人基因组YAC克隆DNA的Alu—PCR反应条件的系统研究

在人基因组ＹＡＣ克隆的Ａｌｕ－ＰＣＲ指纹分析中要求ＤＮＡ扩增带具有ＹＡＣ特征性;在Ａｌｕ－ＰＣＲ方法对ＹＡＣ克隆中的人类基因组ＤＮＡ片段进行特异的同位素标记时则要求被增标记的ＤＮＡ序列在插入片段中具有一定弥散性,我们建立了两种不同的Ａｌｕ－ＰＣＲ反应体系以满足这一不同要求,并已得到较为满意的结果,根据不同条件下的Ａｌｕ－ＰＣＲ结果,分析了多引发位点ＰＣＲ中的一些现象,并作了解释。     

人基因组YAC克隆DNA的Alu－PCR反应条件的系统研究

在人基因组ＹＡＣ克隆的Ａｌｕ－ＰＣＲ指纹分析中要求ＤＮＡ且扩增带具有ＹＡＣ特征性;在用ＡｌＵ－ＰＣＲ方法对ＹＡＣ克隆中的人类基因组ＤＮＡ片段进行特异的同位素标记时则要求被扩增标记的ＤＮＡ序列在插入片段中具有一定的弥散性。我们建立了两种不同的Ａｌｕ－ＰＣＲ反应体系以满足这一不同要求,并已得到较为满意的结果。根据不同条件下的Ａｌｕ－ＰＣＲ结果,分析了多引发位点ＰＣＲ中的一些现象,并作出了解释。     

Ds因子在烟草染色体插入位点旁邻顺序的克隆

用Ｎｅｓｔｅｄ－ＰＣＲ方法从含Ｄｓ因子的转基因烟草ＤＮＡ中克隆了Ｄｓ因子在烟草染色体插入位点的９个旁邻ＤＮＡ片段,以这些片段作探针,和野生型烟草的ＤＮＡ进行Ｓｏｕｔｈｅｒｎ杂交,以检测这些片段在烟草染色体上的低拷贝ＤＮＡ。另外,对这些ＤＮＡ片段进行核苷酸序列测定,并将它们的顺序与Ｇｅｎｂａｎｋ数据中已有的核苷酸序列相比较,其中长度为１２８核苷酸的片段１和荷兰芹的４ＣＬ－２基因的一个区段有５７．８％     

大豆单染色体的显微分离及体外扩增

采用玻璃针分离法,通过显微操作器成功地分离到大豆（ＧｌｙｃｉｎｅｍａｘＬ．）单染色体。将分离到的两条大豆染色体分别放入两个０．５ｍＬＥｐｐｅｎｄｏｒｆ管中,经Ｓａｕ３Ａ酶切,并在染色体ＤＮＡ片段两端加上Ｓａｕ３Ａ人工接头后,进行两轮ＰＣＲ扩增,得到０．３～３ｋｂ之间的ＤＮＡ片段。Ｓｏｕｔｈｅｒｎ杂交表明,这些大豆单染色体扩增片段与大豆基因组ＤＮＡ之间有同源性,从而证明两条单染色体ＤＮＡ确实已被成功地扩增了,同时表明两条不同的大豆单染色体扩增产物存在一定的差异。在常规的倒置显微镜下对小型染色体进行了显微分离,为小型单染色体ＤＮＡ的体外扩增及微克隆奠定了基础。     

血沉标本中人巨细胞病毒DNA的检出

用聚合酶链反应（ＰＣＲ）和地高辛标记探针（ｄｉｇ－ｐｒｏｂｅ）检测临床血沉标本中人巨细胞病毒（ＨＣＭＶ）ＤＮＡ。结果表明,人群血标本中ＨＣＭＶ－ＤＮＡ携带率较高;ＰＣＲ技术较ｄｉｇ－ｐｒｏｂｅ更敏感、快速、简便,二者检出ＨＣＭＶ－ＤＮＡ阳性率分别为８３．３％和６０．３％;ＨＣＭＶ－ＤＮＡ检出率、ＨＣＭＶ－ＩｇＭ检出率与血沉值高低之间无相关性。     

