PCR防污染技术的研究进展

聚合酶链式反应（PCR）是一种高灵敏核酸扩增技术,广泛应用于核酸检测中。但在实际应用过程中,扩增产物及其他核酸片段的污染会导致假阳性的结果,制约了PCR在临床检测中的应用。为了解决这一问题,建立了许多PCR防污染的方法,除了早期建立的并已得到广泛应用的物理隔绝法、光照法及水解法外,近年来还发展了酶消化法、化学修饰法及DEAE纤维素法。本文对PCR防污染技术的原理、应用及进展进行了综述。     

核酸诊断技术规范化的研究

针对PCR技术应用中的一些问题,从下述几方面开展了核酸诊断技术标准化的研究:①探讨了设计引物的影响因素,发现根据同一基因设计的不同引物对PCR敏感性影响较大,可相差20倍,进一步研究表明,引物的自由能,尤其是引物3'端6个碱基的自由能可能决定着PCR的敏感性;②研制成功室温稳定的PCR试剂,将所有PCR成分(加入一种酶保护剂)配制并分装于微量离心管中,并干燥,试剂室温放置8个月,37℃破坏2周对检测结果无任何影响;③因尿嘧啶糖基化酶(UDG)可特异降解DNA双链中的尿密啶核苷,PCR体系中以dUTP代替dTTP,并在PCR扩增前用UDG消化15 min,就可以特异防止PCR产物的污染.对炭疽杆菌、鼠疫杆菌、土拉杆菌和布鲁氏菌扩增结果表明,0.1 U的UDG可完全消化103～108个产物分子的污染;④建立了微孔板杂交技术代替电泳方法检测扩增产物,将PCR产物克隆作为捕获探针包被聚乙烯微孔板,PCR引物5'末端生物素标记,扩增后作为待检测探针杂交,通过比较影响微孔板杂交的包被、杂交和显色等因素,建立了PCR-EIA技术.通过比较包被缓冲液发现镁离子及其离子强度是影响DNA包被的重要因素,包被的DNA以线型质粒最佳,每孔包被300ng左右的DNA 杂交效果最好;杂交液中加和不加甲酰胺对杂交影响不大;用链霉亲和素化的辣根过氧化物酶或碱性磷酸酶酶联显色均能达到检测杂交体的目的,但前者显色较快,更为实用.确定了PCR-EIA技术的最佳的包被、杂交和显色的条件,比常规的PCR-电泳检测敏感性高10倍;⑤比较了不同标本处理方法,确定了各种临床标本和动物组织的较为理想的处理方法.通过上述不同方面的研究,确定了从引物设计、试剂配制、标本处理、UDG防污染和产物微孔板杂交-酶联显色检测等方面的优化条件,建立起敏感性高、特异性强、操作简便和检测客观的核酸检测技术,为临床实验室的常规应用和反生物战病原微生物的核酸诊断奠定了基础.     

PCR增强剂在核酸体外扩增检测技术的研究进展

在各种高致病性病原体、禽流感病毒、食源性微生物等引起的疾病随时大规模流行的背景下,利用聚合酶链式反应（polymerase chain reaction,PCR）技术对第一例或第一波病例的快速实验室诊断显得尤为重要,同时发展出多种以PCR技术为基础的检测技术以便更加快速、高通量、敏感地对疾病进行诊断、预防或预测。然而,在实际病原体检测中,常常出现灵敏度低、准确性差的结果。PCR增强剂是在PCR及PCR衍生技术中添加的一类物质,其可从产率、特异性、灵敏度等方面提高核酸扩增性能,从而优化核酸检测,解决病原体检测的应用瓶颈,为第一例病原体检出节约宝贵的时间。结合以PCR为基础的核酸体外扩增检测技术对PCR增强剂在其中的应用、优缺点、作用机理进行介绍,以期为病原体核酸检测的实际应用提供一些参考。     

用重组酶介导扩增技术快速扩增核酸

体外核酸快速扩增技术是一种可使微量核酸在体外高效快速扩增的技术, 自问世以来, 被广泛应用于分子生物学、医学和法理鉴定等领域, 并被不断改进, 以使其功能和适应性更为广泛. 重组酶介导扩增法是在现有体外核酸扩增原理的基础上发展起来的恒温体外快速扩增核酸技术. RAA法利用重组酶、单链结合蛋白和DNA聚合酶代替了传统PCR的热循环解链过程, 实现了在37℃恒温下的核酸快速扩增, 无需特殊的辅助仪器, 对操作人员的要求也不高, 具备简单、节能、便携、快速等特点, 有望在不远的将来取代传统的热循环PCR反应.     

