单引物PCR法引入定点突变 *

目的:利用单个突变引物,在含人呼吸道合胞病毒F蛋白基因编码序列的pcDNA3.1(+)-F质粒中,通过单次环形PCR在特定序列位置引入定点突变。 方法: 以双链环状的pcDNA3.1(+)-F质粒DNA为模板,设计分别含有三种目的突变N70Q, I431N, Q270T的三条单引物,分别进行单次PCR。用甲基化DNA特异的限制性内切酶Dpn I处理PCR产物后转化大肠杆菌DH5α,进行克隆筛选,酶切鉴定和测序分析。 结果: 酶切鉴定结果和测序结果均符合预期,利用单引物PCR法成功在含人呼吸道合胞病毒F蛋白基因编码序列的pcDNA3.1(+)-F质粒DNA 中引入了单碱基突变、两个间隔碱基突变及相邻三碱基突变三种目的突变。 结论: 单引物PCR法解决了常规定点突变方法中多个PCR反应,程序繁琐及突变效率低等问题,是一种简便、快速、有效的基因工程定点突变新方法。     

A partial-complementary adapter for an improved and simplified ligation-mediated suppression PCR technique

Ligation-mediated suppression PCR (LMS-PCR) is a powerful tool for walking in unknown genomic DNA regions from known adjacent sequences. This approach has made it feasible to obtain promoter sequences and to enable researchers to identify full-length gene sequences or isoforms of multigene families. However, the advantages of LMS-PCR can be obviated by the presence of incomplete base modifications on the suppression adapters. We propose here that a 'partial-complementary adapter' is a more reliable suppression adapter, demanding only 5'-end phosphorylation. We also describe a simplified procedure for the easier preparation of PCR templates with very small quantities of DNA and a fast and direct characterization of the suppression-PCR products. A set of practical guidelines is proposed for pre-checking the efficiency of the adapter modification using two model systems: bacteriophage lambda (lambda) and Arabidopsis.     

Presymptomatic and quantitative detection of Mycosphaerella graminicola development in wheat using a real-time PCR assay

Presymptomatic and accurate diagnosis of Mycosphaerella graminicola leaf blotch is desirable for the disease prediction and the timely application of fungicides. To develop a sensitive PCR assay, four specific primer pairs were designed. They were more specific than three known specific primer pairs. Three of them could detect as little as 0.5 pg M. graminicola DNA in a conventional PCR. A real-time PCR assay was applied for monitoring the disease progression in both inoculated and naturally infected wheat plants using the primer pair ST-rRNA F/R. In inoculated plants, M. graminicola DNA could be detected immediately after inoculation and a steady increase was detected before visible symptoms appeared at 8 days. The rapid growth period took place between 6 and 16 days postinoculation. In the field, the disease progression in the top three leaf layers was followed during the epidemic period. The results were significantly correlated to the disease indices (R=0.8986) and also to the number of pycnidia per leaf (R=0.9227). These suggest that the real-time PCR assay is a reliable approach for the presymptomatic and accurate detection of M. graminicola development in the field.     

应用于染色体步移的PCR扩增技术的研究进展

各种建立在PCR基础上染色体步移的方法能够根据已知的基因序列得到侧翼的基因序列。染色体步移技术主要应用于克隆启动子、步查获得新物种中基因的非保守区域、鉴定T-DNA或转座子的插入位点、染色体测序工作中的空隙填补,从而获得完整的基因组序列等方面。其方法主要有3种：反向PCR的方法,连接法介导的PCR的方法以及特异引物PCR的方法。文章就各种方法进行举例说明并加以分析比较。     

