限制性内切酶介导的重叠延伸在人环氧合酶-1(COX-1)基因克隆中的应用

建立一种用于克隆全长基因的、限制性内切酶介导的重叠延伸法 .对全长基因进行分段扩增 ,并利用适当的限制性内切酶对基因序列内相应的限制性位点进行酶切 ,从而使分段扩增片段得以重叠并互为模板 ,在DNA聚合酶的作用下延伸获得全长基因 .将环氧合酶 1 (COX 1 )基因的外显子 9巧妙地拼接到了缺失外显子 9的COX 1cDNA片段中 ,获得了COX 1基因的全长cDNA .该方法分 3步进行 .首先 ,通过RT PCR分别扩增跨外显子 9的cDNA片段和缺失外显子 9的cDNA片段 ,并克隆到pMD1 8 T载体上 ;其次 ,PCR扩增外显子 9片段 ,限制性内切酶StuI酶切缺失外显子9cDNA片段的重组质粒 ,二者以一定的比例混合 ,互为模板 ,在pfuDNA聚合酶的作用下进行延伸 ,从而产生一个双链的DNA分子 .最后 ,以延伸产物为模板 ,用COX 1cDNA两端的引物进行PCR扩增 ,产生包含外显子 9的COX 1基因的全长cDNA .这种限制性内切酶介导的重叠延伸方法 ,对于克隆mRNA剪接水平上受调控的基因尤为有用 ,同时也为基因的重组和修饰提供一个新的思路     

鹅源新城疫病毒ZJI株基因组cDNA克隆的序列修饰

将鹅源新城疫病毒ZJI株全基因组cDNA克隆通过酶切切下包含T7启动子区域和转录载体的片段,将其自身环化后获得约6．5kb的质粒。设计引物,利用基因定点突变技术,在此质粒上T7启动子与NDV Leader序列之间突变插入额外的3个G碱基,将此突变最终引入到原基因组cDNA克隆中。应用RT—PCR技术从尿囊液中扩增NDV基因组F／HN基因区域部分片段,利用限制性内切酶BsmBI将扩增片段连接,最终将原cDNA克隆中相应片段替换下。测序结果表明,原基因组cDNA克隆中特定位置碱基插入突变成功,F／HN基因区域碱基突变均得以纠正。以上cDNA克隆的修饰与替换为该毒株的反向遗传研究打下了基础。     

肺炎支原体双蛋白多抗原表位表达载体的构建

目的构建肺炎支原体(Mp)双蛋白多特异抗原表位表达载体,提高重组蛋白抗原的敏感性。方法应用生物信息学方法筛选Mp P116粘附蛋白抗原表位序列,PCR点突变技术获取P116蛋白基因片段,与pMD-T载体重组,转入大肠埃希菌JM109,通过限制性酶切图谱和基因序列分析鉴定重组质粒。酶切回收P116基因片段与pGEX 6P-1-P1 DNA重组,转入大肠埃希菌JM109菌株。用Glutathione Sepharose 4B纯化重组蛋白,SDS-PAGE分析表达产物的相对分子量,用Mp免疫血清进行免疫印迹试验,鉴定重组蛋白的免疫原性。结果 PCR点突变扩增Mp黏附蛋白P116的基因片段为597 bp,该基因片段与已知的基因库序列分析比较,除两个突变位点由UAG突变为UGG外,其余核苷酸序列同源性为100%。SDS-PAGE分析多表位重组蛋白相对分子质量(Mr)为77.8 kDa。免疫印迹结果显示,Mp兔多价血清能与纯化的78KDa的重组蛋白发生免疫反应。结论本研究成功构建了Mp双蛋白多表位的表达载体。该表达载体表达的重组蛋白具有Mp特异的免疫反应性。重组蛋白的敏感性有待进一步鉴定。     

