纳米金对PCR扩增效率影响的机制探讨

近年来,纳米金粒子对聚合酶链式反应（polymerasechainreaction,PCR）的增效作用倍受关注,但是其具体的机制仍未明确提出。研究发现在PCR反应中,纳米粒子的增效作用是存在最佳浓度的,增加DNA聚合酶或者小牛血清蛋白（BSA）可以消除纳米金粒子导致的抑制。我们认为,纳米金粒子可能起到了类似于聚合酶B亚基的作用,提高了DNA聚合酶的延伸能力;而过量纳米金对PCR的抑制作用可能与纳米金结合单链DNA产生的位阻效应有关。     

Detection of Various Variant Verotoxin Genes in Escherichia coli by Polymerase Chain Reaction

We constructed common primers for the polymerase chain reaction to detect the genes for various Verotoxins reported, that is, VT1 (or SLT-I), VT2 (or SLT-II), VT2vha, VT2vhb, SLT-IIv (or VT2vp1, VTe) and SLT-IIva (or VT2vp2). A total of 80 Verocytotoxin-producing Escherichia coli strains isolated from humans, domestic animals and meats gave a positive result by PCR with the designed common primers. Digestion by restriction endonucleases BglII and EcoT14I of the amplicon of the VT2vp2 gene gave specific bands of the expected sizes, but not of the amplicons of other VT genes, suggesting a possible method for identification of the VT2vp2 gene. Application of the PCR with the designed primers in diagnostic and epidemiological studies on VTEC infection is also discussed.     

运用PCR对小鼠植入前胚胎进行性别诊断

根据C57BL6小鼠Y染色体重复序列145C5的碱基顺序,设计并合成一对引物,运用PCR扩增昆明白小鼠入前胚胎卵裂球DNA,以确定其性别,共对108枚活检胚胎的相应卵裂球进行了性别诊断,获雄性胚46枚,雌性胚62枚,移植后分别获雄性仔鼠4只,准确率100％（4／4）,雌性仔鼠9只,准确率70％（9／13）,本研究结果表明小鼠Y染色体重复序列145C5的碱基顺序在C57BL6小鼠和昆明白小鼠中基本一致,为农牧业动物进行性别选择和运用PCR进行单基因病植入前遗传学诊断提供了方法学基础。     

Amplification of Nucleic Acids by Polymerase Chain Reaction (PCR) and Other Methods and their Applications

Abstract

The in vitro replication of DNA, principally using the polymerase chain reaction (PCR), permits the amplification of defined sequences of DNA. By exponentially amplifying a target sequence, PCR significantly enhances the probability of detecting target gene sequences in complex mixtures of DNA. It also facilitates the cloning and sequencing of genes. Amplification of DNA by PCR and other newly developed methods has been applied in many areas of biological research, including molecular biology, biotechnology, and medicine, permitting studies that were not possible before. Nucleic acid amplification has added a new and revolutionary dimension to molecular biology. This review examines PCR and other in vitro nucleic acid amplification methodologies—examining the critical parameters and variations and their widespread applications—giving the strengths and limitations of these methodologies.     

Micro-droplet Digital Polymerase Chain Reaction and Real-Time Quantitative Polymerase Chain Reaction Technologies Provide Highly Sensitive and Accurate Detection of Zika Virus

The establishment of highly sensitive diagnostic methods is critical in the early diagnosis and control of Zika virus(ZIKV)and in preventing serious neurological complications of ZIKV infection. In this study, we established micro-droplet digital polymerase chain reaction(ddPCR) and real-time quantitative PCR(RT-qPCR) protocols for the detection of ZIKV based on the amplification of the NS5 gene. For the ZIKV standard plasmid, the RT-qPCR results showed that the cycle threshold(Ct) value was linear from 10~1 to 10~8 copy/l L, with a standard curve R~2 of 0.999 and amplification efficiency of 92.203%;however, a concentration as low as 1 copy/l L could not be detected. In comparison with RT-qPCR, the dd PCR method resulted in a linear range of 10~1–10~4 copy/l L and was able to detect concentrations as low as 1 copy/l L. Thus, for detecting ZIKV from clinical samples, RT-qPCR is a better choice for high-concentration samples(above 10~1 copy/l L),while ddPCR has excellent accuracy and sensitivity for low-concentration samples. These results indicate that the ddPCR method should be of considerable use in the early diagnosis, laboratory study, and monitoring of ZIKV.     