De Novo synthesis of DNA-like molecules by polynucleotide phosphorylase in vitro

In the presence of Mg²⁺ ions, polynucleotide phosphorylase (PNPase, EC 2.7.7.8) is known to synthesize RNA-like polymers using ribonucleoside-5′-diphosphate (NDP) substrates but to be unable to utilize deoxyribonucleoside substrates. Our experiments show that when MgCl₂ is replaced by FeCl₃, PNPase becomes able to synthesize deoxyheteropolymers using deoxyribonucleoside-5′-diphosphates (dNDPs). The deoxyheteropolymer formed from the four dNDPs is degraded by pancreatic DNase, but not by RNase, and is readily used as a template by DNA-dependent DNA polymerase. Synthesis of this DNA-like polymer is accomplished de novo without the help of any primer or preexisting template. What is more, dA/dG and dC/dT ratios of polymers synthesized by different bacterial PNPases closely match ratios found in DNA of the bacterial species the enzyme came from.     

Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi

A set of PCR primers that should amplify all subgroups of arbuscular mycorrhizal fungi (AMF, Glomeromycota), but exclude sequences from other organisms, was designed to facilitate rapid detection and identification directly from field-grown plant roots. The small subunit rRNA gene was targeted for the new primers (AML1 and AML2) because phylogenetic relationships among the Glomeromycota are well understood for this gene. Sequence comparisons indicate that the new primers should amplify all published AMF sequences except those from Archaeospora trappei. The specificity of the new primers was tested using 23 different AMF spore morphotypes from trap cultures and Miscanthus sinensis, Glycine max and Panax ginseng roots sampled from the field. Non-AMF DNA of 14 plants, 14 Basidiomycota and 18 Ascomycota was also tested as negative controls. Sequences amplified from roots using the new primers were compared with those obtained using the established NS31 and AM1 primer combination. The new primers have much better specificity and coverage of all known AMF groups.     

Comparison of DNA extraction methods for multiplex polymerase chain reaction

We compared six DNA extraction methods for obtaining DNA from whole blood and saliva for use in multiplex polymerase chain reaction (PCR) assays. The aim was to evaluate saliva sampling as an alternative to blood sampling to obtain DNA for molecular diagnostics, genetic genealogy, and research purposes. The DNA quantity, DNA purity (A_260/280), PCR inhibition ratio, and mitochondrial DNA/genomic DNA ratio were measured to compare the extraction methods. The different extraction methods resulted in variable DNA quantity and purity, but there were no significant differences in the efficiency of multiplex PCR and oligomicroarray signals after single-base extension on the arrayed primer extension 2 (APEX-2).     

Development of a 16S rDNA-targeted PCR assay for monitoring of Lactobacillus plantarum and Lact. rhamnosus during co-cultivation for production of inoculants for silages

AIMS: This paper reports a simple, rapid approach for the parallel detection of Lactobacillus plantarum and Lact. rhamnosus in co-culture in order to produce an inoculant mixture for silage purposes. METHODS AND RESULTS: The 16S rDNA-targeted PCR primers were established for parallel detection of Lact. plantarum and Lact. rhamnosus in a single multiplex PCR. A protocol for application of these primers in direct PCR as well as colony-direct (CD) PCR was developed. These primers were also applicable for the estimation of the relative amount of each DNA type in mixed probes (semi-quantitative PCR). CONCLUSIONS: The PCR assay presented in this study is a robust, fast and semi-quantitative approach for detection of Lact. plantarum and Lact. rhamnosus in liquid cultures as well as on agar plates. SIGNIFICANCE AND IMPACT OF THE STUDY: This method provides an effective tool for the establishment of a regime for co-cultivation of Lact. plantarum and Lact. rhamnosus. This would enable faster and thus cost-reduced production of ensiling inoculants.     

