Ligase-free subcloning: a versatile method to subclone polymerase chain reaction (PCR) products in a single day.

Often, it is convenient to subclone polymerase chain reaction (PCR) products into a plasmid vector for subsequent replication in bacteria, but conventional subcloning methods often fail. We report a rapid and versatile method to subclone PCR products directionally into a specific site of virtually any plasmid vector. The procedure requires only four primers, does not require DNA ligase, and may be accomplished in a single day. Ligase-free subcloning is performed by incorporating into the PCR primers sequences at the 5' ends that result in PCR products whose 3' ends are complementary to the 3' ends of the recipient linearized plasmid. The PCR product and the linearized plasmid are spliced together in a second PCR reaction in which Taq polymerase extends the complementary overlapping 3' ends (ligation by overlap extension). Denaturation followed by heterologous reannealing and cyclization results in a cyclic recombinant plasmid with two nicks that may be used directly to transform competent Escherichia coli. In our hands, ligase-free subcloning is rapid, and offers many advantages over existing strategies.     

东方田鼠部分BAC文库的微卫星筛选

目的 从东方田鼠的部分BAC文库中筛选微卫星.方法 应用非放射性的菌落杂交方法和磁珠富集法从东方田鼠的BAC文库中筛选高质量的微卫星标记.结果 以地高辛标记的寡聚核苷酸(CA)20为探针,通过菌落杂交法从136个东方田鼠BAC克隆中筛选出杂交信号最强的20个阳性克隆.再将这20个阳性克隆分别通过链霉亲和素磁珠法构建亚克隆文库,从中选取400个经PCR鉴定为阳性的亚克隆进一步测序分析,共得到220个微卫星序列,阳性率55％.选取重复次数高,侧翼序列完整的微卫星序列设计74对引物,共有35对引物能扩增出清晰的条带,其中16对引物具有多态性.结论 成功且高效地从阳性BAC克隆中筛选出微卫星序列,这些微卫星和阳性BAC克隆可用于后续的定位研究.     

A DNA sequencing strategy

A modification of Lin's systematic DNA sequencing strategy is described. A method based on the religation of compatible cohesive ends generated by Sau3AI and BamHI was developed. The original procedure has been simplified and the yield of transfectant has been greatly improved. After complete digestion with BamHI and limited cleavage with Sau3AI, the single-cut linear DNA does not have to be separated from the supercoil or the open circular DNA on an agarose gel. After ligation, the DNA is digested with the restriction enzyme between the cloning site and BamHI site again. The original intact DNA is linearized, whereas the deleted subclone is not. Therefore the background is decreased to an undetectable level. This DNA sequencing strategy was tested on a 1.4-kb cDNA fragment containing the haptoglobin-related sequences. It is not necessary to purify large amounts of RF DNA (500 ng is enough) to get enough subclones. A set of subclones was produced in 1 day and the yield of plaques was about sixfold higher than that published.     

Isolation and characterization of a gp 70+ non producer Friend tumor cell clone

Viral expression was analyzed in ten cell clones of a Friend erythroleukemia cell line (HFL/b cell line [3]), which had lost its capacity to produce infectious particles. All the ten subclones were non producers but expressed spleen focus forming virus (SFFV) polypeptides in the form of p48-p50gag and gp50-gp52env. One subclone (subclone 9) expressed the gp70env of the Friend-MuLV helper component of the Friend virus complex. Comparative analysis of viral RNA expression in one gp70- subclone (subclone 2) and in the gp70+ subclone (subclone 9) was performed using specific ecotropic env gene probe and MCF/xenotropic env gene probe. In both subclones 2 and 9, the MCF/xenotropic env gene probe detected 32S SFFV genomic RNA, 20S SFFV env gene mRNA and a 34S RNA. The ecotropic env probe failed to characterize any 38S F-MuLV genomic RNA in both clones but detected 34S RNA and 24S env mRNA in the gp70+ subclone 9. These data show that expression of a complete F-MuLV genome is not required for synthesis of env gene products.     

