脓肿分支枝杆菌embB基因耐乙胺丁醇的分析

目的 分析脓肿分支枝杆菌的embB基因,以探讨其耐乙胺丁醇的分子机制.方法 用16S rRNA基因序列分析法鉴定5株脓肿分枝杆菌临床株,测定乙胺丁醇对临床株及标准株( ATCC 19977)的最低抑菌浓度(MIC).PCR扩增embB基因的全序列,将所测序列进行生物信息学分析.结果 乙胺丁醇对5株脓肿分支杆菌标准株和临床株的MIC均为128μg/mL.,属高度耐药.从脓肿分支枝杆菌的标准株和临床株均扩增出约3200 bp片段,与GenBank中脓肿分支枝杆菌标准株的embB基因大小一致.5株临床株与标准株比较,其核苷酸序列存在9个点突变,在突变位点所编码的氨基酸序列中,仅第18位、87位、770位密码子编码与标准株不同的氨基酸.6株脓肿分支枝杆菌的embB基因与对EMB敏感的结核分支杆菌标准株(H37RV)的相应基因序列比较,第303-305位密码子的核苷酸序列存在差异,但仅第303、304位核苷酸编码的氨基酸序列不同,第306位密码子的核苷酸序列无差异.结论 脓肿分支杆菌对乙胺丁醇的耐药并非embB基因的突变所致,为embB基因天然存在结构的不同,属于天然耐药.结构的差异与第306位密码子无关,可能与第303、304密码子有关.     

人和小鼠resistin基因的克隆与序列测定

构建人和小鼠resistin基因cDNA克隆,并进行序列分析,为进一步进行resistin表达和生物学活性研究奠定基础。用RT－PCR方法扩增人和小鼠resistin基因cDNA,获得的片段边疆至pGEM-T载体,转化大肠杆菌JM109,并经过敏过鉴定和序列测定。结果成功地构建了人和小鼠resistin基因cDNA克隆,人和小鼠resistin的氨基酸序列具有共同的结构特征CX28CX12CX8CXCX3CX10CXCXCX9CC,克隆的人resistin cDNA在编码序列第133位的A被T代替,导致45位密码子编码的丝氨酸由半胱氨酸代替,小鼠resistin cDNA在第16位的T被C取代,导致第6位密码子编码的苯丙氨酸改变为亮氨酸。密码子发生改变的生物学意义还有待于进一步研究。     

应用寡聚核苷酸检测c-Ha-ras癌基因点突变

人工合成的寡聚核苷酸探针能够准确地检测出克隆的c-Ha-ras癌基因第12位密码子是否发生点突变。将多聚酶DNA链延伸反应(PCR)与寡聚核苷酸探针结合起来测定组织或细胞株中的单拷贝基因c-Ha-ras第12位密码子的点突变,获得满意的结果。此方法的建立,有助于肿瘤的早期诊断、分型等方面的研究。     

脂蛋白脂酶基因的克隆、序列测定及定点突变

 以人的脂肪组织总RNA为模板 ,参考已报道的脂蛋白脂酶 (lipoproteinlipase ,LPL)cDNA设计引物 ,利用RT PCR方法扩增得到了LPLcDNA ,并经序列测定证实其序列是正确的 .在冠心病患者LPL基因第 5外显子的 830位碱基处发现了G→A的转换 ,该变异导致LPL基因第 192位的密码子CGA被CAA取代 ,使LPL第 192位精氨酸改变为谷氨酰胺 .在变异碱基附近设计合成两条引物 ,其中一条包含所要改变的碱基 ,利用基于PCR的定点突变技术和体外重组的方法获得了G830A变异的LPLcDNA     

人血小板生成素氨基端功能区cDNA的克隆及其定点突变

以Nested－PCR方法从人肝cDNA基因文库中扩增出编码人血小板生成素（hTPO）前153个氨基酸的氨基端功能区cDNA;在扩增中,采用非连续多核甘酸定点突变的方法．将翻译起始的七个氨基酸的原核中不常用的密码子同又突变成使用频率较高的密码子,以便于其在大肠杆菌中表达。序列测定证实了预期的结果。     

