Dideoxy sequencing method using denatured plasmid templates

The dideoxy sequencing method in which denatured plasmid DNA is used as a template was improved. The method is simple and rapid: the recombinant plasmid DNA is extracted and purified by rapid alkaline lysis followed by ribonuclease treatment. The plasmid DNA is then immediately denatured with alkali and subjected to a sequencing reaction utilizing synthetic oligonucleotide primers. It takes only several hours from the start of the plasmid extraction to the end of the sequencing reaction. We examined each step of the procedure, and several points were found to be crucial for making the method reproducible and powerful: (i) the plasmid DNA should be free from RNA and open circular (or linear) DNA; (ii) a heptadecamer rather than a pentadecamer is recommended as a primer; and (iii) the sequencing reaction should be done at 37 degrees C or higher rather than at room temperature. The method enabled us to determine the sequence of more than a thousand nucleotides from a single template DNA.     

The use of cetyltrimethylammonium bromide for the rapid isolation from Staphylococcus aureus of relaxable and non-relaxable plasmid DNA suitable for in vitro manipulation

Plasmid DNA was isolated from Staphylococcus aureus by a rapid method that depends on the precipitation of DNA from cleared lysates by cetyltrimethylammonium bromide at low salt concentrations. The method was validated by its ability to provide DNA for restriction analysis of a highly relaxable plasmid species that is not isolated by more traditional techniques. The DNA can be digested with restriction endonucleases and used for transformation without further purification. The method also provides the basis for analysing staphylococcal plasmids that display a high frequency of deletion after transfer. Simple modifications of the technique allow plasmid DNA to be isolated from other bacteria and the rapid purification of DNA samples before in vitro manipulation.     

A rapid procedure for the isolation of plasmid DNA from environmental bacteria.

The INSTA-MINI-PREP method, a rapid protocol for plasmid DNA extraction, was originally developed to prepare plasmid DNA from 1 to 3 ml miniprep Escherichia coli cultures. Direct extraction of plasmid DNA is achieved by a two-phase solution which is separated by centrifugation in the presence of the INSTA-PREP gel barrier material. This method has been successfully tested on various environmental Salmonella strains, although it was not suitable for Pseudomonas aeruginosa and enterococci strains. The INSTA-MINI-PREP method is a new alternative procedure to screen plasmid contents of Salmonella and E. coli strains rapidly and easily.     

Rapid quantitation and monitoring of plasmid DNA using an ultrasensitive DNA-binding dye

A sensitive fluorescence-based method for monitoring plasmid DNA during production was investigated. This simple method of assaying for plasmid DNA allows rapid monitoring of plasmid yields from a recombinant Escherichia coli fed-batch fermentation. The assay has several advantages over traditional methods of plasmid DNA measurement. The fluorescent dye is highly specific and can measure total plasmid DNA concentration in about 5 min. The assay is sensitive over a wide range of plasmid concentrations of between 15 and 280 ng/mL, even in the presence of impurities that occur within alkaline lysate preparations. The technique can also be applied to monitoring fermentation and downstream purification steps.     

Vertical dye-buoyant density gradients for rapid analysis and preparation of plasmid DNA

A rapid and easy method for the isolation of plasmid DNA, both in analytical and preparative scale, is described. Using dye-buoyant density-gradient centrifugation in a vertical rotor, separation of covalently closed, supercoiled plasmid DNA from relaxed circular and linear DNA is completed within 1 to 2 h.     

Rapid purification of plasmid DNAs by hydroxyapatite chromatography.

A method is described for the rapid preparation of plasmid DNAs of molecular weight up to 14 X 10(6). This method involves the chromatography, at room temperature, of bacterial cleared lysates on hydroxyapatite in the presence of high concentrations of phosphate and urea. All detectable protein and RNA contamination of plasmid DNA is removed by this procedure and the conformation of the plasmid DNA is unaffected. Less than 0.5% chromosomal DNA is present in the purified preparation and even this can be removed if necessary by a simple extention of the procedure to include a heat-denaturation step. The method is extremely rapid and amenable to large-scale plasmid preparation; 5 mg ColE1 DNA have been purified within 40 min. The yield of plasmid DNA is similar to that obtained with the conventional dye-centrifugation technique, however the purity is greater.     