用PCR扩增和克隆鸡传染性贫血病毒全基因组DNA

根据已发表的序列,分别在鸡贫血病毒（ＣＡＶ）环形基因组ＤＮＡ（全长２．３ｋｂ）的ＥｃｏＲＩ位点和ＢａｍＨＩ位点的两侧选择适当序列合成两对引物,用ＰＣＲ技术,从斑点杂交检测到病毒核酸的ＣＡＶ感染的ＭＤＣＣＲＰ１细胞基因组ＤＮＡ中,分别扩增出包含ＥｃｏＲＩ和ＢａｍＨＩ分割开的病毒基因组两部分（１．５ｋｂ和０．８ｋｂ）约１．５ｋｂ和约１．２５ｋｂ的两个片段。再将其中相应序列拼接克隆进ｐＵＣ１８载体,获得包含ＣＡＶ全基因组序列ＤＮＡ片段的克隆质粒ｐＣＡＶ２．４。酶切分析表明,该质粒具有预期的ＢａｍＨＩ位点、ＰｓｔＩ位点、ＨｉｎｄⅢ位点,而预期的ＥｃｏＲＩ位点消失。重组质粒插入ＤＮＡ片段的两端序列分析表明,质粒ｐＣＡＶ２．４是包含ＣＡＶ全基因组序列的重组质粒,插入ＤＮＡ片段序列中的ＥｃｏＲＩ位点序列发生了一个碱基突变。     

戊型肝炎病毒细胞分离株部分核苷酸序列分析

用抗原捕获／多聚酶链反应（ＡＣ／ＰＣＲ）对戊型肝炎病毒（ＨＥＶ）细胞分离株ＭＪ９０和Ｒ２５基因组的部分核苷酸序列进行扩增,获得了与ＨＥＶ缅甸株ＥＴ１·１相同的ｃＤＮＡ扩增带。该ｃＤＮＡ扩增带纯化后用双脱氧核苷酸ＤＮＡ链末端终止法测序,ＣＪ９０、Ｒ２５株的核苷酸和氨基酸序列与ＥＴ１·１克隆的同源性分别为９９．６％、１００％和９９％、９９％,从而证明ＭＪ９０和Ｒ２５毒株为ＨＥＶ．     

噬菌体6肽随机表面表达文库的构建

体外合成编码６肽的随机ＤＮＡ片段以及用于随机ＤＮＡ片段扩增了一对ＰＣＲ引物,再经ＰＣＲ扩增,ＢｇＩＩ酶切扩增产物,获得编码６肽的随机ＤＮＡ克隆片段,并利用已构建的噬菌体表面表达载体,经抗性和插入复活筛选,获得１．６×１０＾８个独立克隆,构成库的克隆经酶切,ＰＣＲ扩增,斑点杂交,序列测定,亲和素富集等方法的综合鉴定和评定,以及６肽随机克隆体外增殖和表达特性观察,结果均表明,我们成功构建了编码６肽的     

非连续多核苷酸定点突变的方法

以人粒巨噬细胞集落刺激因子（ｈＧＭ-ＣＳＦ）、人α８干扰素（ｈＩＦＮ-α８）和分裂细胞核抗原（ＰＣＮＡ）的ｃＤＮＡ定点突变为例,建立了一种新的大区域非连续多核苷酸同步定点突变的方法。经碱变性后的质粒ＤＮＡ,先用突变引物延伸单链,然后通过ＰＣＲ扩增得到突变双链ＤＮＡ。用该方法成功地改造了ｈＧＭ-ＣＳＦ基因５′端３６个核苷酸中的９个位点、ＩＦＮ-α８基因５′端３９个核苷酸中的９个位点和ＰＣＮＡ基因ＳＤ顺序两侧６个和７个核苷酸。与经典的含Ｕ单链寡核苷酸定点突变方法相比,本方法突变效率高,并省去了对突变克隆杂交筛选的操作     