重组人载脂蛋白AI米兰突变体在大肠杆菌中的高表达

用RT-PCR法从人肝总RNA库中克隆出人载脂蛋白Al的cDNA序列,再通过重叠PCR将载脂蛋白AI的第179位精氨酸密码子突变成半胱氨酸密码子,即载胎蛋白AI米兰突变体基因。将此目的基因克隆至表达载体pQE30,重组质粒转化JMl09宿主菌,经表达试验筛选出高表达克隆;工程菌经诱导后表达出含6个氨基酸前肽的载脂蛋白AI米兰突变体。表达产物主要以可溶形式存在,但也有部分为包涵体。     

PCR-RFLP 方法测定 ras 癌基因点突变

曾使用 PCR-RFLP 方法分析过 c-Ha-ras 癌基因第12密码子的点突变.因N-ras 基因第12位密码子、K-ras 基因第12和13位密码子无已知的限制性内切酶的酶切位点,不能使用 PCR-RFLP 方法分析这些位点的突变.在 PCR 引物的3′端引入一个误配的碱基使之正好成为某限制性内切酶的酶切位点,这样便能使用PCR-RFLP 技术分析 c-Ha-ras 基因第61位、N-ras 基因第12位、K-ras 基因第12和13位密码子的点突变.     

组织型纤溶酶原激活剂（t－PA）cDNA序列的测定

已经从ｍｅｌａｎｏｍａ细胞系中成功地获得了人组织型纤溶酶原激活剂（ｔ－ＰＡ）ｃＤＮＡ,在此基础上用双脱氧终止法测定了ｔ－ＰＡｃＤＮＡ编码区全序列及３′非编码区部分序列,并发现与Ｐｅｎｎｉｃａ等发表的ｔ－ＰＡｃＤＮＡ序列相比,有两处差异,其一是第１７２５位核苷酸残基为Ｃ而非Ａ,并使此处序列与Ｐｅｎｎｉｃａ序列相比新产生一个ＳｔｙＩ切点,但由于差异发生在密码子第三位,没有引起编码的氨基酸变化;其二是第１７７７位核苷酸残基（终止密码子后第４位核苷酸残基）为Ｔ而非Ｇ,使与终止密码子相隔３个核苷酸残基处产生了一个新的ＴＧＡ,与Ｐｅｎｎｉｃａ序列相比此处的ＢｓｔＮＩ切点也消失了。     

长春花钙调素基因克隆及其假基因的识别

以长春花[Catharanthus roseus(L.)G.Don]叶片cDNA和基因组DNA为模板,利用PCR技术扩增得到了长春花钙调素基因447 bp的全长编码cDNA序列和2个大小不同的DNA片段.序列分析表明,DNA长片段全长1 551 bp,由2个外显子和1个内含子构成,为长春花钙调素基因编码区DNA片段;DNA小片段全长447 bp,与447 bp的长春花钙调素基因cDNA核苷酸一致性高达87%,有56个碱基的差异,其中位于226 bp处的碱基A突变为T,即由AAG突变为终止密码子TAG使翻译提前终止.推测此447 bp的DNA小片段可能为长春花钙调素基因的假基因,命名为CCaMP1.     

翘嘴鳜线粒体DNA细胞色素b基因序列分析

测定了翘嘴鳜（Siniperca chuatsi）的线粒体细胞色素b基因编码区全序列1140个核苷酸序列,并且由此推导出对应的氨基酸序列,A/T所占比例为53.4％,G C约占46.6％。该基因中密码子第1位核苷酸中4种碱基组成较为均衡,第2位核苷酸中T的使用率较高,G的使用率较低;而密码子第3位C/A的使用率高,而G的使用率仅为3.7％;在氨基酸序列中Leu所占比例16.36％,远高于其它氨基酸;而Cys使用比例仅为0.79％。本研究为鳜类的系统发育,资源保护和利用提供了核苷酸序列方面的资料,至于翘嘴鳜线粒体细胞色素b基本序列中密码子不同位置碱基使用比率以及氨基酸组成是翘嘴鳜特有还是鳜类共有特征,尚有待进一步研究。     

蜂毒溶血肽基因的定点诱变及其在大肠杆菌中的表达

从蜜蜂毒腺中提取总ＲＮＡ,通过ＲＴ－ＰＣＲ方法扩增得到了蜂毒溶血肽前体蛋白的ｃＤＮＡ,再进一步通过定点诱变在蜂毒溶血肽序列前引入了羟胺裂解位点,构建了与β－半乳糖苷酶部分序列相融合的蜂毒溶血肽诱变蛋白表达载体,序列分析结果表明,成功地引入了目的密码子且与β－半乳糖苷酶部分序列构成正确的读码框,并在大肠杆菌中表达了诱变蛋白,为基因工程生产蜂毒溶血肽提供了新途径。     