Greater Amount of HCV-RNA in Tears Compared to Blood

Plasma, tear fluid and swabs from eye, nose and pharynx of 33 patients were examined for presence of hepatitis C virus (HCV) RNA by polymerase chain reaction (PCR). All samples from plasma, tear fluid and eyeswabs were found to show a positive reaction in HCV-RNA PCR. Remarkably, we regularly found greater amounts of amplification products in tear fluid and eyeswabs compared to plasma using the same conditions for sample preparation.     

Molecular Characterization of Human Rotavirus VP4 Genes by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism Assay

A restriction fragment length polymorphism (RFLP) assay was developed to examine the genetic variability and similarity of the VP4 genes of human rotaviruses. The VP4 genes of 14 human rotavirus strains, including VP4 serotype P1A strains (Wa, P, VA70), serotype P1B strain (DS-1), serotype P2 strains (M37, 1076, McN, ST3) and serotype P3 strains (AU-1, AU228, K8, PA151, PCP5, MZ58), and those of 2 feline strains (FRV-1 and Cat2) were reverse-transcribed and amplified by the polymerase chain reaction (PCR). The amplified VP4 cDNAs were then digested with a panel of restriction endonucleases (HindIII, NruI, HaeIII, and EcoRI), resulting in the identification of at least one enzyme with which digestion produced an RFLP profile specific for a particular P serotype. Of interest was the presence of two distinct RFLP patterns within the serotype P3 VP4 genes: one corresponding to the VP4 gene carried by the members of the AU-1 genogroup and the other corresponding to the VP4 genes carried by naturally-occurring reassortants between members of the AU-1 and other genogroups.     

Development of A Rapid Method for the Diagnosis of Citrus Greening Disease using the Polymerase Chain Reaction

The fastidious bacterium causing citrus greening disease occurs in uneven and low concentrations in the sieve tubes of host plants. A rapid and sensitive assay based on the polymerase chain reaction (PCR) has been developed using the primers derived from the sequences of the cloned DNA fragment of greening fastidious bacterium (GFB) to detect GFB infection in citrus. One set of the primer pairs (named 226-primer pair), which generates a 226 bp GFB-specific fragment from total DNA templates purified from diseased citrus plants, was tested and chosen for PCR amplification. The PCR-based assay using this 226-primer pair effectively detected GFB infection in various citrus cultivars collected from different Asian countries. This detection technique, which can be completed within 6 h, offers a rapid and efficient method for accurate diagnosis of citrus greening disease.     

Detection of the protozoan Neospora caninum Using in situ Polymerase Chain Reaction

A new method to detect the protozoan Neospora caninum using indirect in situ polymerase chain reaction (PCR) is described. In situ PCR combines the advantages of the extraordinarily high sensitivity and specificity of PCR and the in situ representation of immunohistochemical methods. We describe an indirect in situ PCR, whereby the amplified products were detected using a primed in situ (PRINS) reaction with hapten-labeled nucleotides and visualized using fluorochrome-labeled antibodies. This technique was carried out in both infected cell cultures and formalin fixed, paraffin embedded tissues. Clear signals were obtained in the N. caninum positive samples using in situ PCR, whereas control slides with Toxoplasma gondii infected tissues always yielded negative results.     

