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。     

基于DNA功能化金属有机框架材料的荧光探针对瓣状核酸内切酶1的检测和成像研究

结构特异性核酸酶瓣状核酸内切酶1 (Flap enduclease 1, FEN1)在多种癌细胞中过度表达,被认为是癌症临床诊断的潜在生物标志物。FEN1的精确检测对于癌症早期诊断和预后具有重要意义。荧光法具有操作简单、灵敏度高等优势,被广泛应用于FEN1检测,但基于比率荧光信号检测FEN1的策略尚未见报道。本研究设计了一种基于DNA功能化金属有机框架材料(MOFs)的比率荧光探针(FAM-RhB@UiO-66-NH₂),用于细胞内FEN1的检测和成像。其中,罗丹明B(RhB)被封装在MOFs中,荧光团FAM修饰的DNA链通过Zr—O—P相互作用与MOFs结合,形成基于荧光共振能量转移(FRET)的纳米探针。在FEN1存在的情况下,DNA链被酶切割,FRET体系被破坏,荧光比率发生变化,从而可实现对FEN1的检测。在最佳实验条件下,检测FEN1的线性范围为0.01～3.0 U,线性方程为y=0.1314x+1.6107,检出限低至0.004 U(3σ)。将此探针用于细胞内FEN1成像,能够区分癌细胞和正常细胞。     

基于核酸侵入反应偶联PCR的粪便样本基因甲基化定量分析方法及用于结直肠癌无创筛查

从粪便中检测BMP3基因甲基化水平可实现对结直肠癌的无创筛查,但对检测方法的灵敏度与特异性要求很高。本研究将核酸侵入反应与实时荧光聚合酶链式反应(PCR)偶联,建立了BMP3基因甲基化检测方法,以ACTB基因作为参比基因,通过优化反应体系中探针浓度、Flap核酸内切酶与Taq酶用量,提高BMP3目标基因与ACTB参比基因的扩增效率至接近100%,实现了利用ΔCT法进行BMP3基因甲基化水平的相对定量,可对低至10 copies的甲基化BMP3基因进行检测,并可从非甲基化模板中准确定量0.01%的甲基化模板,非甲基化模板不产生非特异性信号,表明本方法具有极高的灵敏度与良好的特异性。将本方法用于16例结直肠癌患者、7例结直肠腺瘤患者及19例健康人粪便样本中BMP3基因甲基化检测,结果表明,有5例结直肠癌患者的粪便样本检出BMP3基因甲基化,2例结直肠腺瘤患者的粪便样本检出BMP3甲基化,健康人的粪便样本均没有检出甲基化,表明本方法可用于检测粪便样本中基因的甲基化水平,为临床开展基于粪便中基因甲基化检测的无创结直肠癌筛查提供了新方法。     

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.     

一种基于磁性颗粒和通用连接子扩增技术的单核苷酸多态性分型方法

提出了一种应用磁性颗粒和通用连接子扩增技术(Linker-PCR)的多位点单核苷酸多态性(SNP)分型方法. 该方法首先通过酶切将样本基因组DNA打断, 然后将通用连接子通过T4 DNA连接酶与各个酶切片段连接, 利用生物素标记的通用引物将样本进行全基因组扩增. 扩增后, 将生物素标记的Linker-PCR扩增产物固定到亲合素修饰的磁性颗粒表面, 通过与双色荧光标记的等位基因特异性探针杂交, 对待测位点进行分型. 利用该方法, 我们对10个样本MTHFR基因上的2个SNP位点进行了分型, 分型结果准确、正错配信号比大于3. 由于利用Linker-PCR技术来实现对靶序列的全基因组扩增, 该方法非常适用于大量样本的多基因多位点的SNP分型研究.     

基于电沉积导电聚合物薄膜的高灵敏DNA电化学传感器

利用电沉积导电聚合物薄膜,提出了一种对乳腺癌相关的BRCA-1基因的高灵敏检测方法．以Au电极表面自组装DNA捕获探针,利用电沉积在DNA修饰电极表面固定含Ss^2＋/3＋的导电高分子作为电子传递媒介体．通过夹心法杂交目标靶DNA及辣根过氧化物酶标记的信号DNA探针．靶DNA杂交的信号探针上的辣根过氧化物酶与检测溶液中的过氧化氢反应,采用时间．电流（T-I）法,可以灵敏检测BRCA-1基因,其检测限可以达到10fM．     

