PSF不同功能片段融合蛋白的构建及其在细胞内的分布

目的将人类PSF基因的不同功能片段定向连入pEGFP—C2质粒,使PSF蛋白的各功能片段与绿色荧光蛋白在HeLa细胞内融合表达,观察其在HeLa细胞中的表达及定位。方法以重组质粒pEGFP—C2-PSF为模板,PCR法扩增出目的基因,将扩增片段双酶切后连接到质粒pEGFP—C2上,构建重组质粒pEGFP—C2-PSF（I—V）。将构建成功的pEGFP—C2-PSF（I—V）质粒脂质体法转染HeLa细胞,Western印迹检测融合蛋白的表达,并在荧光显微镜下观察融合蛋白的定位与分布。结果成功构建质粒pEGFP—C2-PSF（I～V）,并在HeLa细胞中实现表达;Western印迹检测到融合蛋白GFP—PSF（I～V）;在激光共聚焦显微镜下观察到绿色的融合蛋白表达和定位。结论人类PSF基因的不同功能片段的重组质粒pEG—FP—C2-PSF（I～V）构建成功,可用于标记PSF蛋白的不同功能片段,为进一步研究PSF在信号转导中的作用机制以及其生物学功能奠定基础。     

Left-handed Z-DNA helices in polymers, restriction fragments, and recombinant plasmids

Studies on DNA polymers, restriction fragments, and recombinant plasmids have revealed the following: A) A family of left-handed DNA conformations exists for (dC-dG)n.(dC-dG)n. The observation of a particular conformation is dependent on the salt, the salt concentration and dehydrating agent. B) In sodium acetate solutions, (dC-dG)n.(dC-dG)n forms left-handed, psi(+)-condensed structures as detected by Raman spectroscopy and circular dichroism. C) (dT-dG)n.(dC-dA)n undergoes a right-to-left-handed transition only when reacted with AAF and at high salt concentrations. D) Transitions observed for polymer DNAs also are observed for restriction fragments containing both (dC-dG).(dC-dG) and (dT-dG).(dC-dA) sequences, but the transitions in the fragments generally require higher salt concentrations than observed for the polymers. E) Studies with recombinant plasmids containing (dC-dG) sequences from 10 to 58 bp in length demonstrate that left-handed Z-DNA segments can exist contiguous to B-DNA segments. F) Negative supercoil density (sigma less than or equal to -0.072) is sufficient to convert the (dC-dG) regions in those plasmids into left-handed structures under physiological ionic conditions (200 mM NaCl). G) The favorable free energy contribution of methylation in stabilizing the Z form in fragments and plasmids is approximately offset by the unfavorable free energy contributions of the B/Z junctions. H) Sl and BAL 31 nucleases recognize aberrant structural features at the confluence of the B and Z regions. I) Detailed mapping of Sl nuclease cleavage on supercoiled plasmids shows that the nuclease sensitive regions extend over at least five to ten bp. J) Even though the (dT-dG)n.(dC-dA)n polymer requires base modification and high salt conditions to undergo the R----L transition, supercoiling (sigma less than or equal to -0.07) can supply enough energy to allow a plasmid containing the intervening sequence of a human fetal globin gene with (dT-dG).(dC-dA) sequences to undergo a R----L transition.     

P100蛋白及其片段重组质粒构建与表达

目的分别将人类p100基因,p100的SN基因片段和TD片段定向连入pERFP-CI质粒,使它们可与红色荧光蛋白在HeLa细胞内融合表达,从而为进一步研究P100蛋白及其片段的定位、功能及与其它蛋白的相互关系奠定实验基础。方法PCR分别扩增出P100蛋白全长,SN片段和TD片段基因的序列,定向克隆至真核表达载体pERFP-CI,构建相应的3种重组质粒。将构建成功的质粒转染入HeLa细胞,荧光显微镜下可观察红色荧光融合蛋白表达。结果①PCR法获得P100基因序列,长度为2659bp,SN基因片段1918bp,TD基因片段741bp;②将重组质粒直接进行双酶切鉴定可见P100片段,将经过蓝白斑筛选后的重组子经双酶切再与pERFP-CI载体连接并酶切得到SN片段和TD片段;③转染重组质粒后可观察到红色荧光蛋白的表达。结论3种外源片段成功载人pERFP-CI质粒;P100全长、SN片段、TD片段均可与红色荧光蛋白在HeLa细胞中融合表达。     

Left-handed Z-DNA regions are present in negatively supercoiled bacteriophage PM2 DNA

