PCR引物特异性核查系统(PSC)的构建与应用

聚合酶链式反应(PCR)虽已广泛用于分子生物学研究中,然而PCR实验中的非特异性产物问题将直接影响PCR的效率,在多重PCR实验中更是如此。为了最大限度地降低非特异性产物的出现率,同时避免用户频繁使用Blast比对检查非特异性,我们开发了基于NCBI-Blast的引物评估和模板DNA特异性结合能力评估的核查系统PSC(Primer Specificity Checking,http://biocompute.bmi.ac.cn/PSC),并基于虚拟PCR实验确定了用于引物质量核查计算的多种参数,能够在线提供多个物种的引物特异性核查结果。该系统可以有效地对引物序列可能产生的所有非特异性扩增进行预测,有助于实验前引物优化或者对非特异扩增结果进行解释,最终达到提高PCR效率的目的。     

染色体步移技术研究进展

染色体步移技术是一种常用的克隆已知片段旁侧序列的技术.综述了近年来染色体步移技术的发展情况,介绍了结合基因组文库的染色体步移技术和基于PCR的染色体步移技术.同时总结了物理剪切法和限制性内切酶法构建亚克隆文库的优化步骤,以及连接成环PCR法、外源接头介导PCR法和半随机引物PCR法的原理,并且比较分析了他们之间的优缺点,以期对实际操作起到借鉴作用.     

通用引物双重PCR在节肢动物物种鉴定中的应用

【目的】本研究旨在使用基于线粒体基因通用引物的双重PCR技术同时扩增单一样本中两条标记基因,从而达到简化节肢动物物种鉴定流程的目的。【方法】在一次PCR实验中同时加入可扩增线粒体COI基因和16S rDNA两个不同分子标记的引物,对3纲8目14科的14种节肢动物物种标本的基因组DNA进行扩增;扩增产物经电泳和胶回收后测序,并BLAST在线搜索相似序列,验证基于通用引物的双重PCR在不同的动物类群中用于物种鉴定的有效性。【结果】应用基于COI和16S rDNA的引物从分属于3纲8目14科的14种节肢动物基因组DNA中均可成功扩增目的基因;扩增产物测序结果进一步证实了扩增的准确性。【结论】通过本方法进行物种的分子鉴定,不仅可以保证物种鉴定的高准确率,还可以明显减少时间与DNA样本量的消耗,这对需要快速准确鉴定物种或珍稀的材料样本十分重要。     

用三引物法提高PCR的扩增效率及特异性

聚合酶链反应(PCR)现已广泛应用于分子生物学研究的各个领域。对于模板量较低的样品及单拷贝基因,通常通过增加扩增的次数或多次PCR提高扩增的效率,但这样往往出现非特异性反应。本文采用三引物双扩增法大大提高了PCR扩增的效率及特异性。 1 材料与方法 Melanoma细胞由本室保存,能分泌人组织型纤溶酶原激活剂(t-PA)。RT PCR所用引物与t-PA     

随机引物在分子生物学研究中的应用

随机引物指非特异序列的寡聚核苷酸作为DNA合成过程中的引物, 是相对于特异引物的概念.90年代它与PCR技术结合衍生了几项新技术:采用不同长度随机引物进行DNA指纹分析而衍生出的RAPD、AP-PCR及DAF方法; 进行mRNA多态分析的“差异显示”; 以及rPCR, T-PCR等技术. 以RAPD为例介绍了随机引物PCR的技术特点及其在分子生物学研究中的应用.     

基因侧翼序列扩增技术的应用进展

扩增基因的侧翼序列在分子生物学研究中具有重要作用。到目前为止,克隆基因侧翼序列的方法主要可以分为3类:反向PCR、外源接头介导PCR、半随机引物PCR。对这些技术的原理以及近期的应用情况进行了较为系统的综述,旨在为研究者选择更可靠、更合理的方法提供依据。     