Comparison of two aposymbiotic ciliate clones of Climacostomum virens by their ability for reinfection

The ability of two aposymbiotic (algae-free) subclones of the same green clone of C. virens to establish a stable symbiotic association with Chlorella sp. has been studied by light and electron microscopy. Alga-free subclone No. 1 was obtained from the original green clone by a long-term cultivation in darkness, while subclone No. 2 originated from one cell that spontaneously lost the algae and was found among normal green cells during daily inspection. For infection, algae isolated from ciliates with chlorellae of parental clone of C. virens were used. 5-10 minutes after feeding with Chlorella, specimens of both subclones show numerous algae mostly inside food vacuoles, but some rare algae (3-4 per cell) may occur in individual perialgal vacuoles. Later on, the number of symbiotic chlorellae in ciliates of subclone No. 1 increased, and a stable symbiotic association was reestablished. Unlike, in specimens of subclone No. 2 all newly ingested algae were seen digested within food vacuoles. Within 24-28 h all the ciliates investigated appeared free of algae. However, obviously stable symbiotic ciliate-algae systems in this subclone were obtained after improving the microinjection technique. Injection of algae into alga-free ciliates resulted in maintenance of intact chlorellae in these ciliates. The algae were seen to be located individually within perialgal vacuoles, being presumably protected against host lytic enzyme attack. The endosymbiont population in ciliates was established from as many as 3-5 originally injected algae. The number of symbiotic chlorellae increased steadily reaching the value equal to that in the parental clone 28-30 days after the start of experiment.     

A yeast artificial chromosome contig containing the complete Duchenne muscular dystrophy gene.

A contig of 36 overlapping yeast artificial chromosome (YAC) clones has been constructed for the complete Duchenne muscular dystrophy (DMD) gene in Xp21. The YACs were isolated from a human 48,XXXX YAC library using the DMD cDNA and brain promoter fragments as hybridization probes. The YAC clones were characterized for exon content using HindIII or EcoRI digests, hybridization of individual DMD cDNA probes, and polymerase chain reaction (PCR) amplification of specific exons near the 5' end of the gene. For comparison to the known long-range restriction map of the DMD gene, YAC clones were digested with SfiI and hybridized with DMD cDNA probes. The combined analysis of the exon content and the SfiI map allowed an approximately 3.2-Mb YAC contig to be constructed. The complete 2.4-Mb DMD gene could be represented in a minimum set of 7 overlapping YAC clones.     

Walking into the unknown: a 'step down' PCR-based technique leading to the direct sequence analysis of flanking genomic DNA

We describe a novel and efficient PCR-based technique for walking into unknown flanking genomic DNA without recourse to protracted laborious library screening for overlapping sequences. This two component 'hot start' and 'step down' PCR method uses 6x1 microg of genomic DNA (ca 20kb in length) restricted with six different endonucleases and ligated to adaptors with the inclusion of two further restriction enzymes to prevent self-ligation. This allowed us to walk, in a single step, up to 6kb into flanking DNA and gave sufficient PCR products for up to 200 different walking experiments. This technology enabled us to clone and characterize the previously elusive 5' sequence of the barley powdery mildew chitin synthase gene, BgChs2, which includes a myosin motor-like sequence fused to a type V chitin synthase gene.     

A physical map of the viral genome for infectious pancreatic necrosis virus Sp: analysis of cell-free translation products derived from viral cDNA clones.

The two segments of double-stranded RNA from infectious pancreatic necrosis virus Sp were cloned into the plasmid vector pUC8. Two sets of overlapping clones were identified by restriction enzyme and Southern blot analyses. Each of these sets was shown by Northern blot analysis to be exclusively related to either segment A or B of the genomic RNA. The entire lengths of the cloned segments were estimated to be 2.9 and 2.6 kilobases, respectively. Sequences from the two segments of viral cDNA were subcloned into the bacteriophage T7 RNA polymerase vectors pT71 and pT72. The activity of the single-stranded RNAs transcribed from these subclones in a rabbit reticulocyte lysate translation system provided information on the polarity of and the protein products coded for by each subclone. The four proteins encoded by the genome of infectious pancreatic necrosis virus were identified among the translation products of the individual cloned segments by immunoprecipitation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. By constructing plasmids containing deletions in the sequences from either the 5' or 3' end of segment A, we were able to construct a physical map for the larger segment of double-stranded RNA. The proteins derived from these plasmids indicated that the linear gene order for viral proteins encoded in segment A is beta, gamma 2, and gamma 1.     