Efficient procedure for site-directed mutagenesis mediated by PCR insertion of a novel restriction site

Better understanding of proteins'' structure/function relationship and dissecting their functional domains are still challenges yet to be mastered. Site-directed mutagenesis approaches that can alter bases at precise positions on the gene sequence can help to reach this goal. This article describes an efficient strategy that can be applied not only for both deletion and substitution of target amino acids, but also for insertion of point mutations in promoter regions to study cis-regulating elements. This method takes advantage of the plasticity of the genetic code and the use of compatible restriction sites.Key words: site-directed mutagenesis, restriction site, cloning, PCRUnderstanding the proteins structure/function relationship and dissecting their functional domains is one of the biggest challenges to current proteomic studies.¹ This is mainly achieved by site-directed mutagenesis experiments that can alter bases at precise positions on the gene sequence.² Modifying DNA sequences has become feasible with PCR amplification.³ During the last decade, several strategies have been developed to simplify this approach and increase its efficiency.⁴ The introduction of a site-directed mutation can be realized by one or more PCR reactions. Most of the strategies used in site-directed mutagenesis are based on a substitution of a single base, which leads to a change in one amino acid. This article describes an efficient strategy that can be applied for either deletion or substitution of target amino acids. This strategy is based on performing PCR reactions to create a new restriction site in the sequence of origin, corresponding to the desired mutation. The choice of the restriction site to be created depends on the nature of the amino acid that one desires to introduce in the protein sequence. Since such restriction sites may extend beyond the mutated codon. The preservation of the other codon is done by taking advantage of the plasticity of the genetic code where one amino acid can be encoded by multiple codons.This method was performed in two steps (Fig. 1). In the first step, the DNA sequence of interest, cloned in a plasmid, served as a template for two PCR reactions. Two PCR products are generated. The first one consists of the beginning of the sequence, from the start codon to the mutagenized amino acid codon, where the forward primer bears the start codon region and the reverse primer bears the newly introduced restriction site at the same location of the mutagenized codon. The second PCR product consists of the end of the coding sequence, from the mutagenized amino acid codon to the stop codon. This fragment is generated using a forward primer bearing the same new restriction site as the first PCR product''s reverse primer, and a reverse primer bearing the stop codon region. The two PCR products were cloned separately into a vector in the appropriate orientation. In the second step, the cloning vector bearing the first PCR product was digested with a restriction enzyme site in the vector, and by the restriction enzyme corresponding to the restriction site created by the reverse primer used in the PCR reaction. The resulting fragment was cloned into the vector containing the second PCR fragment, predigested with same two restriction enzymes. The whole mutagenized coding sequence is reassembled by in-frame subcloning of the 3′ end of the coding sequence downstream the 5′ end. All the PCR products were generated using the high fidelity Pfu DNA Polymerase (Promega, Madison, WI USA). For any site-directed mutagenesis experiment, this two-step cloning procedure requires the use of appropriate PCR primers that harbor the desired mutation of the target amino acid. These primers are partially overlapping and contain a common or complementary restriction site enabling the in-frame assembly of the whole coding sequence.Open in a separate windowFigure 1Mutagenesis strategy by restriction enzyme site insertion. (A) In the first step, two PCR products were generated using the full length coding sequence as template. The mutation is carried by the two primers b and c, which are flanked by the same or compatible restriction enzyme''s site (white segment). Both PCR products are separately cloned in the cloning vector in the appropriate orientation. In the second step, the whole mutagenized coding sequence is reassembled by in-frame sub cloning of the 3′ end of the coding sequence downstream the 5′ end. (B) Substitution of threonine by arginine as a result of the insertion of a BglII restriction site. DNA sequencing is carried out to make sure that only the desired change is introduced in the coding sequence. (B-1) The sequence of the native cDNA. (B-2) the sequence of the mutagenized cDNA included BglII restriction site sequence.This approach has been used in a recent study to address the structure/function relationship of the STAS domain of the Arabidopsis thaliana Sultr1;2 sulfate transporter.⁵ A good example of this approach is the replacement of the threonine-serine couple at position 587–588 with an arginine-serine couple. The codon for threonine is: TGT, and that for arginine is: TCT. Serine can be encoded by both TCA and AGA codons. The chosen restriction site used for the reassembly of the whole coding sequence is that of the BglII enzyme: TCT AGA. The insertion of this restriction site enables the substitution of the Thr in position 587 with an Arg while preserving the serine residue in position 588. The BglII restriction site is introduced in the reverse primer and the forward primer used to generate the first and second PCR products respectively. The DNA sequence of the reassembled mutagenized cDNA was checked by sequencing. Than it was expressed, under pGAL1O promoter bearing by pYES2 vector, in yeast mutant deficient in sulfate transporter and the mutagenic protein was detected by imunodetection.Bioinformatic study reveals that this method can be applied to checked a large number of substitutions, insertions or deletions and that finding the right restriction site is not a limiting factor (data no shown).In conclusion, this article describes an efficient two-step procedure for site-directed mutagenesis using primers bearing a restriction site, which is absent from the sequence of origin. The primers flanked by sequences introducing the same or compatible restriction sites mediate the incorporation of the mutation at the selection site. The choice of the restriction site depends on the nature of the desired mutation: insertion, substitution or deletion of an amino acid in a particular position. This strategy can be also used to insert point mutations in promoter regions to study cis-regulating elements.     