Bacteriophage PM2 DNA is a 10-kb covalently closed circular (ccc) molecule with a reported superhelical density of sigma = -0.12. Here we describe the binding of anti-Z-DNA antibodies to PM2 form I DNA under high and low salt conditions. The binding to PM2 DNA has been demonstrated by competitive radioimmunoassay (RIA), retardation of the DNA:antibody complexes in agarose gels and visualization by electron microscopy. The antibody binding is dependent on the degree of negative supercoiling. Thus, PM2 form II and form III did not bind the antibody. The low salt RIA results indicated the presence of 200-400 bp of left-handed DNA per PM2 molecule. This could reduce the effective superhelical density to sigma = -0.04 to -0.08, a range comparable with those found for other ccc DNAs in vivo. Electron microscopy revealed that a maximum of 22 antibody molecules bind to PM2. Single-site restriction with HpaII of the fixed DNA:antibody complex showed a cluster of four to five antibody molecules bound near one end of the linear DNA molecule. The evidence presented indicates that PM2 DNA contains regions of left-handed conformation under physiological conditions (low salt concentration) as well as at high salt concentrations. In addition, electrophoretic analyses of PM2 topoisomers indicate the presence of left-handed regions at superhelical densities less than that of isolated PM2 DNA.     

Three Dimensional Association of Double-Stranded Helices Are Produced in Conditions for Z-DNA Formation

Abstract

The Z form of alternating poly(dG-dC)·poly(dG-dC) can be induced when the concentration of NaCl, MgCl₂ or ethanol are increased. In order to obtain more information concerning this Z structure, the B?Z transition is analyzed on the same sample, both by UV spectrophotometry and electron microscopy. The procedures used in this work provide high resolution images with minimal alterations of the molecules. It is shown that at high vlaues of cations or ethanol, the polymer makes complex associations of numerous molecules stuck together parallelly. By decreasing the salt or ethanol concentrations, a progressive decondensation of the molecules is obtained. At low concentrations of Mg⁺⁺ (2.10^?2 M), alterations of the linear secondary structure of the molecules are observed, although the UV spectrum is of the B-type. In the presence of that low concentration of Mg⁺⁺, natural DNAs (øX174 and yeast mitochondrial DNA fragment inserted in pBR) exhibit structural modifications similar to those observed with the poly(dG-dC)·poly(dG-dC). These structures mainly consist in four-stranded hairpins and loops built up by the sticking of two segments of DNA. The correlation between these intertwining of short DNA segments and the presence of potentially Z-forming sequences is discussed.     

一种经济、简便和准确鉴定重组质粒的方法

目的：提高重组质粒的筛选效率,探讨一种经济、快速并准确的重组质粒鉴定方法。方法：取200μl菌液于Eppendorf管中高速离心1min,倒出上清,沉淀中加入20μl裂解缓冲液以裂解细胞并释放出内部质粒,10000r/min离心10min后取5～10μl上清液进行琼脂糖凝胶电泳,并比较其迁移位置来以判断重组质粒。结果：该方法鉴定结果和PCR鉴定结果完全一致。结论：该方法具有成本低廉、简便快速的特点,在对大量样品进行鉴定时具明显优势,适合在常规实验室推广。     

Left-handed Z-DNA and intramolecular triplex formation at the site of an unequal sister chromatid exchange

An unequal sister chromatid exchange (USCE) in the mouse myeloma cell line MPC-11 between 3' regions of the C gamma 2a and C gamma 2b heavy chain genes results in duplication of the C gamma 2a heavy chain gene and generation of a novel recombination joint. The USCE occurs between (TC)n tracts adjacent to alternating purine-pyrimidine tracts. We have investigated the capacity of both the donor regions and the recombinant product involved in this event to adopt left-handed Z-DNA and intramolecular triplexes. The results of chemical probing with diethylpyrocarbonate and osmium tetroxide at the base pair level demonstrate that under the influence of negative supercoiling the alternating purine-pyrimidine regions of these plasmids can adopt Z-DNA at neutral pH, and the oligopurine.oligopyrimidine (pur.pyr) regions of these regions can adopt intramolecular triplexes at low pH (less than or equal to pH 6.0). At intermediate pH values, mixtures of both structures are present. Increasing the negative superhelical density of the plasmid does not increase the amount of triplex present at neutral pH indicating that the presence of long Z-DNA segments adjacent to pur.pyr tract prevents intramolecular triplex formation. In summary, we conclude that the sequences involved in the USCE can form either an intramolecular triplex in the (TC)n tract or Z-DNA in the alternating purine-pyrimidine tract and that Z-DNA will predominate under physiological conditions. The presence of segments which adopt Z-DNA at a site of USCE suggests that formation of this structure may enhance recombination between adjacent pur.pyr tracts.     