肺炎支原体P1蛋白羧基端基因片段在大肠杆菌中克隆的研究

在大肠杆菌中克隆肺炎支原体P1蛋白羧基端基因片段,为P1蛋白基因片段的扩增、表达及探讨羧基端基因片段功能打基础.采用PCR扩增方法获取P1结构基因.扩增产物用SalI和EcoRI酶切消化,回收1kb大小的DNA片段并与pUC19DNA连接,转入大肠杆菌JM109菌株.用X-gal平板及质粒图谱分析方法筛选重组克隆株,再用限制性核酸内切酶酶切图谱分析鉴定.经PCR扩增MPDNA获得1条5.0kbDNA片段.重组质粒限制性内切酶指纹图谱显示出2条带,1条为pUC19载体DNA带,另1条是1kb的插入片段.实验获得肺炎支原体P1蛋白结构基因及含P1蛋白羧基端DNA片段的重组克隆株.     

基因突变的检测

1985年以前对基因中显著的缺失、插入、重排,可以用Southern杂交法来鉴定。一些小的变异,包括单碱基改变,只有当它们位于限制性内切酶的切点上时,方可被检出(如RFLP,限制性片段长度多态性)。如果这些小的变异不是位于限制性内切酶的切点上,那么只有对整个的基因进行顺序测定,当然,这是费时费力的。检测基因中的未知突变较为有效的方法于1985年     

甘蔗花叶病毒E株系外壳蛋白基因原核表达载体的构建与表达

目的:用原核表达的方法获取大量带6个His标记的甘蔗花叶病毒E株系(ScMV-E)外壳蛋白(CP)。方法:用带有BamHⅠ和SalⅠ酶切位点的特异引物,以带有多个基因的重组质粒pNUSCP为模板,扩增出片段长度为942bp的ScMV-E外壳蛋白基因,亚克隆到pMD18-T载体上,转化E.coliDH5α,经双酶切检测获得阳性克隆。BamHⅠ和SalⅠ双酶切阳性克隆质粒,回收目的片段ScMV-E的CP基因。把目的片段插入表达载体pET29a( ),转化E.coliBL21(DE3),测序。结果:阳性质粒pET29a-CP在E.coliBL21(DE3)中得到大量特异表达。SDS-PAGE分析表明,该蛋白的相对分子质量约36000,与预测一致。结论:以上方法可以得到带6个His标记的目的蛋白,有利于纯化并获取高纯度的ScMV-E的外壳蛋白。     

C型产气荚膜梭菌β1毒素基因表达

利用PCR技术,从C型产气荚膜梭菌染色体DNA中扩增出β1毒素基因,然后用限制性核酸内切酶BamHI和EcoRI对其进行双酶切处理,回收0．95kb的β1毒素基因片段,最后将其定向克隆在事先经同样内切酶处理的载体pET-28c中相应位点上,转化至受体菌B121(DE3)qh。经BamHI和Eco RI双酶切鉴定和核苷酸序列测定证实,构建的重组质粒pETXBl含有B毒素基因,并且具有正确的基因序列和阅读框架。重组菌株BI21(DE3)(pETXB1)经IPIG诱导后,其表达产物经ELISA检测和SDS-PAGE分析,结果表明重组菌株可以高效表达β1毒素蛋白,该蛋白占菌体总蛋白相对含量的12．24％。     

鹅源新城疫病毒ZJI株基因组cDNA克隆的序列修饰*

将鹅源新城疫病毒ZJI株全基因组cDNA克隆通过酶切切下包含T7启动子区域和转录载体的片段,将其自身环化后获得约6.5kb的质粒。设计引物,利用基因定点突变技术,在此质粒上T7启动子与NDV Leader序列之间突变插入额外的3个G碱基,将此突变最终引入到原基因组cDNA克隆中。应用RT-PCR技术从尿囊液中扩增NDV基因组F/HN基因区域部分片段,利用限制性内切酶BsmB I将扩增片段连接,最终将原cDNA克隆中相应片段替换下。测序结果表明,原基因组cDNA克隆中特定位置碱基     

