEN1酶用量为1.5 U,野生型检测探针用量为0.125μmol/L,0.5μmol/L Invader突变型检测探针,各0.25μmol/L通用野生型( VIC)和突变型( FAM)荧光共振转移发卡探针,显著降低了野生型样本和突变型样本背景信号,避免了背景信号对检测结果分型的干扰。采用本方法对编码乙醛脱氢酶2( ALDH2)基因ALDH2*2位点21例样本、细胞色素P4502C19基因CYP2C19*2和CYP2C19*3位点各19例样本进行分型检测,结果表明, AL-DH2*2位点GG纯合10例,GA杂合8例,AA纯合3例;CYP2C19*2位点GG纯合9例,GA杂合8例,AA纯合2例;CYP2C19*3位点GG纯合18例,GA杂合1例。使用焦磷酸测序进行验证,两种方法检测结果一致。本方法特异性好、操作简便、耗时短、成本低,可实现对SNP单管闭管无污染的分型检测。     

Multiple genotyping based on multiplex PCR and microarray

The genetic variability has obtained more and more attention in the process of diagnosis and treatment of tumors.Herein,we have described a multiple genotyping method based on magnetic enrichmentmultiplex PCR (MEM-PCR) and microarray technology.Monodisperse magnetic beads were fabricated and modified with streptavidin.Four loci on two genes (M235T and A-6G loci on AGT gene,A1298C and C677T loci on MTHFR gene) were selected to study single nucleotide polymorphisms (SNP).Target sequences of these SNP loci were amplified using Cy3-labeled primers through multiplex PCR in one tube after the templates were enriched and purified by functional magnetic beads (MB).Four pairs of NH₂-labeled probes,corresponding to each locus,were fixed on CHO-modified glass slide by covalent binding.Hybridization between target sequences and probes was performed under suitable conditions.The spotting locations on microarray and the ratio of fluorescence intensity,produced by different loci,were used to distinguish the SNP genotypes.Finally,three of gastric cancer samples were collected and genotyping analysis for these four SNP loci was carried out successfully simultaneously by this method.     

Rapid single nucleotide polymorphism analysis by primer extension and capillary electrophoresis using polyvinyl pyrrolidone matrix

Rapid molecular diagnosis of 21-hydroxylase deficiency by detecting the most common mutation in the 21-hydroxylase gene is presented using primer extension and capillary electrophoresis with a polyvinyl pyrrolidone matrix. DNA samples were subjected to polymerase chain reaction (PCR) in order to amplify a 422 bp fragment of the CYP21 gene containing the single nucleotide polymorphism (SNP) site. This product served as a template in the primer extension reaction using a fluorescently labeled primer in close proximity to the SNP. ddGTP was used to block the extension if the mutation was present and the other three dNTPs to enable elongation of the primer. Fast analysis of the resulting fragments was performed by capillary electrophoresis using 10% polyvinylpyrrolidone as sieving and wall coating matrix. The Cy5-labeled primer and the two possible primer extension products (mutant and wild type) were completely separated in 90 s.     

八元瓜环对氯化矢车菊素溶解性、稳定性及抗氧化性的影响

采用核磁共振氢谱(¹H NMR)、 红外光谱及紫外吸收光谱等方法考察了八元瓜环(Q[8])对氯化矢车菊素(Cy)的包结作用. 结果表明, 在pH=0.8的盐酸介质中, Q[8]可与Cy形成摩尔比为1:1的主客体配合物, 紫外吸收光谱法测得的主-客体结合常数为1.51×10⁶ . 相溶解度研究结果表明, Q[8]能使饱和Cy溶液的溶解度增大, 当Q[8]浓度为100 μmol/L时, 可使Cy的溶解度增大12.21倍. 紫外吸收光谱随时间变化结果表明, 在较为稳定存在形态及相同实验条件下, Q[8]/Cy溶液比Cy溶液的稳定性提高了2.58倍. 抗氧化性实验结果表明, Q[8]/Cy包合物和Cy均表现出较好的抗氧化活性.     

Multiplexed SNP genotyping using nanobarcode particle technology

Single-nucleotide polymorphisms (SNP) are the most common form of sequence variation in the human genome. Large-scale studies demand high-throughput SNP genotyping platforms. Here we demonstrate the potential of encoded nanowires for use in a particles-based universal array for high-throughput SNP genotyping. The particles are encoded sub-micron metallic nanorods manufactured by electroplating inert metals such as gold and silver into templates and releasing the resulting striped nanoparticles. The power of this technology is that the particles are intrinsically encoded by virtue of the different reflectivity of adjacent metal stripes, enabling the generation of many thousands of unique encoded substrates. Using SNP found within the cytochrome P450 gene family, and a universal short oligonucleotide ligation strategy, we have demonstrated the simultaneous genotyping of 15 SNP; a format requiring discrimination of 30 encoded nanowires (one per allele). To demonstrate applicability to real-world applications, 160 genotypes were determined from multiplex PCR products from 20 genomic DNA samples.     