同步PCR技术及其在植物核酸分子定量中的应用

同步PCR是一种集生化、光电和计算机技术于一体的封闭式DNA扩增系统,采用荧光染料将扩增与检测过程结合在一起,实现了在PCR过程中在线显示PCR反应,通过检测荧光强度来绝对定量起始模板的拷贝数.该技术大大简化和加速了核酸分子的定量过程,不仅快速、灵敏、准确、重复性好,而且很容易计算出待测样品中核酸分子的绝对起始拷贝数.同微阵列等分子生物技术一起,同步PCR技术将会在功能基因解析和病害分子诊断等方面发挥重要作用.本综述除了介绍同步PCR技术的原理和应用外,还介绍了定量拟南芥Aux/IAA基因的转录水平的实验,并就同步PCR操作过程中的问题进行了讨论.     

数字PCR在功能核酸精准检测中的研究进展

数字PCR是近年来迅速发展起来的一种定量分析技术。该技术结果判定不依赖于扩增曲线的循环阈值(Ct),不受扩增效率的影响,具有很好的准确度和重现性,并且可以实现绝对定量分析。数字PCR已经在功能核酸检测、鉴定等研究领域显示出巨大的技术优势和应用前景。在对数字PCR技术的基本原理和定量方法介绍的基础上,对该技术在功能核酸检测的主要应用领域进行综述,并对数字PCR在功能核酸检测领域中的研究前景做出了展望。     

可视化分析在病原体核酸现场快速检测中的研究进展

核酸检测因灵敏度高、特异性强而被广泛应用于病原体筛查与检测。随着检测需求的增加和扩增技术的发展，核酸检测方法逐渐向简单、快速、低成本方向发展。作为核酸检测“金标准”的实时荧光定量PCR法依赖昂贵的荧光读取设备和专业的操作人员，并不适用于病原体的现场快速检测。可视化检测方法无需依赖激发光源或复杂的设备，将可视化检测方法与快速、高效的扩增技术结合，能够以更直观、便携的方式呈现检测结果，具有即时检测(point-of-care testing,POCT)的潜力。本文对与扩增技术、CRISPR/Cas技术结合的可视化分析在病原体核酸快速检测中的应用及优缺点展开综述，以期为基于病原体核酸的POCT策略提供参考。     

PCR—ELISA检测HBV DNA的研究

目的：建立一种敏感、特异的乙型肝炎病毒（HBV）DNA检测方法。方法：应用PCR扩增技术和核酸杂交技术结合酶促显色技术（即PCR－ELISA技术）来检测血清中的HBV DNA。结果：应用PCR－ELISA技术能够检出许多PCR琼脂张胶电泳所检测不到的HBV DNA,大大地提高了检出率,而且,特异性强。结论：PCR－ELISA方法灵敏度高,行异性强,检测结果数据化,不受主观因素的影响。     

高灵敏可视化核酸试纸条法快速检测 HBV DNA

目的:本研究旨在建立一种基于试纸条的快速、灵敏及可视化检测乙型肝炎病毒核酸的方法.方法:利用聚合酶链反应扩增乙肝病毒的保守区,其中上、下游引物的5'端分别修饰异硫氰酸荧光素和生物素.核酸试纸条上的胶体金以及检测线处分别标记有链霉亲和素以及抗荧光素抗体.将扩增产物与展开液混合后点样,10min 后即可用肉眼判读结果.在优化了展开液成分、上样体积以及上样浓度之后,对该方法的灵敏度进行了评价.最后收集15例阴性样本及33例HBsAg 阳性样本,按血清标志物结果进行分类后使用核酸试纸条进行检测,并与实时荧光PCR的结果进行了比较.结果:试纸条检测乙肝病毒核酸的灵敏度为250eopies/mL.在临床样本的测定中,该方法与实时荧光定量PCR的特异性均为100%.且两种方法检测不同血清标志物类型的阳性检出率无差异.结论:核酸试纸条技术能够用于乙肝病毒核酸的可视化检测,与实时荧光PCR相比检测速度快,具有较好的灵敏度和特异性,适合流行病学调查以及在基层医院体检使用.     

快速检测HBV DNA的环状介导等温DNA扩增法

环状介导等温DNA扩增（LAMP）技术是一种新的核酸扩增方法,它能够高特异性、高效、快速地进行核酸的扩增。利用LAMP法检测乙型肝炎病毒（HBV）,能够在等温条件下于1h内将少量的基因拷贝数扩增至10^9,在对65份临床标本的检测中显示了较高的特异性。与现有的PCR技术相比,LAMP法更加简便快速,且在等温条件下进行,不需要复杂的仪器设备,为临床检测乙肝病毒提供了一个快速筒便的新方法。     

Ultrasensitive nucleic acid biosensors for early cancer diagnostics

We have developed ultrasensitive nucleic acid detection systems involving an amplification step where the analytical signal correlates directly to the amount of nucleic acid in the solution So far, we have performed nucleic acid quantification on several breast cancer susceptibility genes and were able to detect nucleic acid amounts that ranged from 0.1–1.0 fg of nucleic acid, which is at least 1000 times more sensitive than conventional fluorescent detection methods. The biosensors are so sensitive that they can be used for direct detection of breast cancer susceptibility genes in mRNA without involving a PCR step.     