一种测定癌基因c-Ha-ras点突变的简易方法——PCR-RFLP法

利用多聚酶DNA链延伸反应与限制性内切酶酶解片段长度多态性分析相结合,可简单、迅速、准确地对胃癌组织及细胞株DNA中癌基因c-Ha-ras第12位密码子是否存在点突变进行测定。这个方法是使用非同位素方法对单拷贝基因点突变进行检测的首次报道。     

PCR-RFLP和PCR-SSCP方法对弱精子症精子mtATPase6基因突变的检测

为了检测弱精子症精子mtATPase6基因突变,采用PCR方法扩增了17例弱精子症mtDNA8602～9416区域815bp目的片段,用MspI和HaeⅢ限制性内切酶酶切,分别用琼脂糖凝胶电泳、聚丙烯酰胺凝胶电泳和单链构像多态性(SSCP)筛查突变。筛选出3例突变标本,经测序确认突变位点和突变性质。结果显示17例标本全部扩增出mtDNA8602～9416的815bp目的片段,PCR产物经MspI限制性内切酶酶切后电泳结果与剑桥序列预期酶切图谱相一致。PCR产物经HaeⅢ酶切,聚丙烯酰胺凝胶电泳图谱上出现泳动带的异常,在17例弱精子症中共筛选出2例酶切片段异常标本。PCR-HaeⅢ酶切产物的SSCP电泳图谱分析结果显示,在PCR-RFLP(HaeⅢ)电泳图谱正常的15例弱精子症标本中筛选出1例异常。两种方法在弱精子症精子标本中筛选出mtATPase6基因突变3例(3/17,17.7%)。3例测序结果发现A8701G、C8943T、C8964T、T8966C、G9053A、C9060A、C9075T、A9120G、C9296T共9个点突变,其中A8701G、T8966C、G9053A三个突变为错义突变,其余均为同义突变。上述结果提示,弱精子症精子mtATPase6基因存在较高突变率;PCR-RFLP和PCR-SSCP能简单、快速、灵敏地筛选mtATPase6基因突变。     

Identification of point mutations by mispairing PCR as exemplified in MERRF disease

The point mutation in the tRNA(Lys) gene of mitochondrial DNA (mtDNA) from patients with myoclonic epilepsy and ragged red fibers (MERRF) was quantitatively analyzed after digestion with the restriction endonuclease Nae I of the PCR amplified DNA. Since the point mutation is not part of a restriction site for a commonly available restriction endonuclease, the Nae I restriction site was introduced by PCR using a mispairing primer. The percentage of mutated mtDNA was determined in a few hairs of five members of an affected family by counting the radioactivity of the fragments after PCR amplification with labelled dATP.     

Site-directed mutagenesis by combination of homologous recombination and DpnI digestion of the plasmid template in Escherichia coli

A rapid site-directed mutagenesis strategy using homologous recombination and DpnI digestion of the template in Escherichia coli is described. Briefly, inverse polymerase chain reaction amplification of the entire circular plasmid was performed by mutagenic primers with overlapping sequences ( approximately 15 bp) for generating PCR products with approximately 15 bp of homology on the terminal ends. On direct transformation of the amplified PCR products into restriction endonuclease DpnI-expressing E. coli BUNDpnI, homologous recombination occurs in E. coli while the original templates are removed via DpnI digestion in vivo, thus yielding clones harboring mutated circular plasmids. Nearly 100% efficiency was attained when this strategy was used to modify DNA sequences.     

Cloning of the BssHII restriction-modification system in Escherichia coli : BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs.

