Isolation of bacterial plasmids by density gradient centrifugation in cesium trifluoroacetate (CsTFA) without the use of ethidium bromide

Plasmids extracted from bacterial cells by alkaline extraction can easily be isolated from linear DNA by isopycnic centrifugation in CsTFA. This is a fast and simple method which circumvents the use of the intercalating dye, ethidium bromide, and consequently the problems associated with its removal. The buoyant densities for covalently closed circular DNA and linear DNA in CsTFA are 1.60 g/ml and 1.65 g/ml, respectively. The isolation is achieved regardless of plasmid size and can be accomplished at temperatures of between 4 and 30 degrees C. Plasmid DNA isolated in gradients of CsTFA are of a high purity and have been found to be intact when cleaved with restriction enzymes and ligated with T4 DNA ligase.     

Purification of mucin glycoproteins by density gradient centrifugation in cesium trifluoroacetate.

A procedure for the rapid isolation of mucin glycoprotein by density gradient centrifugation in cesium trifluoroacetate (CsTFA) is described. The separation of mixtures of rat tracheobronchial mucin, DNA, hyaluronic acid, and bovine serum albumin in CsTFA gradients was superior to that in cesium bromide gradients. Inclusion of guanidinium chloride or urea in the gradient had no influence on the separation obtained. The mucins isolated from sputum samples of cystic fibrosis patients by this procedure are largely free of nucleic acid, nonglycosylated proteins, and glycosaminoglycans. The results of the use of CsTFA gradient centrifugation for the isolation of mucin from extracts of bovine submaxillary gland are also presented. The CsTFA method is particularly suitable for the high-yield isolation of mucin from individual samples which are available in limited quantities.     

Rapid preparation of covalently closed circular DNA by acridine yellow affinity chromatography

Covalently closed circular DNA can be isolated rapidly from cell lysates in a two-step process. Hydroxylapatite chromatography to prepurify the plasmid DNA from contaminating protein and RNA is followed by a step gradient elution of covalently closed circular (CCC) plasmid DNA from an acridine yellow affinity column. This procedure results in CCC DNA of a purity comparable to that obtained from ethidium bromide-CsCl gradients without lengthy centrifugation and free of contaimination by intercalating dye. Up to 250 μg of CCC pBR 322 can be isolated from 500 ml of bacterial culture in 4–6 h.     

Isolation of DNA-free RNA, DNA, and proteins by cesium trifluoroacetate centrifugation

The ability to simultaneously isolate intact DNA-free RNA, genomic DNA, and proteins from a biological specimen can be useful in cloning genes and analyzing gene expression. Equilibrium density gradient centrifugation with CsCl is a useful tool for fractionating, quantitatively separating, and characterizing RNA, DNA, and the total quota of proteins, respectively, based on differences in their buoyant densities. In the present study we have reexamined the rarely used cesium salt, cesium trifluoroacetate, for the same purpose. A significant advantage of CsTFA lies in the fact that, unlike in CsCl, RNA can be recovered from a single, soluble fraction of the CsTFA gradient. Furthermore, unlike CsCl, CsTFA is freely soluble in ethanol so that co-precipitation of the salt in the recovered RNA upon alcohol precipitation does not take place. Hence, the RNA is recovered with minimum manipulations. The one-step separation of cellular macromolecule classes free of each other in small amount of starting materials provides a major advantage over other methods currently in use.     

Fractionation of nucleic acids from Penicillium chrysogenum and associated ribonucleic acid viruses by selective exclusion and retention in agarose gels

Double-stranded nucleic acids from a strain of Penicillium chrysogenum containing RNA viruses were isolated by agarose-gel filtration, and separated into DNA and double-stranded RNA fractions by agarose-gel chromatography in 2.5m-NaCl. The DNA fraction contained less than 1% alkali-labile polynucleotides, and sedimented homogeneously at 8-10S in alkaline sucrose gradients. In CsCl gradients it tended to band in the density region of 1.66-1.72g/ml. It had a ;melting' temperature (T(m)) of 75 degrees C in 0.015m-NaCl-0.0015m-trisodium citrate, corresponding to 51.5mol% of G+C. The double-stranded RNA fraction did not contain detectable DNA. It could not band in CsCl up to a density of 1.78g/ml, and mainly consisted of a 14-15S RNA species with a T(m) of 88.5 degrees C in the above solvent, and a G+C content of 49.3 mol%.     