De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species

Scutellaria L. (family Lamiaceae) includes approximately 470 species found in most parts of the world and is commonly known as skullcaps. Scutellaria L. is a medicinal herb used as a folk remedy in Korea and East Asia, but it is difficult to identify and classify various subspecies by morphological methods. Since Scutellaria L. has not been studied genetically, to expand the knowledge of species in the genus Scutellaria L., de novo whole-genome assembly was performed in Scutellaria indica var. tsusimensis (H. Hara) Ohwi using the Illumina sequencing platform. We aimed to develop a molecular method that could be used to classify S. indica var. tsusimensis (H. Hara) Ohwi, S. indica L. and three other Scutellaria L. species. The assembly results for S. indica var. tsusimensis (H. Hara) Ohwi revealed a genome size of 318,741,328 bp and a scaffold N50 of 78,430. The assembly contained 92.08% of the conserved BUSCO core gene set and was estimated to cover 94.65% of the genome. The obtained genes were compared with previously registered Scutellaria nucleotide sequences and similar regions using the NCBI BLAST service, and a total of 279 similar nucleotide sequences were detected. By selecting the 279 similar nucleotide sequences and nine chloroplast DNA barcode genes, primers were prepared so that the size of the PCR product was 100 to 1000 bp. As a result, a species-specific primer set capable of distinguishing five species of Scutellaria L. was developed.     

Asymmetric overlap extension PCR method bypassing intermediate purification and the amplification of wild-type template in site-directed mutagenesis

By combining asymmetric PCR and overlap extension, we developed a novel asymmetric overlap extension PCR (AOE-PCR) method for site-directed mutagenesis which bypassed the need for intermediate purification and excluded the amplification of a wild-type template. This method was used to introduce single base mutations into a small GTPase gene from cotton and to simultaneously introduce two mutations just by repeating this method using the first round AOE-PCR products as template. Our results suggested that the AOE-PCR method represents a valuable improvement of the original overlap extension PCR for site-directed mutagenesis.     

不同牛分枝杆菌特异性基因PCR方法的比较

【背景】牛结核病是我国二类动物疫病,世界动物卫生组织将其列为法定报告的动物疫病。牛主要通过患病牛呼吸道分泌物和咳嗽所产生的气溶胶感染;人则主要通过食用未经高温处理的病牛的肉或奶感染。因此,经过病原学PCR检测对疑似患病牛牛奶或屠宰组织样品进行快速检验确诊,能够最大限度地减少奶牛养殖中乳品生产业的经济损失。【目的】研究并确定适宜的牛分枝杆菌PCR扩增引物及参数,为临床快速准确诊断牛结核病提供参考。【方法】对已报道的5对PCR引物,运用降落(touch down) PCR法确定适宜退火温度(Tm);运用梯度稀释的牛分枝杆菌C68001株(国内牛结核菌素生产用菌株)基因组DNA以及不同菌液含量的人工模拟临床样本(淋巴结、肺脏和牛奶),确定不同引物PCR方法的敏感性;同时以6种常见牛感染菌(牛种布鲁氏菌2308、羊种布鲁氏菌Rev.1、牛分枝杆菌C68001和AN5、禽分枝杆菌C68202、副结核分枝杆菌C68681和胞内分枝杆菌C68226)核酸样本,确定不同引物PCR方法的特异性。【结果】所有引物在53-63℃均含有目的条带,确定引物的最佳退火温度是60℃。在细菌核酸敏感性检验中,1号和3...     

一种适用于昆虫痕量DNA模板制备的方法

近年来分子生物学技术在昆虫学各领域中得到了广泛地运用 ,从昆虫样品中有效地获得DNA模板是实验成功的前提。但是由于许多昆虫体形微小 ,许多研究需要取单个个体的样品 ,用传统的酚∶氯仿抽提法难以从痕量样品中获得总DNA ,而某些生物公司的试剂盒相对而言价格昂贵。该文介绍一种快速简便、广泛适用于不同种类昆虫、各种不同保存方法保存的昆虫样品和标本的微量DNA模板制备方法     

PCR primers useful for nucleotide sequencing of rDNA of the powdery mildew fungi

Four PCR primers that are useful to determine the nucleotide sequences of the rDNA of the powdery mildew fungi were newly designed. These primers provide both enough stability to work on a wide range of powdery mildews and enough specificity to eliminate contaminating DNA by PCR. DNA sequences of the rDNA ITS region were successfully obtained from specimens that were contaminated by other fungi. In addition, sequence results of the 18S and 28S rDNA were dramatically improved by using these primers in most of the specimens examined.     