数字PCR技术在核酸标准物质研制中的应用

在标准物质研制领域,生物标准物质的研制逐渐成为了研究热点,同时基于核酸的检测技术的开发与应用又推动了核酸标准物质的进程。核酸标准物质需要高级别、精准的定值方法,数字PCR作为单分子定量技术得到了广泛的应用。数字PCR是一种测定核酸分子的绝对定量方法,如微滴式数字PCR是采用油包水形成的微滴作为反应室,将含有DNA模板的反应溶液分配到大量独立的反应室中进行扩增反应,再通过统计反应室中的阳性信号来定量DNA的拷贝数,从而达到精确定量核酸拷贝数的目的。综述了近年来关于数字PCR及其在核酸标准物质研究领域的最新应用进展,重点综述了其在转基因检测、医疗诊断等领域的应用进展,以期为核酸标准物质的研制提供参考。     

Reproducible and inexpensive probe preparation for oligonucleotide arrays

We present a new protocol for the preparation of nucleic acids for microarray hybridization. DNA is fragmented quantitatively and reproducibly by using a hydroxyl radical-based reaction, which is initiated by hydrogen peroxide, iron(II)-EDTA and ascorbic acid. Following fragmentation, the nucleic acid fragments are densely biotinylated using a biotinylated psoralen analog plus UVA light and hybridized on microarrays. This non-enzymatic protocol circumvents several practical difficulties associated with DNA preparation for microarrays: the lack of reproducible fragmentation patterns associated with enzymatic methods; the large amount of labeled nucleic acids required by some array designs, which is often combined with a limited amount of starting material; and the high cost associated with currently used biotinylation methods. The method is applicable to any form of nucleic acid, but is particularly useful when applying double-stranded DNA on oligonucleotide arrays. Validation of this protocol is demonstrated by hybridizing PCR products with oligonucleotide-coated microspheres and PCR amplified cDNA with Affymetrix Cancer GeneChip microarrays.     

丙型肝炎病毒RNA打点杂交检测方法同RT－PCR方法的比较

采用ＨＣＶ基因组结构区Ｃ区ｃＤＮＡ探针和非结构区ＮＳ３－４区ｃＤＮＡ探针,建立了用打点杂交（ｄｏｔｂｌｏｔｈｙｂｒｉｄｉｚａｔｉｏｎ）检测血清中ＨＣＶＲＮＡ的方法,同采用ＨＣＶ基因组５’端非编码区的一对寡核苷酸引物通过逆转录－聚合酶链式反应（ＲＴ－ＰＣＲ）检测血清中ＨＣＶＲＮＡ的方法相比较,发现两种方法都能快速早期和特异地检出血清中ＨＣＶＲＮＡ,但ＲＴ－ＰＣＲ法敏感性优于ＲＮＡ打点杂交法。对于无血清学指标的慢性ＮＡＮＢ肝炎病人的诊断,可采用这两种方法。这两种方法的敏感性在很大程度上依赖于引物和探针的敏感性,以及ＲＮＡ提取方法。ＲＴ－ＰＣＲ法适用于诊断病毒血症和复制,打点杂交法适用于研究ＨＣＶＲＮＡ量的变化,对治疗的评价,以及为实验筛选较高滴度的ＨＣＶＲＮＡ阳性样本。     

A decade with nucleic acid‐based microbiological methods in safety control of foods

In the last decade, nucleic acid‐based methods gradually started to replace or complement the culture‐based methods and immunochemical assays in routine laboratories involved in food control. In particular, real‐time polymerase chain reaction (PCR) was technically developed to the stage of good speed, sensitivity and reproducibility, at minimized risk of carry‐over contamination. Basic advantages provided by nucleic acid‐based methods are higher speed and added information, such as subspecies identification, information on the presence of genes important for virulence or antibiotic resistance. Nucleic acid‐based methods are attractive also to detect important foodborne pathogens for which no classical counterparts are available, namely foodborne pathogenic viruses. This review briefly summarizes currently available or developing molecular technologies that may be candidates for involvement in microbiological molecular methods in the next decade. Potential of nonamplification as well as amplification methods is discussed, including fluorescent in situ hybridization, alternative PCR chemistries, alternative amplification technologies, digital PCR and nanotechnologies.     