Local heating of discrete droplets using magnetic porous silicon-based photonic crystals

This paper describes a method for local heating of discrete microliter-scale liquid droplets. The droplets are covered with magnetic porous Si microparticles, and heating is achieved by application of an external alternating electromagnetic field. The magnetic porous Si microparticles consist of two layers. The top layer contains a photonic code and it is hydrophobic, with surface-grafted dodecyl moieties. The bottom layer consists of a hydrophilic silicon oxide host layer that is infused with Fe3O4 nanoparticles. The amphiphilic microparticles spontaneously align at the interface of a water droplet immersed in mineral oil, allowing manipulation of the droplets by application of a magnetic field. Application of an oscillating magnetic field (338 kHz, 18 A rms current in a coil surrounding the experiment) generates heat in the superparamagnetic particles that can raise the temperature of the enclosed water droplet to >80 degrees C within 5 min. A simple microfluidics application is demonstrated: combining complementary DNA strands contained in separate droplets and then thermally inducing dehybridization of the conjugate. The complementary oligonucleotides were conjugated with the cyanine dye fluorophores Cy3 and Cy5 to quantify the melting/rebinding reaction by fluorescence resonance energy transfer (FRET). The magnetic porous Si microparticles were prepared as photonic crystals, containing spectral codes that allowed the identification of the droplets by reflectivity spectroscopy. The technique demonstrates the feasibility of tagging, manipulating, and heating small volumes of liquids without the use of conventional microfluidic channel and heating systems.     

Anomalous electrophoretic migration of short oligodeoxynucleotides labelled with 5′‐terminal Cy5 dyes

By using a fluorescent exonuclease assay, we reported unusual electrophoretic mobility of 5′‐indocarbo‐cyanine 5 (5′‐Cy5) labelled DNA fragments in denaturing polyacrylamide gels. Incubation time and enzyme concentration were two parameters involved in the formation of 5′‐Cy5‐labelled degradation products, while the structure of the substrate was slightly interfering. Replacement of positively charged 5′‐Cy5‐labelled DNA oligonucleotides (DNA oligos) by electrically neutral 5′‐carboxyfluorescein (5′‐FAM) labelled DNA oligos abolished the anomalous migration pattern of degradation products. MS analysis demonstrated that anomalously migrating products were in fact 5′‐labelled DNA fragments ranging from 1 to 8 nucleotides. Longer 5′‐Cy5‐labelled DNA fragments migrated at the expected position. Altogether, these data highlighted, for the first time, the influence of the mass/charge ratio of 5′‐Cy5‐labelled DNA oligos on their electrophoretic mobility. Although obtained by performing 3′ to 5′ exonuclease assays with the family B DNA polymerase from Pyrococcus abyssi, these observations represent a major concern in DNA technology involving most DNA degrading enzymes.     

高密度噬菌体抗体芯片对细胞表面蛋白的识别

采用正常人和白血病患者的白细胞对人源噬菌体抗体库进行淘选, 以获得对两种细胞表面蛋白特异的抗体. 通过pVIII展示系统, 使抗体以多价展示于重组噬菌体颗粒表面, 从上述两组中各挑选出48个克隆分别固定于环氧基片上, 并以空白噬菌体和牛血清白蛋白作为对照, 制成高密度噬菌体抗体芯片. 取来自3名正常人和3名白血病患者的白细胞裂解物样品, 用荧光染料Cy3标记, 与噬菌体抗体芯片反应, 对微阵共聚焦扫描得到的荧光图谱进行分析. 在白血病白细胞表面蛋白的识别图谱中有8组斑点显著不同于正常图谱. 由此表明, 噬菌体抗体芯片可用于识别细胞表面蛋白.     

水溶性Fe3O4磁性纳米催化剂的合成及应用

利用对氨基苯磺酸氟硼酸重氮盐与Fe₃O₄磁性纳米粒子(MNPs)的偶联反应,非常方便地制备出表面含有磺酸基的Fe₃O₄磁性纳米粒子。 透射电子显微镜(TEM) 测试结果表明,粒子的平均粒径在 20 nm左右。 溶解性实验表明,该纳米粒子具有较好的水溶性,但不溶于常用的有机溶剂,因此可利用其磁性回收并循环使用。 将该纳米粒子用于催化羧酸与醇的酯化反应,产物酯的收率为71%~86%。 催化剂在酯化反应中的最优使用量为1.5%(质量分数)。 同时,该催化剂可催化果糖合成5-羟甲基糠醛(HMF),收率为32%。