A quantitative TaqMan PCR assay for the detection of Mycoplasma suis

Aim: To develop a TaqMan probe‐based, highly sensitive and specific quantitative PCR (qPCR) assay for the detection and quantification of Mycoplasma suis in the blood of pigs. Methods and Results: Primers and probes specific to Myc. suis 16S rRNA gene were designed. The qPCR assay’s specificity, detection limit, intra‐ and inter‐assay variability were evaluated and its performance was compared with a Myc. suis conventional PCR assay (cPCR). Blood of two experimentally infected pigs, 40 Indiana pigs, 40 Brazilian sows and 28 peccaries were tested. The assay detected as few as ten copies of Myc. suis plasmids and was 100‐fold more sensitive than the cPCR. No cross‐reactivity with nontarget pig mycoplasmas was observed. An average of 1·62 × 10¹¹ and 2·75 × 10⁸ target copies ml^?1 of blood were detected in the acutely and chronically infected pigs, respectively. Three (7·5%) pigs and 32 (80·0%) sows were positive while all peccaries were negative for Myc. suis. Conclusion: The developed qPCR assay is highly sensitive and specific for Myc. suis detection and quantification. Significance and Impact of the Study: TaqMan qPCR is an accurate and quick test for detection of Myc. suis infected pigs, which can be used on varied instrumentation platforms.     

Enzymatic activity of the SARS coronavirus main proteinase dimer

The enzymatic activity of the SARS coronavirus main proteinase dimer was characterized by a sensitive, quantitative assay. The new, fluorogenic substrate, (Ala-Arg-Leu-Gln-NH)(2)-Rhodamine, contained a severe acute respiratory syndrome coronavirus (SARS CoV) main proteinase consensus cleavage sequence and Rhodamine 110, one of the most detectable compounds known, as the reporter group. The gene for the enzyme was cloned in the absence of purification tags, expressed in Escherichia coli and the enzyme purified. Enzyme activity from the SARS CoV main proteinase dimer could readily be detected at low pM concentrations. The enzyme exhibited a high K(m), and is unusually sensitive to ionic strength and reducing agents.     

Species-specific DNA probe and development of a quantitative PCR assay for the detection of Morganella morganii

Aims: To develop a SYBR Green quantitative PCR assay (qPCR) for the specific detection of Morganella morganii, a fish pathogen responsible for the Histamine Fish Poisoning. Methods and Results: A new primer set, amplifying a 179‐bp fragment of the 16S rRNA gene, was selected for specificity, and 14 M. morganii strains and 32 non‐Morganella strains were evaluated. The melting temperature of 84°C was consistently specific for the amplicon. Two standard curves were constructed: the minimum detection sensitivity was 0·563 pg of pure DNA, corresponding to DNA extracted from nine cells of M. morganii. The qPCR assay was evaluated in experiments with seeded fish samples, and the regression coefficient values were calculated. Conclusions: A highly specific and rapid assay was developed for the detection of M. morganii in tuna fish samples. Significance and Impact of the Study: This method represents the first study about the quantification of pathogenic M. morganii in fish products. This approach can be utilized to prevent the presence of this undesirable species in the food chain.     