Stereochemical Effects of Methylphosphonate in B- and Z-DNA Helices: Variation in Hydrophobicity and Effective Widths of Grooves

Abstract

Stereochemical effects of methylphosphonate (MP) in B-DNA and Z-DNA duplexes are studied through molecular mechanics approach. Duplexes of different lengths, tetramers, hexamers, dodecamers are examined to assess the interstrand and intrastrand electrostatic effects due to MPs vis-a-vis phosphates. A variety of models which include duplexes with alternating S-MP and R-MP, alternating phosphate and MP and, duplexes posessing MPs in only one of the strands, are examined by considering both the S- and R-stereoisomers. Majority of the calculations are performed with CG sequences to delineate factors responsible for the stability of B- and Z-DNA as well as B × Z-DNA transition under nonionic conditions. The results show that both B- and Z-DNA duplexes are energetically favoured in the presence of MP due to overwhelming reduction in intrastrand as well as interstrand electrostatic repulsive interactions. The effect is distinct in oligomers longer than tetramers. Comparison of energetics of MP B- and Z-DNA duplexes suggests that an oligodeoxynucleotide such as d(CG)₆ with all phosphates replaced by MPs may favour equally both B- and Z-DNA conformations. The analysis further provides an estimate of electrostatic interactions, operating at the grooves under a variety of conditions. Several specific and localised effects due to S-MP and R-MP are seen at CG and GC steps in various B-DNA and Z-DNA models. S-MP in B- DNA reduces the effective major groove width by nearly 3 Å hence denying access to the functional groups of endonucleases thereby enhancing the resistance of MP-DNA to enzymatic digestion. Further, methyl groups of MP render the surface of the DNA helix to be significantly hydrophobic which may explain higher permeability of MP-DNA in membranes as well as its less soluble nature in aqueous media.     

Restriction Enzyme-Resistant High Molecular Weight Telomeric DNA Fragments in Tobacco

Restriction endonuclease-resistant high-molecular-weight (HMW)DNA fragments were isolated from nuclear DNA fragments in tobacco.The size of the fragments produced by EcoRI, HindIII, AfaI,and HaeIII ranged from 20 kb to over 166 kb. The kinetics ofdigestion by Bal31 nuclease showed that most of the HMW fragmentsare chromosome ends. The consensus sequence for tobacco telomererepeats was determined to be CCCTAAA by genomic sequencing usingthe HMW fragments and by sequencing after cloning. Besides thetelomere sequence, 9 tandem repeats of a 45-bp sequence wereidentified, in which a 35-bp unit sequence (AGTCAGCATTAGGGTTTTAAACCCTAAACTGAACT)formed a stem structure. The front of the stem is composed ofa palindrome of the telomere repeats. This highly conservedunit is surrounded by less conserved internal sequences thatare around 10–11 bp in size and contain a TTTT stretch.The internal sequences resemble the 10–11 bp consensusfor the scaffold attachment regions found in yeast and drosophila.The characteristic 45-bp sequence was abundant on the ends ofchromosomes. The shortest distance between the repeats containingtelomeric stem and the telomere was less than 20 kb. This architectureof the tobacco chromosome end region resembles the end regionof yeast chromosomes in which autonomous replication sequencesare present frequently.     

Stability of Recombinant Plasmids in Transgenic Microorganisms under Different Environmental Conditions

The copy number of R plasmids weakly depends on the selective pressure of the respective antibiotic but does depend on the physiology of the host species and the type of plasmids and cloned genes, whose expression leads to a further load on the biosynthetic apparatus of cells. The last factor is critical in the maintenance of recombinant plasmids in transgenic microorganisms.     

Genotyping of Staphylococcus epidermidis by Small-Fragment Restriction Endonuclease Analysis and Pulsed-Field Gel Electrophoresis of Genomic Restriction Fragments

Small-fragment restriction endonuclease analysis (SF-REA) was established as a typing tool for Staphylococcus epidermidis. A total of 60 isolates comprising 48 epidemiologically nonrelated strains and 12 putatively linked isolates from 7 patients in 2 wards were analyzed. Nonrelated isolates were characterized by unique fingerprints when DNA was cleaved with EcoRI or ClaI, electrophoretically separated in a polyacrylamide gel, and silver stained. Three blood culture isolates from one patient in an intensive care unit, 4 isolates obtained from a child over a span of 2 weeks, and 5 isolates from 5 newborns in the same ward were grouped into 3 DNA pattern types, indicating identity of sequential isolates from 2 patients and nosocomial transmission of one Staphylococcus epidermidis strain between 5 babies. Results from pulsed-field gel electrophoresis of SmaI and SacII DNA digests and conventional marker systems such as antibiogram and plasmid profile were in accordance with these interpretations, whereas slight variation was observed in the biotypes of several strains. From the results of this study, we conclude that SF-REA is a precise and efficient method for the genotypic characterization of Staphylococcus epidermidis strains that can be used as a rapid and reliable typing tool.     