Localisation of identical organophosphorus pesticide degrading (opd) genes on genetically dissimilar indigenous plasmids of soil bacteria: PCR amplification,cloning and sequencing of opd gene from Flavobacterium balustinum

Plasmid borne organophosphorus pesticide degrading (opd) gene of Flavobacterium balustinum has been amplified using polymerase chain reaction (PCR) and the resulting PCR product (1.25 Kb) was cloned in pUC18. Further, a detailed restriction map was determined to PCR product and subcloned as overlapping restriction fragments. The nucleotide sequence was determined for all subclones to obtain complete sequence of PCR amplified fragment. The sequence showed 98% similarity to opd genes cloned from other soil bacteria isolated from diversified geographical regions. The protein sequence predicted from the nucleotide sequence was almost identical to parathion hydrolase, a triesterase involved in hydrolysis of triester bond found in variety of op-pesticides. The signal sequence of parathion hydrolase contained recently discovered twin arginine transport (tat) motif. It appears that tat motif plays a critical role in membrane targeting of parathion hydrolase.     

A complete set of overlapping cosmid clones of M-ABA virus derived from nasopharyngeal carcinoma and its similarity to other Epstein-Barr virus isolates

DNA of the transforming, nondefective Epstein-Barr virus (EBV) strain M-ABA, which is derived from nasopharyngeal carcinoma cells, was cloned as large overlapping pieces into the cosmid pHC79. The termini were cloned from closed circular virus DNA molecules out of M-ABA cell DNA in phage λL47. The large overlapping clones were used to prepare a library of subclones with inserts of 1–15 kb. A detailed restriction enzyme map of M-ABA virus DNA reveals the close similarity to isolates from other sources. The high number of tandem repeats in EBV DNA stresses the importance of using cloning vectors that can be propagated in recA^?Escherichia coli hosts.     

Infectivity of Proviral DNA from Avian Sarcoma Virus-Transformed Mammalian Cells

The number of Rous viral genomes in the cellular DNA from two subclones (RS2/3, RS2/6) derived from the same clone of hamster BHK-21 cells transformed by Rous sarcoma virus was determined by hybridization with viral complementary DNA made in vitro, and the capacity of the cellular DNA to infect (transfect) chicken embryo fibroblasts was compared before and after shearing this DNA to about the size of the provirus (6 x 10(6) to 7 x 10(6) daltons). The two subclones differed widely both in their capacity to give rise to virus (inducibility) after fusion with chicken embryo fibroblasts and in level of expression of viral proteins. It was shown that cells of both subclones contain a single copy of Rous DNA and yield infectious DNA. However, whereas transfection of chicken embryo fibroblasts was successful with both unsheared (>/=18 x 10(6) daltons) and sheared DNA from the most inducible subclone (RS2/3 subclone), which also expresses viral proteins to an appreciable amount, transfection with DNA from the least inducible subclone (RS2/6 subclone), in which viral proteins are not expressed, succeeded only with sheared DNA. It was then about as successful as with sheared or unsheared RS2/3 DNA. The lack of infectivity of unsheared RS2/6 DNA may be explained by the hypothesis proposed by Cooper and Temin (G. M. Cooper and H. T. Temin, J. Virol. 17:422-430, 1976) to explain the lack of infectivity of DNA from certain chicken cells producing spontaneously low amounts of RAV-0 and resistant to exogenous RAV-0 infection, that is, that the viral genome (proviral DNA) is linked to a cis-acting control element which blocks its expression. This linkage might originate, in RS2/6 cells, from translocation of cellular DNA containing the single proviral copy.     

Use of Alu-PCR to characterize hybrids containing multiple fragments and to generate new Xp21.3-p22.2 markers.

Irradiation fragment hybrids potentially provide highly enriched sources of region-specific human DNA. However, such hybrids often contain multiple human pieces, not all of which can be easily detected. To develop specific resources for rapidly generating markers from Xp21.3-p22.2, we have single cell cloned two previously constructed irradiation hybrids that contain markers in this region and have achieved segregation of the different known fragments originally retained. Alu-PCR products were generated from subclones positive or negative for Xp21.3-p22.2 markers, and comparison of the ethidium bromide patterns between sister subclones facilitated identification of bands likely to map to particular regions; in contrast, subclones that shared markers but were derived from independent lines showed no overlap in ethidium bromide pattern. All Alu-PCR products from one subclone, 50K-19E, in which only three closely linked markers were detected (DXS41, DXS208, DXS274) were mapped back to their region of origin. Of 28 products, 15 mapped to Xp21.2-p22.2, and these make up a new set of regionally assigned markers. However, the mapping data identified four separate Xp fragments in 50K-19E, only one of which had been picked up by marker analysis. Mapping back gel-isolated Alu-PCR products from an irradiation hybrid prior to any cloning or screening generates a comprehensive profile of the human DNA retained and permits rapid selection of sequences derived only from the region of interest.     