基于纳米金与纳米银簇间表面等离子增强能量转移效应特异性检测microRNA

microRNAs(miRNAs)的灵敏检测对临床诊断具有十分重要的意义.本研究采用偶联DNA聚合酶和核酸内切酶介导的恒温扩增反应实现靶标循环再生的策略,利用纳米金(AuNPs)与纳米银簇(AgNCs)间表面等离子增强能量转移效应,开发了一种miRNA定量检测方法.在AuNPs表面组装两种探针(Probe a和Probe b)制备响应元件Probe b-Probe a-AuNP,其中Probe a通过3′端巯基共价偶联到AuNPs表面,此外具有靶标miRNA互补序列、核酸内切酶酶切序列和Probe b互补序列,Probe b为荧光AgNCs合成模板.靶标miRNA存在时,启动酶级联恒温扩增反应,导致Probe b脱离AuNPs表面,抑制了Probe b为模板合成的AgNCs与AuNPs间表面等离子增强能量转移效应,使得反应体系荧光信号增强.本方法的检出限为2.5×10-11 mol/L,与miRNAs商业化检测试剂盒相比,避免了逆转录反应,而且操作简单,检测成本低,可应用于生物样本中miRNAs分析.     

指数线性聚合酶链式反应法制备焦磷酸测序反应的单链模板

建立了一种简单的焦磷酸测序用单链模板制备方法,以包含SNP6位点一段78bp序列为对象,采用非热启动Taq酶进行指数线性PCR扩增,通过加入甘油、BSA等PCR增强剂增加反应的效率和特异性,设计反应液A和B处理PCR产物中干扰焦测序的限制性引物、未完全反应的产物、焦磷酸和dNTPs等杂质, 处理后1～2 μL PCR产物就可直接用于焦测序检测.测定了BRCA1基因中5个乳腺癌相关的SNP位点,获得的图谱无非特异性信号,测得序列与参考序列一致,能够进行SNP分析,表明本方法可以制备高质量焦测序单链模板,且使焦测序的成本显著降低,操作更为简便,减少了操作过程中样本间的交叉污染,有利于焦测序样品预处理的自动化.     

用于高度降解mRNA样本的非反转录基因表达量测定方法

许多生物样本(如石蜡包埋组织样本)中的mRNA易断裂为小片段,利用传统方法检测较困难。为了测定高度降解的mRNA,本研究针对待测mRNA短片段设计一对探针,当探针与待测模板杂交后,通过连接反应将两条探针5’与3’端相连,连接产物作为PCR扩增模板进行实时荧光定量检测,从而对待测mRNA进行定量测定。以人ACTB基因为待测靶标,通过测定不同浓度的待测靶标及与待测靶标序列不同的RNA片段,分别考察方法的灵敏度与特异性,并检测肺癌石蜡切片样本中ACTB基因的表达量,与传统的反转录定量PCR检测结果进行了对比。本方法的检出限为150 fmol/L,定量线性范围为150 fmol/L～300 pmol/L,并且具有良好的特异性。在对石蜡包埋组织样本中的基因表达量检测时,本方法扩增检测CT值比反转录实时定量PCR小,表明本方法更适合对高度降解的mRNA样本进行定量测定。     

发卡型万能传导在基于核酸分子线路的基因诊断中的应用和性能优化

核酸等温扩增技术作为核酸体外扩增技术,其反应过程始终维持在恒定温度下。与聚合酶链反应相比,核酸等温扩增反应具有优异的便携型,因而被视为最有望实现基因快检甚至即时快检的体外基因扩增方法。然而,由于反应过程中假阳性扩增频发、反应后对产物的检测方法缺乏特异性和灵敏度等缺点,限制了其在实际分析检测中的应用。通过构建发卡型结构万能中转探针,成功地将恒温扩增产物转到一套性能良好的已知核酸分子线路上;借助核酸分子线路的百倍放大性能和序列特异性,实现对上游基因序列信息的精准识别和放大信号输出。针对不同的待测序列,仅需改变发卡型中转探针的序列,即可实现对不同序列目标物的检测。基于中转探针的重要性,本研究对中转探针的设计原理和方法进行了重点阐述,提出并验证了一套行之有效的普适性设计规律,确保中转探针良好的中转效率(信噪比)。利用这一规律获得的中转探针,与核酸分子线路偶联,可成功为低至近单分子(20个拷贝)的模型基因提供显著荧光和电化学信号输出。     

Silica microbeads capture fetal nucleated red blood cells for noninvasive prenatal testing of fetal ABO genotype