Formation of Pseudo-Terminal Restriction Fragments, a PCR-Related Bias Affecting Terminal Restriction Fragment Length Polymorphism Analysis of Microbial Community Structure

Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in molecular microbial ecology. In this study, we show that besides expected terminal restriction fragments (T-RFs), additional secondary T-RFs occur in T-RFLP analysis of amplicons from cloned 16S rRNA genes at high frequency. A total of 50% of 109 bacterial and 78% of 68 archaeal clones from the guts of cetoniid beetle larvae, using MspI and AluI as restriction enzymes, respectively, were affected by the presence of these additional T-RFs. These peaks were called “pseudo-T-RFs” since they can be detected as terminal fluorescently labeled fragments in T-RFLP analysis but do not represent the primary terminal restriction site as indicated by sequence data analysis. Pseudo-T-RFs were also identified in T-RFLP profiles of pure culture and environmental DNA extracts. Digestion of amplicons with the single-strand-specific mung bean nuclease prior to T-RFLP analysis completely eliminated pseudo-T-RFs. This clearly indicates that single-stranded amplicons are the reason for the formation of pseudo-T-RFs, most probably because single-stranded restriction sites cannot be cleaved by restriction enzymes. The strong dependence of pseudo-T-RF formation on the number of cycles used in PCR indicates that (partly) single-stranded amplicons can be formed during amplification of 16S rRNA genes. In a model, we explain how transiently formed secondary structures of single-stranded amplicons may render single-stranded amplicons accessible to restriction enzymes. The occurrence of pseudo-T-RFs has consequences for the interpretation of T-RFLP profiles from environmental samples, since pseudo-T-RFs may lead to an overestimation of microbial diversity. Therefore, it is advisable to establish 16S rRNA gene sequence clone libraries in parallel with T-RFLP analysis from the same sample and to check clones for their in vitro digestion T-RF pattern to facilitate the detection of pseudo-T-RFs.     

小鼠Dppa2基因shRNA载体的构建及干扰效果的检测

目的:构建有效的针对小鼠Dppa2基因的shRNA(short hairpin RNA)干扰载体。方法:设计合成2对针对小鼠Dppa2基因的shRNA序列以及1对与哺乳动物基因组无同源性的shRNA序列作为对照,构建pSUPER.Retro.puro干扰载体并进行PCR,酶切和测序验证。进一步将各干扰载体分别转染小鼠胚胎干细胞(embryonic stem cells,ESCs),RT-PCR检测干扰效率。结果:PCR,酶切和测序验证均表明各shRNA载体构建成功。将空载体及各重组载体分别转染小鼠ESCs发现,干扰组Dppa2基因表达水平相对于空载体对照组和阴性shRNA载体对照组明显下调。结论:成功构建了有效的针对小鼠Dppa2基因的shRNA干扰载体,为进一步研究Dppa2基因在维持小鼠ESCs不分化过程中的作用提供了基础。     

Preparation of Chloroplast DNA from Barley and Lettuce and Comparison of Restriction Fragments

Chloroplast DNA from three barley cultivars and from one lettuce cultivar was prepared from chloroplasts isolated by Conventional differential centrifugation. Barley chloroplast DNA size was sensibly lower (130 kpb) than lettuce chloroplast DNA (150 kpb). Chloroplast DNAs from the three barley cultivars showed similar restriction fragment patterns after digestion with: BamHI, EcoRI or HindIII. The lettuce chloroplast DNA restriction pattern was very different from the barley chloroplast DNA restriction pattern.     