A procedure for the large-scale isolation of highly purified plasmid DNA using alkaline extraction and binding to glass powder

A preparative procedure for obtaining highly purified plasmid DNA from bacterial cells is described. The method is adapted from our earlier procedure, which gave partially purified plasmid in a form suitable for rapid screening of a large number of samples. In the present method, all detectable RNA, chromosomal DNA, and protein are removed without the use of enzymes, phenol extraction, dialysis, or equilibrium centrifugation. Binding of plasmid DNA to glass powder in the presence of 6 m sodium perchlorate is used for the final purification step.     

A simple method for the preparation of the covalently closed circular form of plasmid DNA

We describe a simple, rapid, inexpensive method for isolation of covalently closed circular plasmid DNA. The method involves the electrophoresis of crude DNA preparations in an agarose gel, electrotransfer onto a dialysis membrane and elution of the highly purified circular covalently closed plasmid DNA. Native and recombinant plasmid DNA have been purified by this method and shown to be suitable for restriction enzyme digestion and transformation of bacteria. The yield of this rapid purification procedure makes it a good alternative method to standard centrifugation in cesium chloride ethidium bromide gradients.     

Purification of RNA-free plasmid DNA using alkaline extraction followed by Ultrogel A2 column chromatography

A procedure for extracting RNA-free plasmid DNA from bacterial cells is described. The method is simple and rapid enough to obtain pure plasmid DNA in 8 to 10 h after plasmid amplification. The protocol uses the alkaline extraction procedure described by Birnboim and Doly (1979, Nucl. Acid Res. 7, 1513-1523). Plasmid DNA is then separated from high-molecular-weight RNA by ammonium acetate precipitation and from low-molecular-weight RNA contaminants by Ultrogel A2 column chromatography. The plasmid DNA obtained by this inexpensive technique is sufficiently pure to be used for restriction endonuclease analysis, 5'-end labeling, S1 mapping, DNA sequencing, and colony hydridization.     

氧化硅包裹的磁性纳米粒子纯化质粒DNA

质粒的分离纯化在分子生物学实际工作中占有重要地位.本文采用氧化硅包裹的磁性纳米粒子,平均粒径为20 nm左右,在外加磁场的作用下,从细胞粗提掖中快速分离质粒DNA.用这种方法成功地从大肠杆菌DH5α浓缩和纯化得到了pUC19质粒,该质粒具有生物活性,可直接用于限制性酶切和细胞转化等分子生物学下游操作.     

Purification and separation of various plasmid forms by exclusion chromatography

A chromatographic method for the rapid isolation of preparative amounts of plasmid DNA without the use of cesium chloride centrifugation is described. The protocol uses the alkaline extraction procedure and an exclusion column of Fractogel TSK 75S. From a clear lysate it is possible to obtain plasmid DNA completely free of proteins, RNA, and chromosomal DNA. From partially purified plasmid the procedure allows the separation of the different forms. This technique was successfully applied to different plasmids ranging in size from 2.9 to 17.5 MDa. It is a preparative method yielding easily 500 micrograms of pBR322 from 1 liter of amplified culture. The plasmid is suitable for topoisomerase I, topoisomerase II, and EcoRI assays.     

Separation of genomic DNA from plasmid DNA by selective renaturation with immobilized metal affinity capture

In contrast to proteins, many nucleic acids can undergo reversible modification of their conformations, and this flexibility can be used to facilitate purification. Selective renaturation with capture is a novel method of removing contaminating genomic DNA from plasmid samples. Plasmid DNA quickly renatures after thermal denaturation and cooling (or alkaline denaturation followed by neutralization), whereas genomic DNA remains locally denatured after rapid cooling in mismatch-stabilizing high ionic strength buffer. Partially denatured genomic DNA can be selectively bound to a metal chelate affinity adsorbent through exposed purine bases, while double-stranded renatured plasmid DNA is not bound. Using this method we have readily achieved 1,000,000-fold clearance of 71 wt % contaminating E. coli genomic DNA from plasmid samples.     