BssHII restriction endonuclease cleaves 5'-GCGCGC-3' on double-stranded DNA between the first and second bases to generate a four base 5'overhang. BssHII restriction endonuclease was purified from the native Bacillus stearothermophilus H3 cells and its N-terminal amino acid sequence was determined. Degenerate PCR primers were used to amplify the first 20 codons of the BssHII restriction endonuclease gene. The BssHII restriction endonuclease gene (bssHIIR) and the cognate BssHII methyltransferase gene (bssHIIM) were cloned in Escherichia coli by amplification of Bacillus stearothermophilus genomic DNA using PCR and inverse PCR. BssHII methyltransferase (M.BssHII) contains all 10 conserved cytosine-5 methyltransferase motifs, but motifs IX and X precede motifs I-VIII. Thus, the conserved motifs of M. BssHII are circularly permuted relative to the motif organizations of other cytosine-5 methyltransferases. M.BssHII and the non-cognate multi-specific phiBssHII methyltransferase, M.phiBss HII [Schumann,J. et al . (1995) Gene, 157, 103-104] share 34% identity in amino acid sequences from motifs I-VIII, and 40% identity in motifs IX-X. A conserved arginine is located upstream of a TV dipeptide in the N-terminus of M.BssHII that may be responsible for the recognition of the guanine 5' of the target cytosine. The BssHII restriction endonuclease gene was expressed in E.coli via a T7 expression vector.     

Physical mapping of a large-plaque mutation of adenovirus type 2.

We have developed a simple method based on cotransfection of overlapping DNA restriction fragments for construction of recombinants of adenovirus type 2 (Ad2) and Ad5. When Ad2 DNA digested with restriction endonuclease EcoRI was cotransfected with Ad5 DNA digested with SalI, recombination occurred between Ad2 EcoRI-A (map position 0 to 59) and Ad5 SalI-A (map position 45 to 100). Analysis of the recombinant DNAs by digestion with EcoRI or BamHI restriction endonucleases indicated that, as expected, recombination had occurred in overlapping sequences (map position 45 to 59) between the Ad2 EcoRI-A fragment and the Ad5 SalI-A fragment. By using this method, several recombinants were constructed between a large-plaque (lp) mutant of Ad2 and wild-type Ad5. Cleavage of the recombinant genomes with restriction endonucleases BamHI, EcoRI, and HindIII revealed that the lp mutation is located within the left 41% of Ad2 genome.     

Organization of chicken DNA sequences homologous to the transforming gene of avian myeloblastosis virus. I. Restriction enzyme analysis of total DNA from normal and leukemic cells.

Hybridization probes consisting of cloned DNA recombinants which represent different regions of the leukemogenic sequence (amv) from avian myeloblastosis virus were used to carry out a more detailed restriction endonuclease analysis of the homologous sequences (proto-amv) present in normal and leukemic chicken DNA. The results show that four large introns interrupt the normal cellular proto-amv sequences and that there is no major rearrangement of these sequences in leukemic myeloblasts.     

A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers

A set of mapping markers have been designed for Arabidopsis thaliana that correspond to DNA fragments amplifed by the polymerase chain reaction (PCR). The ecotype of origin of these amplified fragments can be determined by cleavage with a restriction endo-nuclease. Specifically, 18 sets of PCR primers were synthesized, each of which amplifies a single mapped DNA sequence from the Columbia and Landsberg erecta ecotypes. Also identifed was at least one restriction endonuclease for each of these PCR products that generates ecotype-specific digestion patterns. Using these co-dominant cleaved amplified polymorphic sequences (CAPS), an Arabidopsis gene can be unambiguously mapped to one of the 10 Arabidopsis chromosome arms in a single cross using a limited number of F₂ progeny.     

DNA splicing by directed ligation (SDL)

Splicing by directed ligation (SDL) is a method of in-phase joining of PCR-generated DNA fragments that is based on a pre-designed combination of class IIS restriction endonuclease recognition and cleavage sites. Since these enzymes cleave outside of their recognition sites, the resulting sticky end can have any desired sequence, and the site itself can be removed and does not appear in the final spliced DNA product. SDL is based on the addition of class IIS recognition sites onto primers used to amplify DNA sequences. Cleavage of the PCR products results in elimination of the recognition site-containing flanking sequences and leaves the DNA fragments crowned with protruding ends. With careful design of the sticky ends, several segments can be ligated together in a predetermined order in a single reaction. SDL requires fewer rounds of amplification than overlap extension methods, and is particularly useful for creating a series of recombinants that differ in one segment.     