Ds因子在烟草染色体插入位点旁邻顺序的克隆

用ＮｅｓｔｅｄＰＣＲ 方法从含Ｄｓ 因子的转基因烟草ＤＮＡ 中克隆了Ｄｓ 因子在烟草染色体插入位点的９ 个旁邻ＤＮＡ 片段,以这些片段作探针,和野生型烟草的ＤＮＡ 进行Ｓｏｕｔｈｅｒｎ 杂交,以检测这些片段在烟草基因组中的拷贝数,结果表明它们都属于烟草染色体上的低拷贝ＤＮＡ。另外,对这些ＤＮＡ 片段进行核苷酸序列测定,并将它们的顺序与Ｇｅｎｂａｎｋ 数据库中已有的核苷酸序列相比较,其中长度为１２８ 核苷酸的片段１ 和荷兰芹的４ＣＬ２ 基因的一个区段有５７ ．８ ％ 同源性,而另一长度为１６９ 核苷酸的片段３ 和百合中的反转座子的一个区段有６０ ．９ ％ 的同源性。这都表明Ｄｓ 因子在异源植物烟草中插入染色体单拷贝基因的机率很高,这对转座子标签法克隆基因是非常有利的。     

Isolation of thirty-one new porcine microsatellites from a microsatellite enriched microdissected chromosome 8 library

Chromosome 8 (SSC8) is an important one in the swine genome because it has been shown to harbor several economically important quantitative trait loci (QTL). The entire porcine chromosome 8 was microdissected and amplified by degenerate oligonucleotide primer (DOP) PCR. The PCR product was then enriched for (CA)n microsatellites by hybridization to a biotinylated CA repeat oligonucleotide and captured by streptavidin-coated magnetic beads. The captured DNA was cloned into a TA cloning vector. Screening with an isotopically labeled CA oligonucleotide probe resulted in the isolation of 31 informative and polymorphic microsatellite clones. Seventeen of those were mapped to chromosome 8, 12 to chromosome 15, 1 to chromosome 10 and 1 to chromosome X. The markers were all placed on the USDA-MARC porcine genetic linkage map.     

Isolation of thirty‐one new porcine microsatellites from a microsatellite enriched microdissected chromosome 8 library

Abstract

Chromosome 8 (SSC8) is an important one in the swine genome because it has been shown to harbor several economically important quantitative trait loci (QTL). The entire porcine chromosome 8 was microdissected and amplified by degenerate oligonucleotide primer (DOP) PCR. The PCR product was then enriched for (CA)_n microsatellites by hybridization to a biotinylated CA repeat oligonucleotide and captured by streptavidin‐coated magnetic beads. The captured DNA was cloned into a TA cloning vector. Screening with an isotopically labeled CA oligonucleotide probe resulted in the isolation of 31 informative and polymorphic microsatellite clones. Seventeen of those were mapped to chromosome 8, 12 to chromosome 15, 1 to chromosome 10 and 1 to chromosome X. The markers were all placed on the USDA‐MARC porcine genetic linkage map.     

Conjugation in Rhodopseudomonas sphaeroides mediated by R plasmids

Plasmids R68.45, RP4, RP4::Mu cts62, RP1ts::Tn10, RP1ts::Tn9, Rts1 and RP41 were transferred into cells of photosynthetic nitrogen-fixation bacterium Rhodopseudomonas sphaeroides from Escherichia coli and Pseudomonas aeruginosa. The transfer of plasmids occurred with high frequency of 10(-1) to 10(-2) per donor cell in all cases. Mobilization of R. sphaeroides 2R chromosome was obtained by RP4 and Rts1 plasmids at a frequency of 10(-7) to 10(-8) per donor cell in all cases. Mobilization of R. sphaeroides 2R chromosome was obtained by RP4 and Rts1 plasmids at a frequency of 10(-7) to 10(-8) per donor cell. Bacteriophage Mu cts62 could be induced from the plasmid DNA in R. sphaeroides 2R cells and was capable of the lytic growth and producing phage progeny. It was demonstrated that an increase in the efficiency of donor chromosomal genes transfer into recipient cells could be achieved in crosses with the donor carrying RP4::Mcts62 plasmid.     

Role of proofreading and mismatch repair in maintaining the stability of nucleotide repeats in DNA.