Rapid procedure for isolation and detection of Salmonella plasmids

A rapid procedure is described for the isolation of high quality and quantity plasmid DNA from Salmonella. Plasmids of molecular mass ranging from 10 kbp to 147 kbp were isolated. The method yielded enough DNA from the low copy number virulence plasmids of various Salmonella serovars for visualization on an agarose gel. The method is based on the classic alkaline lysis methods, employing the same reagents, but without any incubation steps. Isolation of plasmid DNA was also attempted with the use of rapid DNA isolation kits, but without success. It was reasoned that endonucleases, present in the resin, might have degraded the plasmids. © Rapid Science Ltd. 1998     

A simple procedure for large-scale purification of plasmid DNA

We report a simple, rapid and reliable procedure for large-scale purification of plasmid DNA from non-amplified bacterial cultures. It is a modification of the boiling method of Holmes and Quigley [Anal. Biochem. 114 (1981) 193-197] and involves gel-filtration chromatography using Sephacryl S-1000 for final purification of plasmid DNA. This method does not require CsCl gradients and the recovered plasmids are free of RNA and chromosomal DNA, are supercoiled, retain their biological activity, and are suitable for restriction analysis.     

A rapid method for the isolation of plasmid DNA from bacteria

Summary A rapid method is described for the isolation of plasmid DNA from Escherichia coli and Pseudomonas putida. The effect of heating the cell preparation during plasmid extraction is discussed in relationship to the final plasmid yield.     

Simple method for extracting plasmid DNA from lactic acid bacteria

Rapid screening and large-scale plasmid DNA isolation procedures are described for lactic acid bacteria, using glass beads to break cells. The rapid screening procedure allows one to obtain plasmid DNA pellets in less than 1 h. This method has been successfully tested on various bacteria from the genera Lactococcus, Leuconostoc, Lactobacillus, Pediococcus, Streptococcus, Enterococcus and Propionibacterium. This procedure yields plasmid DNA with minor chromosomal and plasmid DNA-degraded form contaminations.     

Use of a 'Miniprep' for rapid extraction of plasmids from vancomycin- and gentamicin-resistant Enterococcus faecium

Conventional methods of plasmid extraction are largely unsuited to diagnostic laboratories. The 'Miniprep' is a rapid method that utilises a centrifugable column to separate plasmid DNA from chromosomal DNA. We have modified this technique to extract plasmid DNA from seven strains of vancomycin- and gentamicin-resistant Enterococcus faecium (VGREF): 1% mannitol was added to the growth medium and cell lysis was achieved by incubation in 10 mg of lysozyme/ml in 10 mM Tris, 1 mM EDTA and 25% sucrose at pH 8.0. RNase A was added to plasmid eluate rather than at the lytic step. In comparison to a standard phenol/chloroform method, Miniprep completely eliminated chromosomal interference in gel electrophoresis but otherwise produced identical plasmid profiles. Plasmids obtained from the VGREF ranged from 42 to 1.3 Md. Band densities on a single elution from the Miniprep varied from 8.3 to 106.3 relative units. Double elution increased band densities from the same preparation from 30.4 to 196 relative units; mean percentage increases per track between 7.0 and 34.6%. This method is suitable to achieve plasmid DNA extraction from VGREF within 1 h, making the process more suitable for diagnostic laboratories.     

Detection by multiplex polymerase chain reaction and typing of Chlamydia trachomatis isolates

Abstract The multiplex polymerase chain reaction (PCR) was applied for the detection of the Chlamydia trachomatis chromosome and plasmid. The multiplex PCR demonstrated a sensitivity of 0.8 fg of chlamydial DNA, corresponding to the detection of about 5 copies of the plasmid. Analysis of 195 genital specimens collected randomly from a female population, showed that the multiplex PCR is more sensitive and rapid than culturing for detecting Chlamydia trachomatis . Moreover, sequencing of the II variable domain of the ompl gene, directly from DNA of the clinical specimens, appears to be a simple and rapid method for determining serovar isolates.     

A general method for plasmid isolation in lactobacilli

A simple procedure for rapid isolation and detection of plasmid DNA fromLactobacillus species is described. Using an alkaline-detergent lysis method, plasmid DNA was released and characterized from cells treated with either mutanolysin or lysozyme for 1 h at 0°C. Treatment of cells with either enzyme at 37°C for 1h was detrimental to plasmid isolation and charaterization in someLactobacillus species. The procedure was effective with small volumes of cells and allowed rapid characterization of plasmid DNA inLactobacillus plantarum, Lactobacillus acidophilus, Lactobacillus helveticus, andLactobacillus bulgaricus strains.     

简单快速分离无RNA的大肠杆菌质粒DNA的方法

本文介绍一种简单快速分离质粒ＤＮＡ方法。此方法有两个主要步骤。用这种方法分离的质粒ＤＮＡ纯度高、无ＲＮＡ,并可用于酶切、连接等操作。