重组pEGFP—C2-p100-TSN点突变质粒构建及表达

目的将6个不同的p100-TSN．Mutants基因片段分别定向连入PEGFP—C2质粒中,使P100-TSN突变蛋白能够与绿色荧光蛋白在COS7细胞中融合表达,从而为进一步研究p100蛋白TSN结构域的功能奠定实验基础。方法利用EcoR I和Xho I双酶切方法从6个pcDNA3．1（＋）-p100-TSN．Mutants重组质粒中分别获得p100-TSN．Mutants的cDNA片段,将其连人pEGFP—C2质粒载体中,再将成功构建的6个pEGFP—C2-p100-TSN．Mutants质粒分别转染COS7细胞中,荧光显微镜下观察绿色荧光蛋白表达。结果①将重组质粒进行双酶切鉴定可见p100-TSN．Mutants的cDNA片段;②转染重组质粒后可观察到绿色荧光蛋白的表达。结论①6个pEGFP—C2-p100-TSN．Mutants重组质粒构建成功;②p100-TSN突变蛋白可与绿色荧光蛋白在COS7细胞中融合表达。     

基于小鼠MMP-9基因的siRNA的筛选

通过GenBank数据库检索,基于小鼠MMP-9基因设计特异性的siRNA干扰靶点,克隆至pGCsi-U6/Neo/GFP载体中,使用PEI衍生物包裹,转染小鼠黑色素瘤B16细胞,流式细胞仪和激光扫描共聚焦显微镜分析细胞转染情况,RT-PCR检测24,48 h后MMP-9基因转录水平变化,筛选最佳的重组质粒和干扰靶点。结果显示：成功设计和构建了3个MMP-9-siRNA干扰质粒,3个重组质粒对B16细胞的转染率分别为60.04%、63.93%和56.27%,且3个重组质粒均能有效干扰B16细胞MMP-9 mRNA的表达,其中MMP-9-siRNA-2干扰效率最高（63%）,可持续干扰MMP-9基因表达。这些结果提示,MMP-9-siRNA-2为沉默小鼠黑色素瘤细胞MMP-9基因最优的siRNA重组质粒。     

pCMV-BD-ZNF424和pCMV-Tag2-ZNF424缺失突变重组质粒的构建

锌指蛋白基因家族是人类最大的基因家族之一,目前已知的很多锌指蛋白成员都是转录调控因子.KRAB/C2H2型锌指蛋白是一类重要的转录因子,ZNF424是该亚家族的一个新成员.已经初步证明ZNF424具有转录激活作用,为了进一步研究ZNF424各结构域激活程度和在信号途径中的作用,设计出引物,以pCMVB-D-ZNF424重组质粒作为模板,PCR扩增出含ZNF424基因的KRAB、LINK和ZNF的3个含不同结构域的区域,克隆到pMD18T-载体,然后内切酶切下各目的片段,再构建出pCMVB-DK-RAB、pCMVB-DL-INK、pCMVB-D-ZNF、pCMVT-ag2BK-RAB、pCMVT-ag2BL-INK和pCMVT-ag2CZ-NF共6个缺失突变重组质粒,为进一步研究ZNF424基因功能奠定基础.     

ZNF230/荧光蛋白融合基因表达载体的构建及其在Cos细胞中的表达与定位

为了用绿色荧光蛋白标记观察人类无精症相关基因ZNF230在Cos7细胞中的蛋白质表达及定位,用PCR方法扩增得到突变的人和小鼠mt-ZNF230和mt-znf230基因,使其3′端的终止密码TGA突变为TGG,并装入T-载体,双酶切后通过定向克隆将其与真核表达载体pEGFP-N1的绿色荧光蛋白（green fluorescence protein,GFP）基因融合,构建了ZNF230—荧光蛋白融合基因表达载体。然后经真核表达质粒－脂质体介导,导入Cos7细胞系。荧光显微镜观察显示：在空白载体pEGFP-N1转染的Cos细胞中荧光布满整个细胞,而在转染阳性载体pEGFP-ZNF230的Cos细胞中荧光主要聚集在细胞核中。表明转染的Cos细胞系能高效表达人ZNF230和小鼠znf230蛋白,ZNF基因表达的蛋白定位于细胞核内。Abstract: To use green fluorescent protein as a marker to studythe localization of the fusion protein, the mutant full length cDNAs of human ZNF230 and mouse znf230 with their stop codon TGA changed to TGG were obtained by PCR amplification., and then cloned into pGEM-Teasy vector. After the double enzyme cutting, the mutated human and mouse ZNF230(znf230) were inserted into mammalian expression plasmid pEGFP-N1.Thus we constructed the plasmid with fusion gene of ZNF230 and green fluorescent protein(GFP).Then the Cos cell was transfected with the fused gene by liposome. Fluorescence microscopy showed that green fluorescence protein expressed over the whole cell when transfected with vector pEGFP-N1.While after the transfection with pEGFP-ZNF230, the fluorescence located mainly on the nuclei of the cells. We demonstrated that the transfected Cos cell line can express human ZNF230 and mouse znf230 with high efficiency.When transfected with the constructed recombinant pEGFP-ZNF230 vector, the ZNF230 protein localizes mainly on the nucleus.