食品中沙门氏菌分子检测靶点的筛选与评价

[目的]发掘新的沙门氏菌分子检测靶点,筛选检测性能优秀的引物.[方法]利用BLAST程序比较沙门氏菌属内基因组DNA序列的同源性以及沙门氏菌与非沙门氏菌基因组DNA序列之间的特异性,发掘出100多个检测沙门氏菌属的特异性片段,并从中随机挑选出15个片段作为候选靶点,一共设计了27对引物(FS1～FS27),对它们的特异性、灵敏度加以评价,从中筛选检测性能最好的引物.[结果]在27对引物中,检测性能最优的引物为FS23,采用该引物对供试菌株的相应检测靶点进行PCR扩增,44株沙门氏菌都能扩增到一条492 bp特异性片段,而22株非沙门氏菌则不能扩增出这一特异性片段.以FS23为引物建立PCR方法检测猪霍乱沙门氏菌基因组DNA的灵敏度为11.9 fg/μL,细菌纯培养物灵敏度为4.9×102cfu/mL;用猪霍乱沙门氏菌人工污染牛奶样品,如果接种起始菌量为100 cfu/25 mL时,只需要增菌5 h,采用上述方法即能检测出沙门氏菌.[结论]引物FS23对应的基因序列是一个性能优良的新分子检测靶点,具备很高的特异性和灵敏性,能够广泛应用于食品中沙门氏菌的快速检测.     

A PCR based assay for detection and differentiation of African trypanosome species in blood

Direct PCR analysis of trypanosome infected blood samples in the quantities required for large scale epidemiological study has always been problematic. Current methods for identifying and differentiating trypanosomes typically require several species-specific reactions, many of which rely on mouse passaged samples to obtain quality concentrated genomic DNA. As a consequence important epidemiological information may be lost during the sample preparation stage. Here, we report a PCR methodology that reduces processing and improves on the sensitivity of present screening methods. The PCR technique targets the gene encoding the small ribosomal subunit in order to identify and differentiate all clinically important African trypanosome species and some subspecies. The method is more economical, simple, and sensitive than current screening methods, and yields more detailed information, thereby making it a viable tool for large-scale epidemiological studies.     

SARS-CoV核衣壳蛋白的表达与免疫研究

依据GenBank中SARS基因组序列,采用人工合成的方法合成编码SARS病毒N蛋白的全基因(1296bp)序 列,再与设计的CTL特异性表位基因(195bp)重组后,克隆到pET-28a( )质粒中,重组质粒转化到大肠杆菌BL21 (DE3)中诱导表达。利用SARS患者恢复期阳性血清,鉴定表达蛋白。进一步纯化后免疫马,并用ELISA方法检 测血清抗体效价。结果显示SDS-PAGE表明所表达的蛋白相对分子质量约为55000 Da,与预计大小相符;Western blot显示表达的蛋白具有良好的抗原性和特异性。对表达蛋白形成的包涵体进行洗涤,得到的蛋白纯度可达到 70．1％。切胶纯化免疫马后,获得的抗SARS抗体滴度达1:2560。为亚单位疫苗研制和精制抗SARS抗体免疫制 剂提供基础。     

PCR-SSP技术对广东汉族人HLA-DR基因分型

探索具有高分辨率、高特异性和简捷快速的方法对ＨＬＡ－ＤＲ基因分型,为临床器官移植配型和疾病相关性分析提供实用的方法和基础资料．利用ＤＲ１～ＤＲｗ１８序列特异性的１９组引物及１对内参照引物进行ＰＣＲ扩增即ＰＣＲ－ＳＳＰ对ＨＬＡ－ＤＲ进行基因分型,扩增产物经琼脂糖凝胶电泳,溴乙锭染色,在紫外光下观察分型结果．每个被检个体的ＤＲ型别可由特异引物扩增出现的电泳谱带直接判断．双盲检测２２例的结果１００％正确．在１０２例中国广东地区汉族人中,ＤＲ９和ＤＲ２的基因频率最高,分别为０．２２０５和０．１９１２,ＤＲ１０为最低（０．００９８）．与用ＰＣＲ－ＳＳＯ方法分型获得的结果比较,基因型别分布基本一致,但一些等位基因的频率有差异,表明ＨＬＡ－ＤＲ基因频率的分布在不同地区、不同种族的人群间存在着差异．ＰＣＲ－ＳＳＰ法分辨率和特异性虽不及ＰＣＲ－ＳＳＯ法但比血清学方法精细,分型的全过程只需２～４ｈ能满足临床器官移植配型的要求．基因频率调查结果为器官移植配型和疾病相关性分析提供了基础资料．