ABO hemolytic disease of the newborn (ABO-HDN), which may cause neonatal jaundice and polycythemia, or even stillbirth or neonatal death, is widespread in China. Prenatal testing for the fetal ABO blood group can reduce unnecessary concerns or ensure prompt treatment. Herein, we presented a method to employ high-density silica microbeads (SiO₂ MBs) for capturing fetal nucleated red blood cells (fnRBCs) in maternal peripheral blood, and we detected the ABO genotype of the fetus using these captured cells. We evaluated 52 patients using the SiO₂ MBs. Among 26 pregnant women with type O blood, 8 (30.8%) of the fetuses had type A blood, 5 (19.2%) had type B blood, and 13 (50%) had type O blood. SRY genes were detected in all 27 male fetuses. This study represents a simple and effective method for noninvasive prenatal detection of the fetal ABO genotype. We believe that this method has great potential for noninvasive prenatal testing of the fetal Rh blood group and other fetal diseases as well.     

Detection of cell-free fetal DNA in maternal plasma using two types of compound markers

With the discovery of circulating cell-free fetal DNA (cffDNA) in maternal plasma, noninvasive prenatal testing became possible. However, analysis of low-level cffDNA against high background maternal DNA remains complicated and challenging. To circumvent this limitation, selective amplification of cffDNA was used in this study. Two kinds of compound markers (namely DIP-STR and SNP-STR), both based on selective amplification, were used here for targeting fetal DNA. By designing two allele-specific forward primers for DIP-STR and SNP-STR, DNA fragments with different DIP/SNP alleles can be selectively amplified. When analyzing maternal plasma DNA, these markers can selectively target paternally inherited fetal alleles whose DIP/SNP allele was not shared with the mother. In this study, 21 families were studied with six DIP-STRs and 11 SNP-STRs. Fetal DNA was successfully detected across plasma samples for at least one marker. Detection rate varied between DIP-STR and SNP-STR markers, and DIP-STR outperforms SNP-STR. Fetal alleles obtained from maternal plasma were double confirmed by genotyping paternal genomic DNA and fetal genomic DNA from amniocentesis. This study demonstrated that selective amplification strategy can be used to target cffDNA in maternal plasma, which will be a promising method for noninvasive prenatal paternity testing.     

全血直接扩增结合焦磷酸测序法测定亚甲基四氢叶酸还原酶基因多态性

亚甲基四氢叶酸还原酶基因677C>T和1298A>C两个位点的多态性与临床常用抗肿瘤药物甲氨喋呤及氟尿嘧啶的作用密切相关,对这两个位点多态性的检测能指导临床合理用药。为进一步缩短检测时间,降低检测成本,本研究建立了基于全血直接PCR的焦测序检测方法,采用"HpH Buffer"直接扩增全血模板,仅需1μL全血样本即可对两个位点进行高效扩增。扩增产物经碱变性法制备单链模板后进行焦磷酸测序,经过条件优化,仅需5μL扩增产物和1μL微球即可完成高灵敏的焦测序反应。为验证方法的准确性,检测了12例临床样本,均能正确检测两个位点的基因多态性。本研究为临床基因多态性检测提供了一种操作简便,耗时短,成本低,准确度高的方法,本方法可用于指导甲氨喋呤和5-氟尿嘧啶的个体化用药。     

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。     

富含胞嘧啶单链DNA-银纳米簇荧光探针用于S1核酸酶的灵敏检测

以富含胞嘧啶（C）的单链DNA为模板合成银纳米簇,将其作为功能化探针,建立了一种无标记荧光检测S1核酸酶的方法.S1核酸酶可以特异性识别单链DNA,在最适的酶催化反应条件下,可将其降解为单核苷酸或寡核苷酸片段.当S1核酸酶不存在时,富含C的单链DNA可以有效地合成荧光银纳米簇;当S1核酸酶存在时,单链DNA模板被特异性识别并降解,导致无法形成银纳米簇,使体系荧光信号降低.实验结果表明,银纳米簇的荧光强度随着S1核酸酶浓度的增加而降低.在优化的条件下,体系荧光信号（F/F₀）与S1核酸酶的浓度在5.0×10^-5~4.0×10^-3 U/μL范围内呈线性关系,检出限为2.0×10^-6 U/μL.该荧光探针选择性好,可用于RPMI 1640细胞培养基中S1核酸酶的检测,回收率达到91.8%~109.5%.     