基于通用引物的多重PCR对小圆胸小蠹的分子鉴定

本研究利用通用引物的多重PCR方法开展小圆胸小蠹Euwallacea fornicatus的分子鉴定,以期探究多重PCR在昆虫分子鉴定中的可行性,并为开展小圆胸小蠹的有效、准确鉴定及综合防治等提供重要依据。使用多重PCR方法扩增了小圆胸小蠹的COI、16S和28S的3个分子片段,并将获得的目的序列在GenBank中进行BLAST比对;利用MEGA 7计算方胸小蠹属不同种间的遗传距离,并基于邻接法和最大似然法分别构建单基因系统发育树。结果表明：多重PCR可以用于小圆胸小蠹分子序列的获取;基于COI和16S的遗传距离分析表明了小圆胸小蠹的种内遗传距离均小于2%;基于单个基因构建的系统发育树均显示本研究扩增的小圆胸小蠹COI和16S序列与GenBank中获取的小圆胸小蠹COI和16S序列聚为一支。多重PCR可以应用于小圆胸小蠹的分子鉴定,该方法不仅可以提高物种鉴定的准确率,还可以减少PCR过程中的时间和DNA消耗。     

一种利用ISSR开发SSR引物的方法

介绍从简单序列重复间区（ISSR）开发微卫星（SSR）引物的方法。该方法分两步：（1）正向引物的分离,即试材ISSR扩增,产物纯化回收并克隆至T载体,测序后设计正向引物（引物1）和巢式引物（引物2）;（2）反向引物的分离,即基医l组DNA酶切并连接接头,结合抑制PCR技术,对产物克隆测序后设计反向引物。应用该方法前人已在多个物种中开发出多对SSR引物．     

一种基于适配器连接介导的等位基因特异性扩增法测定多重SNP

建立了一种基于DNA适配器连接介导的等位基因特异性扩增法测定多重SNP。以CYP2D6基因中的5个SNP位点（100C>T,1661G>C,1758G>T,2470T>C和2850C>T）为例,用PCR法预扩增得一段含所有待测SNP位点的长片段,然后用限制性内切酶将其消化成短片段,在连接酶的作用下与设计的DNA适配器（adapter）相连;该适配器的一端与限制性内切酶降解后留下的粘性末端相同,另一端带有一段公共序列。在两管中加入与适配器连接的片段作为PCR扩增模板,并分别加入SNP特异性引物和一种适配器特异性的通用引物进行PCR扩增,最后用凝胶电泳法分离PCR扩增产物。由于每管与SNP的两种特异性引物中的一种对应,可以根据每管中扩增片段的大小判断SNP的类型。通过凝胶电泳法可以一次分离与5种SNP类型相对应的引物特异性延伸反应产物;采用该法成功测定了20名健康中国人的CYP2D6基因中5个SNP位点的基因多态性,与限制性片段长度多态性法（RFLP）测定结果完全一致。该方法采用n+1种引物（n种SNP特异性引物和一种通用引物）进行n重PCR反应,极大提高了PCR反应的特异性,结果准确,可用于同时测定多个SNP位点。

     

通用引物PCR分离登革病毒2型cDNA及其插入方向鉴定

逆转录后采用聚合酶链反应(RT/PCR)扩增登革病毒2型中国海南98株(DEN_2HN98)部分包膜糖蛋白(E)基因,PCR产物钝端插入pUC18质粒,获得重组质粒pDEⅡ305。用pUC/M13测序用通用引物,PCR方法又从pDEⅡ305扩增分离DEN_2 E cDNA片段。通过一侧通用引物和另一侧DEN_2 E特异引物配对,引导酶促DNA扩增反应,鉴定了pDEⅡ305中cDNA片段的插入方向,结果与序列分析一致。本文首次报道通用引物PCR方法的建立,实验结果表明该技术可用于pUC/M13系统中插入片段的分离及其方向鉴定。     

Primer design versus PCR bias in methylation independent PCR amplifications

Many protocols in methylation studies utilize one primer set to generate a PCR product from bisulfite modified template regardless of its methylation status (methylation independent amplification MIP). However, proportional amplification of methylated and unmethylated alleles is hard to achieve due to PCR bias favoring amplification of unmethylated relatively GC poor sequence. Two primer design systems have been proposed to overcome PCR bias in methylation independent amplifications. The first advises against including any CpG dinucleoteides into the primer sequence (CpG-free primers) and the second, recently published by us, is based on inclusion of a limited number of CpG sites into the primer sequence. Here we used the Methylation Sensitive High Resolution Melting (MS-HRM) technology to investigate the ability of primers designed according to both of the above mentioned primer design systems to proportionally amplify methylated and unmethylated templates. Ten “CpG-free” primer pairs and twenty primers containing limited number of CpGs were tested. In reconstruction experiments the “CpG-free” primers showed primer specific sensitivity and allowed us to detect methylation levels in the range from 5 to 50%. Whereas while using primers containing limited number of CpG sites we were able to consistently detect 1–0.1% methylation levels and effectively control PCR amplification bias. In conclusion, the primers with limited number of CpG sites are able to effectively reverse PCR bias and therefore detect methylated templates with significantly higher sensitivity than CpG free primers.     