应用PCR技术对先天性长QT综合征KCNQ1 基因进行定点突变的研究

利用聚合酶链反应（PCR）技术对长QT综合征（LQTS）KCNQ1基因进行定点突变的研究。首先设计两对引物（包含预定的突变）,通过3轮PCR扩增,扩增出含有所需突变位点的片段,然后将片段克隆入T载体中,通过酶切连接的方法将突变点引入到pIRES2-EGFP-KCNQ1中,随后用Effectene转染试剂介导转染HEK293细胞。结果在真核表达载体pIRES2-EGFP-KCNQ1基础上获得了KCNQ1 cDNA C934T的突变体,测序表明在序列中发生了预期的突变。将含突变点的pIRES2-EGFP-KCNQ1转染HEK293细胞后,在荧光显微镜下观察到被转染的HEK293细胞发出绿色荧光,表明含突变点的pIRES2-EGFP-KCNQ1得到了表达。Abstract: To study PCR site-directed mutagenesis of long QT syndrome KCNQ1 gene in vitro. The site-directed mutagenesis of LQTS gene KCNQ1 was made by PCR. Two sets of primers were designed according to the sequence of KCNQ1 cDNA, and mismatch was introduced into primers. Mutagenesis was performed in a three-step PCR. The amplified fragments from the third PCR which contained the mutation site were subcloned into the T-vecor PCR2.1.Then the fragments containing the mutation site was obtained from PCR2.1 with restriction enzyme digestion and was inserted into the same restriction site of pIRES2-EGFP-KCNQ1. With Effectene Transfection Reagent, pIRES2-EGFP-KCNQ1 was transfected into HEK293 cell. The sequencing analysis showed that the mutation site was correct. Mutation from T to C in 934 site of KCNQ1 cDNA was found. Under the fluorescence microscope, the green fluorescence was spread in the transfected HEK293 cell, meaning the pIRES2-EGFP-KCNQ1 containing the mutation site was expressed correctly.     

Improvement in the heterogeneous N-termini and the defective N-glycosylation of human interleukin-6 by genetic engineering.

Recombinant human interleukin-6 (IL-6), expressed in Chinese hamster ovary cells, has heterogeneous N-termini of Ala1 and Val3, as does naturally occurring IL-6. This heterogeneity is thought to be caused by difficulty in cleavage of the signal sequence. To obtain homogeneous IL-6, Pro at -1 was exchanged for Ala by site-directed mutagenesis. Alternatively, the signal sequence was replaced with that of human granulocyte-colony-stimulating factor. In both cases, the IL-6 designed to start with Ala1 was still heterogeneous, while the IL-6 designed to start with Val3 showed a homogeneous N-terminus. It is suggested that the heterogeneity of the N-terminus is caused not only by the signal sequence, but also by the succeeding sequences of the mature protein. Only a portion of recombinant human IL-6 is N-glycosylated. Asn46, being exchanged for Gln by site-directed mutagenesis, was confirmed to be partially N-glycosylated. The defective N-glycosylation was assumed to be caused by interference or tension from a disulfide bond near the N-glycosylation site. To verify this hypothesis, the Cys45 and Cys51 forming the disulfide bond were exchanged for Ser. The N-glycosylated species became predominant upon this substitution, suggesting that formation of the disulfide bond is a cause of the defective N-glycosylation.     