基于离子液体修饰碳纳米管电极的碱性磷酸酶电化学检测

利用自制的离子液体修饰碳纳米管电极(CNTs-ILE),在对CNTs-ILE的特性及对碱性磷酸酶(AP)酶促反应的底物磷酸对硝基苯酯(PNPP)和产物对硝基苯酚(PNP)进行电化学研究的基础上,采用安培法对酶促反应进程实现了持续动态的检测.实验表明,CNTs-ILE的循环伏安特性优于传统玻碳电极,且它在检测PNP时呈现出良好的抗钝化特性.当AP浓度范围在1.0～100 U/L时,电流大小与AP的浓度呈良好的线性关系.本方法可快速检测AP浓度,检测时间在20 min内.CNTs-ILE具有良好的抗钝化、操作简单及制作成本低等特点,在碱性磷酸酶的检测领域中有望得到进一步发展.在传统ELISA基础上,利用CNTs-ILE对具体样本最终的AP酶促反应产物进行电化学检测,通过峰值电流大小确定抗原浓度,为检测以AP为标记酶的抗原和抗体提供了理论依据.     

Polymerase chain reaction method to detect canis materials by amplification of species-specific DNA fragment

Rapid identification of mammal materials in feeding stuffs and food is essential for effective control of a potential source of pathogens, such as those that cause bovine spongiform encephalopathy. A convenient polymerase chain reaction (PCR)-based assay was developed for detection and identification of a canis-specific mitochondrial DNA sequence in foodstuffs and food. The amplified canis-specific PCR product was a 213 base pair band from the D-loop DNA fragment of mitochondria, a high copy gene which should improve the possibility of amplifying template molecules of adequate size among the degraded DNA fragments brought about by heat denaturation. The specificity of this method was confirmed by 8 canis blood DNA samples (from different breeds of dog) and 9 noncanis animal blood DNA samples (bovine, sheep, porcine, chicken, fish, donkey, rabbit, deer, horse). This method was able to detect the presence of canis material in foodstuffs and in food mixtures even when the concentration of canis-derived meat was reduced to 0.05%. Furthermore, it did not appear to be affected by prolonged heat treatment. This method was developed for detection of canis materials in feeding stuffs, and occasionally for medical jurisprudence detection of canis-derived materials.     

Diagnostic Accuracy of Serum Hyaluronan for Detecting HCV Infection and Liver Fibrosis in Asymptomatic Blood Donors

Background: The disease caused by hepatitis C virus (HCV) is asymptomatic, silent, and progressive liver disease. In HCV-infected patients the increase in serum HA is associated with the development of hepatic fibrosis and disease progression. Methods: HCV-RNA detection was performed in all serological samples of blood donors that tested positive using HCV Ultra ELISA. Determination of hyaluronan (HA) was performed in positive HCV samples using ELISA-like fluorometric method. The HA content was compared to HCV viral load, genotype of the virus, liver fibrosis as well as ALT and GGT liver biomarkers. Results: Persistently normal ALT (<40 U/L) and GGT (<50 U/L) serum levels were detected in 75% and 69% of the HCV-Infected blood donors, respectively. Based on ROC analysis, the HA value < 34.2 ng/mL is an optimal cut-off point to exclude HCV viremia (specificity = 91%, NPV = 99%). Applying HA value ≥34.2 ng/mL significant liver fibrosis (≥F2) can be estimated in 46% of the HCV-infected blood donors. HA serum level (≥34.2 ng/mL) associated with a high ALT level (>40 U/mL) can correctly identify HCV infection and probable liver fibrosis (sensitivity = 96% and specificity = 90%) in asymptomatic blood donors. Conclusions: A high level of HA (≥34.2 ng/mL) in association with ALT (≥40 U/L) in serum can provide a good clinical opportunity to detect HCV-infected asymptomatic persons that potentially require a liver biopsy confirmation and antiviral treatment to prevent the development of advanced liver fibrosis or cirrhosis.     

Universal optical assays based on multi-component nanoprobes for genomic deoxyribonucleic acid and proteins

In this report, we developed a universal assay method for both genomic DNA and proteins by using enzyme-based multi-component optical nanoprobes. The nanoprobes are gold nanoparticles assembled with bio-recognizing and signaling elements. We firstly demonstrated that the nanoprobes could detect unpurified asymmetric polymerase chain reaction (PCR) product from genomic DNA of Escherichia coli, with the sensitivity approximately 10 times higher than that of quantitative real-time PCR assay. The limit of detection (LOD) of our nanoprobe-based method is less than 10 pg template DNA (target DNA). Using DNA aptamers as recognition elements, we also showed that as few as 0.1 nM thrombin could be colorimetrically detected with high specificity. These results indicated that the enzyme-based multi-component nanoprobes have the capability to work with real biological samples, and have the potential in various biological and clinical applications.