Genome analysis of Peromyscus (Rodentia,Cricetidae)

A satellite DNA fraction from P. eremicus, having a buoyant density of 1.705 g/ml in neutral CsCl density gradients, was isolated. In situ hybridization experiments, using 3H-RNA complementary to this DNA fraction indicated that the short (heterochromatic) arms of most of the autosomes contained this sequence. Conversely, in situ hybridization using 3H-complementary DNA (cDNA) synthesized from the cytoplasmic poly (A) RNA of P. eremicus (comprising a substantial fraction of total messenger RNA) showed that the number of silver grains in the long arms (euchromatin) was significantly higher than that in the short arms. The X chromosomes showed a distinct localization pattern of both sequences.     

Simultaneous isolation of preparative amounts of RNA and DNA from Trichinella spiralis by cesium trifluoroacetate isopycnic centrifugation

A rapid method for simultaneously banding preparative amounts of RNA and DNA from Trichinella spiralis muscle larvae by isopycnic centrifugation in cesium trifluoroacetate (CsTFA) is described. Larvae were homogenized in guanidinium isothiocyanate and the DNA, RNA, glycogen, and denatured protein components were isopycnically separated without prior purification. This procedure resulted in the isolation of nucleic acids suitable for molecular biological application. Agarose gel electrophoresis of gradient fractions indicated the separation of undegraded RNA and DNA where total RNA was of sufficient purity to efficiently direct in vitro translation of parasite protein and total DNA was greater than 20 kb in size and sensitive to restriction endonuclease digestion. Oligo (dT)-purified poly(A)+ mRNA was 3.6% of total RNA with greater than 18% conversion to cDNA.     

Properties of Intracytoplasmic A Particles Isolated from Oncornavirus-Producing Human Cells

A particles with the diameter of 70 to 80 nm were isolated from the cytoplasm of HEp-2, HeLa, and AO cells producing oncornavirus of Mason-Pfizer-like type. Most of the A particles banded at 1.23 to 1.24 g/ml, whereas 3 to 10% banded at 1.29 g/ml in equilibrium sucrose gradients. They banded at 1.30 g/ml in CsCl gradients suggesting that they contained 8% RNA. Individual A particles sedimented at 200 to 250S in velocity sucrose gradients, but their significant part was found aggregated and sedimented at more than 300S. They were resistant to RNase digestion. A particles possessed polymerase activity which was preferentially activated by Mn(2+) rather than by Mg(2+), the RNA template being 60S RNA. Cross-hybridization with two DNA products and immunoassay showed that A particles and Mason-Pfizer-like oncornavirus produced by the same cells contained neither homological RNA sequences nor common antigens, suggesting that A particles are not intracellular precursors of Mason-Pfizer-like oncornavirus but represent an independent oncornavirus. Hybridization of A particle RNA with excess of cellular DNA revealed about 20 proviral copies per HEp-2 cell genome and no proviral copies in human embryo and placenta cell genomes.     

Isolation of dna and rna from Streptococcus sobrinus OMZ176 using CsTFA gradients

• 1.1. A simple procedure for isolation of high molecular weight genomic DNA, and RNA, from Streptococcus sobrinus OMZ176 is described.
• 2.2. Cell cultures were grown aerobically for 10 hr.
• 3.3. Spheroplast formation and lysis was achieved by mutanolysin/lysozyme-dependent digestion of the cell wall, followed by N-lauroylsarcosinate-mediated lysis.
• 4.4. Nucleic acids were isolated directly from cell-lysates using cesium-trifluoroacetate (CsTFA) densitygradient centrifugation.
• 5.5. Three different centrifugation regimes were tested: self-generated density gradients in a fixed angle rotor; self-generated density-gradients in a swinging-bucket rotor; pre-formed density-gradients in a swinging-bucket rotor.
• 6.6. Genomic DNA isolated by the CsTFA-procedure was found to have higher purity as compared to genomic DNA isolated in a conventional CsCl gradient.
• 7.7. Isolated DNA was shown to be of a quality suitable for applications in molecular biology.

     

Rapid isolation of pancreatic islets from collagenase digested pancreas by sedimentation through Percol at unit gravity.