The role of the proofreading exonuclease in maintaining the stability of multiply repeated units in DNA was studied in Escherichia coli. Reversion of plasmids in which the beta-galactosidase alpha complementing sequence was moved +2 out of frame by inserts containing (CA)14, (CA)5, (CA)2 or (TA)6 or +1 by creating a run of 8 C was compared in mutS and mutSdnaQ strains. Proofreading corrects at least half of the frameshift errors for all the plasmids and at least 99% of the errors in the (CA)2 plasmid. The (CA)2 plasmid reverts mostly by +1 frameshifts in the restriction sites flanking the insert. With the (CA)14, (TA)6, (CA)5 and 8C plasmids, reversion is mainly by loss of a repeat unit. The data support the hypothesis that the dnaQgene product recognizes frameshifts close to the DNA growing point. Frameshifts distal to the growing point are mainly corrected by mismatch repair.We speculate that mismatches in mononucleotide repeats are susceptible to proofreading because they can either migrate to a point where they are recognized by the exonuclease or, alternatively, because single nucleotide distortions are more readily detected than dinucleotides.     

Tn4556, a 6.8-kilobase-pair transposable element of Streptomyces fradiae.

A 6.8-kilobase-pair (kbp) transposable element (Tn4556) was found in a neomycin-producing strain of Streptomyces fradiae. This element was first observed in two 30.3-kbp plasmids (pUC1123 and pUC1124) which arose when a thiostrepton resistance gene (1 kbp) was ligated with the BclI-2 fragment (22.5 kbp) that contains the origin of replication of phage SF1. The Tn4556 segment was deleted when these plasmids were transduced into another S. fradiae host with phage SF1. These deletion plasmids (pUC1210 and pUC1211) had copy numbers of less than 1 per chromosome and were unstable. In contrast, pUC1123 and pUC1124, with copy numbers of 12 to 15 per chromosome, respectively, were relatively stable. When pUC1210 and pUC1211 were reintroduced into S. fradiae by protoplast transformation, the Tn4556 element transposed again to the plasmids at numerous new locations in either of two orientations. A copy of Tn4556 was found in the S. fradiae chromosome by hybridization studies. It appears that Tn4556 originated from the chromosome, transposed into unstable pUC1210 and pUC1211, and made stable plasmids. A temperature-sensitive hybrid plasmid carrying a viomycin resistance derivative of Tn4556 (pMT660::Tn4556::vph) was constructed. When Streptomyces lividans UC8390 containing the hybrid plasmid was grown at 39 degrees C, Tn4556::vph (Tn4560) transposed to random positions in the host chromosome.     

Bacillus subtilis soil isolates: plasmid replicon analysis and construction of a new theta-replicating vector

We have searched for plasmids in a collection of 55 Bacillus subtilis strains isolated from various natural sources of the territory of Belarus. Twenty percent of the strains contained one or two plasmids of either 6-8 or approximately 90 kb. Small plasmids were shown to carry a rolling circle replicon of the pC194 type. Four out of the eight large plasmids contained a related theta replicon that has no homolog in databases as shown by sequence determination. A B. subtilis/Escherichia coli shuttle vector based on this replicon was constructed. It has a low copy number (6 units per chromosome) and is stably inherited in B. subtilis. It might thus be a useful tool for DNA cloning. These data extend previous observations, indicating that most of the small plasmids of B. subtilis replicate as rolling circles and belong to the pC194 family. On the contrary, large plasmids appear to form a large pool of theta-replicating determinants, since three different replicons have already been isolated from them.     