Characterization of two clones isolated from the TC-1 murine marrow stromal cell line: growth factor and retrovirus production and physical support of hemopoiesis

We previously reported the isolation of an adherent murine marrow cell line termed TC-1, and the initial characterization of two subclones derived from this line. In this study we report a further characterization of two subclones from the non-cloned TC-1 cell line. One subclone, TC-1-C-3, consisted of large, slow-growing syncytial polypoid cells that grew to relatively low saturation densities, did not form colonies in soft agar and showed desmosome-like junctions. The other subclone, TC-1-C-11, consisted of smaller, rapidly growing fibroblast-like diploid cells which showed anchorage-independent growth in soft agar. Both these subclones produced growth factors which stimulated giant macrophage colonies in soft agar culture in vitro, but only the TC-1-C-3 subclone produced a retrovirus, whose source was most likely the endogenous ecotropic Emv-2 provirus present in chromosomal DNA in C57BL mice. This retrovirus from the TC-1-C-3 subclone did not appear capable of transforming TC-1-C-11 cells. Together, these data suggest that TC-1-C-3 cells have a special capacity for supporting hemopoiesis. The question of whether the mechanism of this support relates to an intrinsic property of the cell or is possibly related to retrovirus production remains unanswered.     

昆虫病原线虫共生菌BP品系杀虫毒素基因簇中各基因与杀虫活性的关系

昆虫病原线虫共生菌Xenorhabdus nematophilus BP的多个杀虫毒素基因集中在一起形成一个约40kb的基因簇。为研究这个基因簇中各基因与杀虫活性的关系,对该共生菌粘粒文库中5个粘粒克隆XnBP76、XnBP83、XnBP203、XnBPp378 和XnBP414及XnBP83的3个亚克隆插入DNA片段的基因结构和它们对棉铃虫的杀虫活性进行了比较,结果显示,xptB1, xptC1和xptA2 3个基因或后两者的联合表达产物具有最强的杀虫效果,缺失其中的任何1个或2个会使杀虫活力大幅度地下降或完全消失;而xptD1和xptA1的缺失对毒素基因簇的表达产物的杀虫活力影响很小;杀虫毒素的物理混合没有明显的增效作用。     

Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries

We present a statistical analysis of the problem of ordering large genomic cloned libraries through overlap detection based on restriction fingerprinting. Such ordering projects involve a large investment of effort involving many repetitious experiments. Our primary purpose here is to provide methods of maximizing the efficiency of such efforts. To this end, we adopt a statistical approach that uses the likelihood ratio as a statistic to detect overlap. The main advantages of this approach are that (1) it allows the relatively straightforward incorporation of the observed statistical properties of the data; (2) it permits the efficiency of a particular experimental method for detecting overlap to be quantitatively defined so that alternative experimental designs may be compared and optimized; and (3) it yields a direct estimate of the probability that any two library members overlap. This estimate is a critical tool for the accurate, automatic assembly of overlapping sets of fragments into islands called "contigs." These contigs must subsequently be connected by other methods to provide an ordered set of overlapping fragments covering the entire genome.     

USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products

We present a method that allows simultaneous fusion and cloning of multiple PCR products in a rapid and efficient manner. The procedure is based on the use of PCR primers that contain a single deoxyuridine residue near their 5′ end. Treatment of the PCR products with a commercial deoxyuridine-excision reagent generates long 3′ overhangs designed to specifically complement each other. The combination of this principle with the improved USER cloning technique provides a simple, fast and very efficient method to simultaneously fuse and clone multiple PCR fragments into a vector of interest. Around 90% positive clones were obtained when three different PCR products were fused and cloned into a USER-compatible vector in a simple procedure that, apart from the single PCR amplification step and the bacterial transformation, took approximately one hour. We expect this method to replace overlapping PCR and the use of type IIS restriction enzymes in many of their applications.     