Locked Nucleic Acid Pentamers as Universal PCR Primers for Genomic DNA Amplification

Background

Multiplexing technologies, which allow for simultaneous detection of multiple nucleic acid sequences in a single reaction, can save a lot of time, cost and labor compared to traditional single reaction detection methods. However, the multiplexing method currently used requires precise handiwork and many complicated steps, making a new, simpler technique desirable. Oligonucleotides containing locked nucleic acid residues are an attractive tool because they have strong affinities for their complementary targets, they have been used to avoid dimer formation and mismatch hybridization and to enhance efficient priming. In this study, we aimed to investigate the use of locked nucleic acid pentamers for genomic DNA amplification and multiplex genotyping.

Results

We designed locked nucleic acid pentamers as universal PCR primers for genomic DNA amplification. The locked nucleic acid pentamers were able to prime amplification of the selected sequences within the investigated genomes, and the resulting products were similar in length to those obtained by restriction digest. In Real Time PCR of genomic DNA from three bacterial species, locked nucleic acid pentamers showed high priming efficiencies. Data from bias tests demonstrated that locked nucleic acid pentamers have equal affinities for each of the six genes tested from the Klebsiella pneumoniae genome. Combined with suspension array genotyping, locked nucleic acid pentamer-based PCR amplification was able to identify a total of 15 strains, including 3 species of bacteria, by gene- and species-specific probes. Among the 32 species used in the assay, 28 species and 50 different genes were clearly identified using this method.

Conclusion

As a novel genomic DNA amplification, the use of locked nucleic acid pentamers as universal primer pairs in conjunction with suspension array genotyping, allows for the identification of multiple distinct genes or species with a single amplification procedure. This demonstrates that locked nucleic acid pentamer-based PCR can be utilized extensively in pathogen identification.     

A comparison of nucleic acid amplification techniques for the assessment of bacterial viability

AIMS: The ability to determine the presence and viability status of bacteria by molecular methods could offer significant advantages to the food, environmental and health sectors, in terms of improved speed and sensitivity of detection. METHODS AND RESULTS: In this study, we have assessed three amplification techniques, PCR, RT-PCR and NASBA, for their ability to detect nucleic acid persistence in an E. coli strain following heat-killing. NASBA offered the greatest sensitivity of the three methods tested. The presence of residual DNA and mRNA could be detected by PCR and NASBA, respectively, for up to 30 h postdeath, by which time cell death had been confirmed by culture methods. Thus a single quantitative measurement based on nucleic acid amplification did not permit unequivocal determination of cell viability. CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: The correlation between cell viability and persistence of nucleic acids must be well characterized for a particular analytical situation before molecular techniques can be substituted for traditional culture methods.     

Extracting nucleic acids from activated sludge which reflect community population diversity

Critical to most studies in molecular microbial ecology is the application of DNA/RNA extraction methods which can reveal the true level of population biodiversity present in samples from the community under investigation. Activated sludge communities have been studied extensively using molecular methods, but rarely have the nucleic acid isolation methods applied been assessed for their ability to achieve this. This study compares eight published RNA and DNA extraction protocols and one commercially available DNA isolation kit for their capacity to provide high quality nucleic acids that reflect the community composition. Each method was assessed on the basis of nucleic acid yield, purity and integrity, and the ability to provide PCR amplifiable RNA and DNA from known marker populations that varied in their resistance to nucleic acid extraction. Only three consistently provided DNA from each of the marker populations known to be present in the samples from fluorescence in situ hybridisation analysis. The failure of the other methods emphasises the need to validate all DNA/RNA extraction protocols. It is recommended that several validated extraction methods be used and the extracts pooled to further minimise any risk of bias.     

基于CRISPR/Cas系统的核酸生物传感器

近年来,CRISPR/Cas系统已经成为转录调控和基因组编辑的重要工具。除了在基因编辑领域的贡献,CRISPR/Cas系统独特的靶核酸顺式切割和非特异性单链核酸反式切割能力,在开发核酸检测的新型生物传感器方面展现出巨大潜力。构建基于CRISPR/Cas系统高灵敏度生物传感器的关键通常依赖其与不同信号扩增策略,诸如核酸扩增技术或特定信号转导方法的结合。基于此,本文旨在通过介绍不同类型的CRISPR/Cas系统,全面概述基于该系统的核酸检测生物传感器的研究进展,并重点对结合核酸扩增技术（PCR、LAMP、RCA、RPA和EXPAR）、灵敏的信号转导方法（电化学和表面增强拉曼光谱）和特殊结构设计生物传感的三大类型信号放大策略的CRISPR/Cas生物传感器进行总结和评论。最后,本文对目前的挑战以及未来的前景进行展望。