Efficient DNA subcloning through selective restriction endonuclease digestion

Described here is a selective restriction endonuclease digestion method that eliminates the electrophoresis step that is usually used during the subcloning of new DNA sequences into typical E. coli-based plasmids. The method increases yield while decreasing laboratory resource and time utilization. By using donor and acceptor sequences that contain unique restriction sites found only outside of the intended recombination sequences, the initial digestion products can be directly combined without electrophoresis if the ligation step is followed by a selective digestion using the unique restriction enzymes before transformation. This system is based on the several order of magnitude decrease in transformation efficiency of linearized compared to circular plasmids. As an example, this method was used to obtain recombinants between a 3.6 kb acceptor plasmid and 3.0 kb insert following one ligation reaction after the failure of nine standard reactions using similar amounts of input DNA. It is particularly applicable to situations in which low subcloning efficiencies are expected. The technique can be extended to a large percentage of planned recombinations by using nonidentical compatible cohesive or blunt-ended fragments, or site-directed mutagenesis.     

Classification of rice germplasm. I. Analysis using ALP and PCR-based RFLP

The potential of using a PCR-based approach to detect DNA polymorphism for rice germplasm classification was compared with that of Southern-based RFLP analysis. Thirty-five Iranian rice varieties were studied along with 2 typical Indica and 3 typical Japonica varieties. Thirteen mapped RFLP markers were used as hybridization probes against Southern blots containing digests of one restriction endonuclease; 12 of the 13 probes detected polymorphism in the varieties. Fifteen sets of oligonucleotides derived from sequences near the ends of the same probes and of two other mapped probes were used as primers for PCR amplification of total genomic DNA of the varieties. Amplicon length polymorphisms (ALPs) were detected with 6 of the 15 sets of primers. To identify additional polymorphism, the PCR products were digested with nine different restriction endonucleases recognizing 4- or 5-bp DNA sequences and analyzed by gel electrophoresis in agarose and polyacrylamide. RFLPs were detected for 11 sets of primers, due to point mutations and to addition/deletion events that were too small to be detected as ALPs. Because PCR products are easily generated and may be analyzed in detail through the use of restriction endonucleases that cut rice DNA frequently, PCR-based RFLP analysis is a useful tool for the classification of rice germplasm.     

A genotypic mutation system measuring mutations in restriction recognition sequences.

The RFLP/PCR approach (restriction fragment length polymorphism/polymerase chain reaction) to genotypic mutation analysis described here measures mutations in restriction recognition sequences. Wild-type DNA is restricted before the resistant, mutated sequences are amplified by PCR and cloned. We tested the capacity of this experimental design to isolate a few copies of a mutated sequence of the human c-Ha-ras1 gene from a large excess of wild-type DNA. For this purpose we constructed a 272 bp fragment with 2 mutations in the PvuII recognition sequence 1727-1732 and studied the rescue by RFLP/PCR of a few copies of this 'PvuII mutant standard'. Following amplification with Taq-polymerase and cloning into lambda gt10, plaques containing wild-type sequence, PvuII mutant standard or Taq-polymerase induced bp changes were quantitated by hybridization with specific oligonucleotide probes. Our results indicate that 10 PvuII mutant standard copies can be rescued from 10(8) to 10(9) wild-type sequences. Taq polymerase errors originating from unrestricted, residual wild-type DNA were sequence dependent and consisted mostly of transversions originating at G.C bp. In contrast to a doubly mutated 'standard' the capacity to rescue single bp mutations by RFLP/PCR is limited by Taq-polymerase errors. Therefore, we assessed the capacity of our protocol to isolate a G to T transversion mutation at base pair 1698 of the MspI-site 1695-1698 of the c-Ha-ras1 gene from excess wild-type ras1 DNA. We found that 100 copies of the mutated ras1 fragment could be readily rescued from 10(8) copies of wild-type DNA.