Apoptosis induced by DNA uptake limits transfection efficiency

Electrotransfection is an effective method for transfecting lymphoid cells. However, the transfection efficiency of certain lymphoid cells is low. L1210 subclones and NFS-70 pro-B cells, which are highly refractory to various transfection methods, were used to identify the limiting factors. Cells were electrotransfected with plasmids coding for green fluorescence protein or luciferase. The luciferase expression of L1210 subclone 3-3 was found to increase 6-12 h after electroporation, but decreased significantly from 12 to 48 h. The lower level of luciferase activity at later time periods correlated with decreases in cell viability, which was shown to be due to apoptosis, as determined by propidium iodide/acrindine orange staining, DNA laddering, and prevention of cell death by addition of caspase inhibitors. Similar results were observed with NFS-70 pro-B cells and select L1210 subclones. In contrast, L1210 parental and L1210 subclone 7-15.6 cells undergo only low levels of apoptosis (< or = 5%). Apoptosis occurred only when DNA (plasmids or salmon sperm DNA) was present during electroporation, but was not dependent on the conformation of the DNA used or the expression of transgenes. Cells pulsed in the presence of dextran sulfate (MW 500,000) did not apoptose. Similar results were observed when L1210 subclone 3-3 was transfected using the cationic lipid 1, 2-dioleoyl-3-trimethylammonium propane, although the transfection efficiency and corresponding rate of apoptosis were significantly lower. Applying the caspase inhibitor fluoromethyl ketone (Boc-ASP-FMK) dramatically improved cell viability and transgene expression of select L1210 subclones and NFS-70 pro-B cells.     

Characterization of chimeric antibody producing CHO cells in the course of dihydrofolate reductase-mediated gene amplification and their stability in the absence of selective pressure

Recombinant Chinese hamster ovary (CHO) cells expressing a high-level of chimeric antibody against S surface antigen of hepatitis B virus were obtained by co-transfection of heavy and light chain cDNA expression vectors into dihydrofolate reductase (dhfr)-deficient CHO cells and subsequent gene amplification in medium containing stepwise increments in methotrexate (MTX) level such as 0.02, 0.08, 0.32, 1.0, and 4.0 microM. The highest producer (HP) subclone was isolated from each MTX level and was characterized with respect to cell growth and antibody production in the corresponding level of MTX. The specific growth rate of the HP subclone was inversely proportional to the MTX level. On the other hand, its specific antibody productivity (qAb) rapidly increased with increasing MTX level up to 0.08 microM, and thereafter, it gradually increased to 20 microg/10(6) cells/day at 4 microM MTX. Southern blot analysis showed that the enhanced qAb at higher MTX level resulted from immunoglobulin (Ig) gene amplification. The stability of the HP subclones isolated at 0.02, 0.08, 0.32, and 1.0 microM MTX in regard to antibody production was investigated during long-term culture in the absence of MTX. The qAb of all subclones significantly decreased during the culture. However, the relative extent of decrease in qAb was variable among the subclones. The HP subclone isolated at 1 microM MTX was most stable and could retain 59% of the initial qAb after 80 days of cultivation. Southern blot analysis showed that this decrease in qAb of the subclones resulted mainly from the loss of Ig gene copies during long-term culture. Despite the decreased qAb, the HP subclone isolated at 1 microM MTX could maintain high volumetric antibody productivity over three months because of improved cell growth rate during long-term culture.     

A Polymerase Chain Reaction Screening Method for Rapid Detection of Microsatellites in Bacterial Artificial Chromosomes

Standard protocols aimed at identifying subclones of interest from bacterial artificial chromosomes (BACs) include the use of hybridization methods that are time consuming and often require the use of radioactive isotopes. Through our efforts to identify microsatellites in BACs from rainbow trout (Oncorhynchus mykiss) we have developed a nonradioactive polymerase chain reaction (PCR)-based screening technique to select microsatellites containing subclones for marker development. Two BACs were subcloned and screened by PCR using a vector-specific primer and a mix of microsatellite repeat primers. The subclones were then sequenced to evaluate the efficiency of the PCR screening method. Correlation between positive PCR amplification and presence of microsatellites varied between the two BACs (21.9% and 71.4%), but still a sufficient number of subclones were identified to enable design and optimization of microsatellite markers.