Primer design for Whole Genome Amplification using genetic algorithms

Whole Genome Amplification (WGA) is an important process to increase limiting amounts of genomic DNA prior to genomic analyses. Current amplification methods based on primer extension or strand displacement principles employ primers of partially or totally random sequence. In this paper, we present a method using Genetic Algorithms to optimize a single primer design to be used in a primer extension reaction to achieve unbiased WGA. Computational simulation and prediction of a suitable primer proposed two candidates NYP6-1 (ATCTCA) and NYP6-2 (TGAGAT). NYP6-1 amplified to a maximum length of 2537 base pairs (bp), had genome coverage of approximately 45.62%, with an average of 493 and variance of 163 amplicons per 1 megabasepairs (Mb). NYP6-2 amplified to a maximum length of 2926 bp and covered 54.35% of the genome with an average of 579 and a variance of 191 amplicons per Mb. In contrast, the original primer used in Degenerate Oligonucleotide-Primed PCR (DOP-PCR) had coverage of 20.93%, an average of 74 and variance of 188 amplicons per Mb when extended up to a length of 2000 bp. Successful WGA of miniscule amounts of genomic DNA requires the amplification method used to resolve issues on efficiency, accurate representation of the whole genome and ability to degraded DNA. The sequence NYP6-2 discovered using our method can be confidently used in a primer extension based protocol to perform quantitatively unbiased WGA.     

A New PCR Method: One Primer Amplification of PCR-CTPP Products

Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) is a convenient method for genotyping single nucleotide polymorphisms, saving time, and costs. It uses four primers for PCR; F1 and R1 for one allele, and F2 and R2 for the other allele, by which three different sizes of DNA are amplified; between F1 and R1, between F2 and R2, and between F1 and R2. To date, we have applied PCR-CTPP successfully for genotyping more than 60 polymorphisms. However, it is not rare that PCR does not produce balanced amplification of allele specific bands. Accordingly, the method was modified by attaching a common sequence at the 5' end of two-pair primers and adding another primer with the common sequence in PCR, in total five different primers in a tube for PCR. The modification allowed one primer amplification for the products of initial PCR with confronting two-pair primers, named as one primer amplification of PCR-CTPP products (OPA-CTPP). This article demonstrates an example for an A/G polymorphism of paraoxonase 1 (PON1) Gln192Arg (rs662). PCR-CTPP failed clear genotyping for the polymorphism, while OPA-CTPP successfully produced PCR products corresponding to the allele. The present example indicated that the OPA-CTPP would be useful in the case that PCR-CTPP failed to produce balanced PCR products specific to each allele.     

Gene walking using sequential hybrid primer polymerase chain reaction

We developed a simple and robust method for removing nonspecific amplification produced during gene walking with a gene-specific primer and a degenerate primer. The primary walking polymerase chain reaction (PCR) was followed by two or three PCR rounds, each incorporating a low concentration of a reverse hybrid primer, where the 3′ end was bound to a target sequence generated in the preceding PCR round and the 5′ end was a new sequence that generated a target sequence for the next PCR round. The low concentration of the hybrid primer and the extent of amplicon stem-loop formation inhibited nonspecific amplification and enabled successful walking along three genes.     

用寡核苷酸本身作为PCR引物检测其重组DNA

以待检测的寡核苷酸本身作为一个引物,加上两个载体特异引物,组成两对PCR引物。含待检测寡核苷酸片段的重组DNA用这两对引物可分别扩增出两个大小不同的片段,而载体DNA只有一对引物（即载体特异引物）可扩增出一个较小的片段。     