Localization of genes conferring resistance to selected groups of antibiotics in methicillin-resistant strains of Staphylococcus aureus

Localization of genes conferring resistance to MLS, tetracyclines, chloramphenicol, gentamycin and neomycin in 80 MRSA strains isolated from hospital specimens was determined. The obtained results were compared to DNA patterns of the examined strains after digestion with SmaI and separation in pulsed field electrophoresis (PFGE). It was shown that genes of resistance to MLS (ErmI+) in the case of 13 strains were located on chromosome and in the case of 37 strains on plasmids (16 strains had ErmI+ and 21 strains had ErmI-). Genes determining resistance to tetracyclines were localised on chromosome in the case of 39 (23 strains possessed TetK, 11 strains had TetM and 5 strains possessed both TetK and TetM determinants) and in the case of 32 strains on plasmids. Chloramphenicol resistance genes were localised on plasmids in all 30 resistant strains. Genes conferring resistance to gentamycin were present in 31 of the investigated strains on chromosome and in two strains on plasmids. Neomycin resistance genes were plasmid in 34 strains. It was shown that the localization of the resistance genes and the PFGE patterns of the investigated strains were highly correlated.     

Interaction (integration and excision) of the pRP19.6 plasmid, a derivative of the RP1 plasmid containing duplicated sequence IS21, with the chromosome of Escherichia coli K12

A pRP19.6 plasmid is the derivative of the temperature sensitive RPlts12 plasmid and contains a duplicated IS21 (IS8) element. Using temperature sensitive pRP19.6 replication, Hfr strains have been obtained by integration of the plasmid into the chromosome of E. coli rec+ and recA- cells and their properties were studied. According to the results obtained, pRP19.6 insertion into the genome of the rec+ bacteria IS reversible, and its integration into the chromosome of the recA- bacteria produced the stable Hfr strains. To elucidate the mechanism of pRP19.6 excision from the bacterial chromosome, plasmids of R+ transconjugates generated with a low frequency in the crosses between the stable Hfr strains and the rec+ recipients were analyzed. It was shown that the stable Hfr clones might produce stable R1 plasmids as well as a family of deletion KmsTra- derivatives of the pRP19.6. The structure of the KmsTra- was investigated and the mechanism of their formation was proposed. In the light of the data obtained, prospects of pRP19.6 practical application are discussed.     

Isolation of large bacterial plasmids and characterization of the P2 incompatibility group plasmids pMG1 and pMG5.

Large plasmids from Agrobacterium tumefaciens, Salmonella typhimurium, Escherichia coli, Pseudomonas putida, and Pseudomonas aeruginosa were routinely and consistently isolated using a procedure which does not require ultracentrifugation but includes steps designed to separate large-plasmid DNA from the bacterial folded chromosome. It also selectively removes fragments of broken chromosome. A variety of large plasmids was readily visualized with agarose gel electorphoresis, including five between 70 and 85 megadaltons (Mdal) in size, six between 90 and 143 Mdal, one that was larger than 200 Mdal, and one that was larger than 300 Mdal. This isolation procedure allowed initial estimation of the molecular sizes of the two IncP2 plasmids, pMG1 and pMG5, which were 312 and 280 Mdal, respectively. A standard curve for size determination by gel electrophoresis including plasmids between 23 and 143 Mdal in size did not extrapolate linearly for plasmids of the 300-Mdal size range. Unique response of different plasmids to the isolation procedure included sensitivity of IncP1 plasmids to high pH and the co-isolation of a 20-Mdal "cryptic" plasmid in conjunction.     

Transfer of chromosomal genes and formation of R'-derivatives using PR4::D312cts15 plasmids in Pseudomonas aeruginosa cells

Several hybrid RP4 plasmids containing the genome of heat-inducible D3112cts15 phage integrated into 2 different sites of RP4 were selected. It was shown that the plasmids RP4::D3112cts15 mobilized the chromosome of Pseudomonas aeruginosa from many sites located in different chromosome regions. Chromosomal recombinants are, formed at frequencies of about 10(-4) per recipient cell. Analysis of coinheritance of unselected markers showed that the majority of recombinants inherited short donor chromosome fragments (about 5 min). R' plasmids can be easily selected by mating with a rec- recipient. For instance, the frequency of selection of R' plasmids containing argH+ locus was about 10(-5) per donor cell. Conjugative transfer of RP4::D3112cts15 into nonlysogenic strains PAO P. aeruginosa results in partial or complete loss of prophage from a hybrid plasmid. The RP4::D3112cts15 plasmids appear to have retained the broad host range of the original RP4 (they are maintained in P. putida and Escherichia coli).