Epitope insertion into the human hypoxanthine phosphoribosyltransferase protein and detection of the mutant protein by an anti-peptide antibody

The translational stop codon TAA of the human hypoxanthine phosphoribosyltransferase (HPRT) cDNA has been changed to GAA by site-specific mutagenesis. This modification extends the open reading frame to a downstream stop codon and results in the addition of a unique negatively charged hexapeptide to the C terminus of human HPRT protein. The mutated cDNA was transferred into HPRT-deficient rodent cells by retroviral vector infection, and the expressed enzyme was found to be fully active. An antibody against a synthetic octapeptide corresponding to the mutated HPRT C terminus precipitated the HPRT protein specifically from cells infected with the mutant virus and not infected with the wild-type HPRT virus. The technique of inserting a novel epitope into a protein by site-directed mutagenesis should be generally applicable in studies of the regulation of gene expression in vitro and in vivo.     

Phenylalanine hydroxylase deficiency caused by a single base substitution in an exon of the human phenylalanine hydroxylase gene

A novel restriction fragment length polymorphism in the phenylalanine hydroxylase (PAH) locus generated by the restriction endonuclease MspI was observed in a German phenylketonuria (PKU) patient. Molecular cloning and DNA sequence analyses revealed that the MspI polymorphism was created by a T to C transition in exon 9 of the human PAH gene, which also resulted in the conversion of a leucine codon to a proline codon. The effect of the amino acid substitution was investigated by creating a corresponding mutation in a full-length human PAH cDNA by site-directed mutagenesis followed by expression analysis in cultured mammalian cells. Results demonstrate that the mutation in the gene causes the synthesis of an unstable protein in the cell corresponding to a CRM- phenotype. Together with the other mutations recently reported in the PAH gene, the data support previous biochemical and clinical observations that PKU is a heterogeneous disorder at the gene level.     

甘油脱氢酶基因在大肠杆菌中的密码子优化表达

[目的]利用密码子优化技术,提高甘油脱氢酶基因gldA在大肠杆菌中的表达水平.[方法]针对gldA起始密码子下游区域,优先选择AT含量最高的同义密码子,从而在不改变氨基酸序列的前提下,提高该区域的AT含量.利用大引物PCR的方法对野生型gldA-WT进行定点突变,获得优化型基因gldA-4,与pET-32a(+)连接后...     

用改进的重叠延伸PCR技术构建三位点突变载体

目的:改进传统重叠延伸PCR方法,实现引入3个不同DNA突变位点的简便的多位点定点突变。方法:根据前期构建的包含人线粒体12S rRNA(NC 01290)3个热点突变位点的野生型质粒序列,利用Muta Primer 2.0软件设计针对3个热点突变位点的3对互补的定点突变引物,以野生型质粒为模板,结合重叠延伸PCR反应和冷冻析出法,产生同时包含3个突变位点的突变目的片段,酶切后克隆到载体中,测序确证是否突变成功。结果:DNA测序证实3个不同突变位点同时成功引入,定点突变载体构建成功。结论:用改进的重叠延伸PCR技术能简便、高效地获得多位点定点突变载体,在分子生物学领域有较高的使用价值。     

A method for clone sequence confirmation using a mismatch-specific DNA endonuclease

Site-directed mutagenesis and polymerase chain reaction (PCR)-based cloning are well-established methods carried out routinely in most modern molecular biology laboratories. Application of these methods requires confirmation of the DNA sequence of the target gene by sequencing of DNA purified from multiple colonies, a laborious process. We have developed an alternative approach to screen DNA amplified directly from colony DNA for both desired and undesired mutations. This approach is based on the use of a plant mismatch DNA endonuclease, Surveyor Nuclease, to directly screen clones derived by site-directed mutagenesis. We have also used this approach to identify error-free clones of three genes from celery cDNA produced by PCR and TOPO cloning. Sequence confirmation using Surveyor Nuclease provides a fast and simple approach to obtain desired clones from site-directed mutagenesis and PCR-based cloning methods without the necessity of sequencing DNAs purified from multiple clones.