A Percoll solution with a density of 1.045 g/ml was used to separate pancreatic islets and exocrine tissue from collagenase-digested human and $\text{ob/ob}$ mouse pancreases by sedimentation at unit gravity. Most exocrine tissue from the mouse was found to range in density from 1.015 to 1.045 g/ml whereas the denser islets lay in a narrower range of 1.065–1.070 g/ml. Up to 400 islets were obtained from each mouse pancreas and 140 islets from 4 g of human pancreas; the isolated islets being essentially free from contamination with exocrine tissue. Glucose-stimulated insulin release was the same whether the mouse islets were isolated with or without Percoll. The simplicity of the method makes it suitable for large-scale islet isolation, a feature of potential importance for the treatment of diabetes by islet transplantation.     

Endogenous and exogenous domain markers of the rat hepatocyte plasma membrane

We have used a combined biochemical and morphological approach to establish the suitability of certain endogenous and exogenous domain markers for monitoring the separation of rat hepatocyte plasma membrane domains in sucrose density gradients. As endogenous domain markers, we employed two of the integral plasma membrane protein antigens, HA 4 and CE 9, localized to the bile canalicular and sinusoidal/lateral domains, respectively, of the hepatocyte plasma membrane in rat liver tissue (Hubbard, A. L., J. R. Bartles, and L. T. Braiterman, 1985, J. Cell Biol., 100:1115-1125). We used immunoelectron microscopy with a colloidal gold probe to demonstrate that HA 4 and CE 9 retained their domain-specific localizations on isolated hepatocyte plasma membrane sheets. When the plasma membrane sheets were vesiculated by sonication and the resulting vesicles were centrifuged to equilibrium in sucrose density gradients, quantitative immunoblotting revealed that the vesicles containing HA 4 and those containing CE 9 exhibited distinct density profiles. The density profile for the bile canalicular vesicles (marked by HA 4) was characterized by a single peak at a density of 1.10 g/cm3. The density profile for the sinusoidal/lateral vesicles (marked by CE 9) was bimodal, with a peak in the body of the gradient at a density of 1.14 g/cm3 and a smaller amount in the pellet (density greater than or equal to 1.17 g/cm3). We used this sucrose gradient fractionation as a diagnostic procedure to assign domain localizations for several other hepatocyte plasma membrane antigens and enzyme activities. In addition, we used the technique to demonstrate that 125I-wheat germ agglutinin, introduced during isolated liver perfusion at 4 degrees C, can serve as an exogenous domain marker for the sinusoidal domain of the rat hepatocyte plasma membrane.     

Separation of dense, polysaccharide-containing vesicles from secreting, cultured oat cells. Characterization of a putative secretory vesicle fracton

Suspension cultured oat (Avena sativa L. cv. Garry) cells, which secrete polysaccharides into the medium, were used as starting material for analyses of Golgi-derived vesicle membranes and plasma membranes isolated during cell fractionation. Vesicles collected by a procedure employing ultrafiltration followed by ultracentrifugation into a sucrose step gradient exhibited an equilibrium density of 1.27 g cm^?3 when run on continuous sucrose gradients, a feature which is most likely attributable to the high concentration of enclosed polysaccharides. Brief sonication lowered the density of these vesicles to about 1.15 g cm^?3, as judged from the coincidence of the protein peak and the marker enzymes for Golgi [Triton-stimulated UDPase, cold-storage IDPase (EC 3.6.1.6)] and plasma membrane [vanadate-inhibited K⁺, Mg²⁺-ATPase (EC 3.6.1.3)]. Sonication of these vesicles also greatly diminished the amount of detectable polysaccharide observed in a colorimetric assay for sugars. Fractionation of a plasma membrane-enriched preparation from these cells on continuous sucrose gradients showed the major protein peak and the peak activity for the plasma membrane marker at 1.17 g cm^?3, however, there was also significant overlap with a mitochondrial [cytochrome c oxidase (EC 1.9.3.1)] peak at 1.18 g cm^?3, Smaller peaks of the Golgi markers were seen at 1.14 g cm^?3. Analyses of marker enzymes for ER and mitochondria (EC 1.6.99.3) showed little contamination of the membranes of presumptive secretory vesicles from these sources, and the lack of significant vanadate-insensitive ATPase activity in the density range from 1.13–1.18 g cm^?3 in either fractionation scheme suggests that these membranes do not include material from the tonoplast. The coincidence of markers for Golgi and plasma membrane with from the tonoplast. The coincidence of markers for Golgi and plasma membrane with the membranes of sonicated, dense vesicles, at a density slightly lower than that of plasma membranes prepared from the same cells, supports the possibility that membranes en route to the plasma membrane are incompletely differentiated.     