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches

The polymerase chain reaction (PCR) is sensitive to mismatches between primer and template, and mismatches can lead to inefficient amplification of targeted regions of DNA template. In PCRs in which a degenerate primer pool is employed, each primer can behave differently. Therefore, inefficiencies due to different primer melting temperatures within a degenerate primer pool, in addition to mismatches between primer binding sites and primers, can lead to a distortion of the true relative abundance of targets in the original DNA pool. A theoretical analysis indicated that a combination of primer-template and primer-amplicon interactions during PCR cycles 3–12 is potentially responsible for this distortion. To test this hypothesis, we developed a novel amplification strategy, entitled “Polymerase-exonuclease (PEX) PCR”, in which primer-template interactions and primer-amplicon interactions are separated. The PEX PCR method substantially and significantly improved the evenness of recovery of sequences from a mock community of known composition, and allowed for amplification of templates with introduced mismatches near the 3’ end of the primer annealing sites. When the PEX PCR method was applied to genomic DNA extracted from complex environmental samples, a significant shift in the observed microbial community was detected. Furthermore, the PEX PCR method provides a mechanism to identify which primers in a primer pool are annealing to target gDNA. Primer utilization patterns revealed that at high annealing temperatures in the PEX PCR method, perfect match annealing predominates, while at lower annealing temperatures, primers with up to four mismatches with templates can contribute substantially to amplification. The PEX PCR method is simple to perform, is limited to PCR mixes and a single exonuclease step which can be performed without reaction cleanup, and is recommended for reactions in which degenerate primer pools are used or when mismatches between primers and template are possible.     

基因组步移法克隆小菜蛾CYP9G2基因的上游序列

利用4种产生平端切头的限制性内切酶消化小菜蛾(Plutella xylostella)的基因组DNA,然后利用DNA连接酶的催化作用,在4种不同平端切头的小菜蛾基因组DNA上连接一个氨基化的基因组步移衔接头序列,针对衔接头及已克隆的CYP9G2基因的序列,设计两对PCR上、下游引物,进行PCR扩增、T-A克隆和阳性克隆的巢式PCR验证,通过测序克隆到了小菜蛾CYP9G2基因上游未知序列约1.8 kb.通过对该基因的上游序列进行信息分析,发现1个可能的节肢动物动物转录起始子(Inr),3个CAAT样盒及1个抗氧化剂样反应因子,共5个可能的顺式调控元件.研究还表明,利用基因组步移方法可以快速地克隆已知序列的上游未知序列,实验操作经济、简便,对于已知cDNA序列或部分基因组序列的基因,其上游调控序列的克隆,基因组步移具有较高的实用价值.     

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design

We have developed a new primer design strategy for PCR amplification of distantly related gene sequences based on consensus-degenerate hybrid oligonucleotide primers (CODEHOPs). An interactive program has been written to design CODEHOP PCR primers from conserved blocks of amino acids within multiply-aligned protein sequences. Each CODEHOP consists of a pool of related primers containing all possible nucleotide sequences encoding 3-4 highly conserved amino acids within a 3' degenerate core. A longer 5' non-degenerate clamp region contains the most probable nucleotide predicted for each flanking codon. CODEHOPs are used in PCR amplification to isolate distantly related sequences encoding the conserved amino acid sequence. The primer design software and the CODEHOP PCR strategy have been utilized for the identification and characterization of new gene orthologs and paralogs in different plant, animal and bacterial species. In addition, this approach has been successful in identifying new pathogen species. The CODEHOP designer (http://blocks.fhcrc.org/codehop.html) is linked to BlockMaker and the Multiple Alignment Processor within the Blocks Database World Wide Web (http://blocks.fhcrc.org).     

Comparative Sensitivity of PCR Primer Sets for Detection of Cryptosporidium parvum

Improved methods for detection of Cryptosporidium oocysts in environmental and clinical samples are urgently needed to improve detection of cryptosporidiosis. We compared the sensitivity of 7 PCR primer sets for detection of Cryptosporidium parvum. Each target gene was amplified by PCR or nested PCR with serially diluted DNA extracted from purified C. parvum oocysts. The target genes included Cryptosporidium oocyst wall protein (COWP), small subunit ribosomal RNA (SSU rRNA), and random amplified polymorphic DNA. The detection limit of the PCR method ranged from 10³ to 10⁴ oocysts, and the nested PCR method was able to detect 10⁰ to 10² oocysts. A second-round amplification of target genes showed that the nested primer set specific for the COWP gene proved to be the most sensitive one compared to the other primer sets tested in this study and would therefore be useful for the detection of C. parvum.