聚合酶链反应技术检测禽网状内皮组织增殖病病毒

目的建立聚合酶链反应(PCR)技术检测禽网状内皮组织增殖病病毒(REV)的方法。方法提取感染REV-T和脾坏死病毒(SNV)的SPF鸡胚成纤维细胞DNA为模板,利用前病毒长末端重复序列(LTR)区引物进行扩增。采集肿瘤病鸡,以及人工感染REV 28 d后鸡肝脏、脾脏、肾脏、心脏、胸腺、法氏囊等器官,进行扩增。同时将采集的脏器组织,进行HE染色和免疫组化试验(IHC)。结果REV-T感染的组织未检测出电泳条带,而SNV感染的细胞中检测到了一条300bp特异而清晰的电泳条带,而且SNV感染的鸡组织中,PCR方法检测到了特异的条带。通过HE染色和免疫组化技术观察到了肿瘤组织,肿瘤细胞的形态、分布。结论PCR检测REV更快捷,特异更好。     

Comparison of a Reversed Passive Latex Agglutination and a Polymerase Chain Reaction for Identification of Cholera Toxin Producing Vibrio cholerae O1

Production of cholera toxin (CT) in AKI medium and conservation of CT gene (ctx) of 49 strains of Vibrio cholerae O1 were compared by reversed passive latex agglutination (RPLA) and polymerase chain reaction (PCR). The production of CT agreed with conservation of the ctx in 48 out of the 49 strains. Ten strains were positive, and 38 strains were negative by both methods. Only one strain was negative in RPLA and positive in PCR. This suggested that the combination of AKI-SW and RPLA is comparable to PCR to identify CT-producing V. cholerae O1.     

用于聚合酶链式反应(PCR)引物设计的计算机程序

 本文报道了两个用于PCR引物设计的计算机程序PCRDESN和PCRDESNA。PCRDESN程序主要从以下4个方面评价用户自己设计的一对引物的质量:(1)引物内的碱基反向重复或发夹结构,(2)两个引物之间的碱基互补配对,(3)两个引物之间的同源性,(4)引物的碱基组成及特点和T_m值计算。通过用多例文献发表的及本院有关实验室提供的引物对序列的验证,确定了程序的运算参数,证明该程序能较好地检验引物对的质量和解释某些PCR实验失败的原因。PCRDESNA程序采用逐级优化的方法和比PCRDESN所选用的更严紧的引物选择参数对用户提供的核酸序列进行快速检索,以确定所有可能的和合适的引物对。     

Specific Detection of Buckwheat Residues in Processed Foods by Polymerase Chain Reaction

A specific and qualitative detection method for buckwheat in foods using the polymerase chain reaction (PCR) was developed. Trace amounts of buckwheat in commercial food products were qualitatively detected by this method. It should be reliable for detecting buckwheat residues in processed foods and practical for monitoring the labeling system for allergenic food materials.     

Degradation of a Polymerase Chain Reaction (PCR) Product by Heat-Stable Deoxyribonuclease (DNase) Produced from Yersinia enterocolitica

When crude deoxyribonucleic acid (DNA) preparations by boiling were used for the polymerase chain reaction (PCR) from pathogenic and non-pathogenic Yersinia enterocolitica strains, the amplified products were degraded after their storage at 4 C. The degradation of products was prevented by the addition of ethylenediaminetetraacetate (EDTA) or treatment with proteinase K. These findings indicate that Y. enterocolitica produced heat-stable deoxyribonuclease (DNase). Proteinase K treatment would be recommended to prevent heat-stable DNase contamination in the DNA preparations for PCR from Y. enterocolitica strains.     

Heterogeneity of HLA-G Genes Identified by Polymerase Chain Reaction/Single Strand Conformational Polymorphism (PCR/SSCP)

A genomic HLA-G clone named 7.0E was isolated from a Japanese placenta. The deduced amino acid sequence of the 7.0E was identical to two HLA-G genomic clones and two cDNA clones previously described. The DNA sequences of α1 and α2 domains of the HLA-G gene from 5 cell lines also encoded the same amino acids. However, a 14 bp insertion, ATTTGTTCATGCCT, was present in the 3′ untranslated region of 7.0E compared with the originally described HLA-G clone (HLA 6.0). Polymerase chain reaction (PCR)/single strand conformational polymorphism (SSCP) analysis of exon 8 allowed the HLA-G gene to be classified into two alternative types, G6.0 and 7.0 E, those correlated to the absence or the presence of the 14 bp stretch. Each group had minor sequence variant(s), and the alleles of the 7.0E-type were more heterogeneous than those of the G6.0- type. The 14 bp deletion is present only in the G6.0-type of HLA-G alleles among HLA class I genes. Thus it was suggested that G6.0 alleles were generated after diversification of the HLA-G.     