Stoichiometry and specificity of binding of Rauscher oncovirus 10,000-dalton (p10) structural protein to nucleic acids.

A structural protein of Rauscher oncovirus of about 8,000 to 10,000 daltons (p10), encoded by the gag gene, has been purified in high yield to apparent homogeneity by a simple three-step procedure. The purified protein was highly basic, with an isoelectric point of more than 9.0, and its immunological antigenicity was chiefly group specific. A distinctive property of the protein was the binding to nucleic acids. The stoichiometry of p10 binding to Rauscher virus RNA was analyzed using both 125I-labeled p10 and 3H-labeled RNA. The protein-RNA complex, cross-linked by formaldehyde, was separated from free RNA and free protein by velocity sedimentation and density gradient centrifugation. A maximum of about 140 mol of p10 was bound per mol of 35S RNA, or about one molecule of p10 per 70 nucleotides. This protein-RNA complex banded at a density of about 1.55 g/ml. The number of nucleic acid sites bound and the affinity of p10 binding differed significantly among the other polynucleotides tested. The protein bound to both RNA and DNA with a preference for single-stranded molecules. Rauscher virus RNA and single-stranded phage fd DNA contained the highest number of binding sites. Binding to fd DNA was saturated with about 30 mol of p10 per mol of fd DNA, an average of about one p10 molecule per 180 nucleotides. The apparent binding constant was 7.3 X 10(7) M(-1). The properties of the p10 place it in a category with other nucleic acid binding proteins that achieve a greater binding density on single-stranded than on double-stranded molecules and appear to act by facilitating changes in polynucleotide conformation.     

Analysis by isopycnic centrifugation of isolated nucleoids of Escherichia coli.

The isolated, formaldehyde-fixed nucleoid of E. coli has been analyzed by isopycnic centrifugation in CsCl density gradients. The membrane-free nucleoid bands at a density of 1.69 +/- 0.02 g/cm3. The membrane-associated nucleoid bands at a density of 1.46 +/- 0.02 g/cm3. Both species sediment to equilibrium as nearly monodisperse bands in CsCl, suggesting that the nucleoid components of DNA, RNA and protein are present in relatively constant ratios. These ratios are constant regardless of the position of the nucleoids in the heterogeneous sedimentation profile of a preparative sucrose gradient. The fixed nucleoids remain condensed during isopycnic centrifugation and there is no detectable loss of RNA from the nucleoid.     

Localization of repeated DNA sequences in CsCl gradients by hybridization with complementary RNA

Single-stranded ends of mouse satellite DNA sequences exposed during the extraction of nuclear DNA, or by mechanical shear, can hybridize with highly labelled RNA, complementary to satellite DNA. In neutral CsCl gradients, the hybrid sediments as a sharp peak at the density of mouse satellite DNA (1.691 g/cm³). The possibility of exploiting this observation in locating and isolating cryptic repetitive DNAs from nuclear DNA or the DNA of heterochromatin is discussed.     

The isolation of pure cholinergic synaptic vesicles from the electric organs of elasmobranch fish of the family Torpedinidae

1. Zonal centrifuging permitted the separation, on the milligram scale and in a form largely free from contamination by soluble cytoplasmic protein or membrane fragments derived from other structures, of synaptic vesicles from the purely cholinergic terminals of the electric organ of Torpedo. Up to 100g of tissue could be processed in a single run. 2. As much as 46% of the bound acetylcholine from the original tissue preparation was recovered as a single peak of density equivalent to 0.38m-sucrose-0.21m-NaCl and with a concentration of up to 680nmol of acetylcholine/mg of protein. 3. The limiting concentration of acetylcholine in isolated vesicles when allowance had been made for non-vesicular protein appeared to be about 600nmol/mg of protein. 4. Vesicle counts by a ;bead-tagging' procedure indicated an acetylcholine content of about 360mumol/ml of vesicles; thus the vesicle protein content would be about 60% (w/v). 5. Calculations showed that the core of the vesicle, accounting for about 55% of the vesicle volume, could be largely filled with acetylcholine and protein.