Comparison of Detection Methods for Legionella Species in Environmental Water by Colony Isolation,Fluorescent Antibody Staining,and Polymerase Chain Reaction

Three detection methods for Legionella species in water samples from cooling towers and a river were examined. Direct counting of bacteria stained with fluorescent antibody (FA) for L. pneumophila (serogroups 1 to 6) could detect the cell of 10⁴ to 10⁶ cell/100 ml in all 14 samples, while colony counting method detected 10 to 10³ CFU/100 ml only in 8 samples from cooling towers. Polymerase chain reaction (PCR) assay with primers to amplify 16S ribosomal DNA sequence of most Legionella species (LEG primer) detected legionellae in 13 samples, while species-specific primers for L. pneumophila detected the DNAs from 3 samples. In laboratory examination, LEG primers could amplify DNAs of 29 species of genus Legionella with high sensitivity, even from 1 cell of L. pneumophila GIFU 9134. The PCR assay with LEG primers was specific and sensitive methods to be satisfied the survey of legionellae. Thus, PCR assay is a suitable method to detect and monitor Legionella species in an environment.     

Development of a Synthetic Positive Control Which Also Detects Plasmid Contamination in Diagnostic Polymerase Chain Reaction

This paper describes a technique for developing a positive control for use in a nested PCR to show that the PCR has functioned correctly with both outer and inner primers designed for the diagnostic amplification of 618 and 317 bp products, respectively. This positive control produces a larger product than the diagnostic sample that can be discriminated on an agarose gel. This technique is advantageous over traditional cloning of the diagnostic PCR product itself by: (1) making it visually easy to detect plasmid contamination and thus prevent false positives from the plasmid; (2) develop a positive control when the target organism is at a very low prevalence, so initial detection is not relied on for cloning positive controls (this will ensure the PCR is working correctly prior to diagnostic sampling, reducing false negatives); or (3) for developing a PCR and determining the sensitivity prior to the use of diagnostic samples. The methods used to produce this nested positive control demonstrate how to use large oligonucleotide primers in PCR without nonspecific binding occurring.     

多重PCR对真菌性角膜炎主要致病菌的菌属鉴定

目的:建立多重PCR体系对真菌性角膜炎主要致病真菌进行快速诊断并同时进行菌属鉴定的方法。方法:建立两个多重PCR体系(体系1和体系2),对真菌性角膜炎九种主要致病真菌DNA进行检测,观察该体系对真菌临床菌株、人类基因组及其他眼部常见致病微生物DNA的检测结果。结果:体系1对镰孢菌属扩增均产生约360bp的特异产物,对曲霉菌属、牵连青霉菌和新月弯孢菌扩增均产生约470bp的特异产物。体系2对镰孢菌属、曲霉菌属均无特异产物,而对牵连青霉菌产生了360bp的特异产物,对新月弯孢霉产生了300bp的特异产物。根据DNA模板在两个多重PCR体系中扩增出的不同特异条带可将九种真菌分为四个菌属。57株真菌临床菌株中55株的鉴定结果与常规鉴定结果一致。两体系对人类基因组及其他眼部常见致病微生物DNA的扩增结果均为阴性。结论:通过两个多重PCR体系检测可将真菌性角膜炎在菌属水平进行诊断及鉴定。该方法具有快速、简便、特异、灵敏的特点,具有较好的临床应用前景。     

人传染性软疣病毒快速PCR检测方法的建立

为了能够对传染性软疣病毒(MCV)感染做出准确快速的实验室诊断,从14例临床MCV患者皮疹处提取获得病毒DNA,设计引物并进行PCR扩增获得预期的167bp的片段,经测序并与已报道的序列比对,完全一致。而使用痘病毒科其他病毒的特异引物(正痘病毒和副痘病毒属)则没有特异扩增条带。将病毒DNA进行系列稀释后行PCR扩增,结果表明PCR检测方法的敏感性为5×10-4ng/μL。