Isolation of high molecular weight DNA from wholeEuglena cells

Summary A method for isolating high quality DNA from wholeEuglena cells is described. The procedure consists in: the weakening of the cell pellicle in glycerol avoiding the mechanical disruption of cells and shearing damage in DNA molecules; the decondensation ofEuglena compact chromatin directly inside the cells; the complete dissociation of cells and nucleoproteins in sarkosyl detergent; the optional digestion of proteins and RNA with DNase-free enzymes and the final purification of DNA by isopycnic banding in CsCl gradients. Degradation of DNA is prevented all along the extraction procedure by glycerol, antioxydants, EDTA and sarkosyl detergent. Using the enzymatic digestion step, DNA containing few single-stranded nicks is obtained with a yield approaching 100%. DNA with no single-stranded nick could be obtained with a 35% yield when the enzymatic digestion step was omitted. In both cases, the double-stranded DNA has an average molecular weight equal or greater than 6×10⁷. It is free of contaminants and could be easily digested with restriction enzymes. After digestion with Eco RI and size-fractionation in agarose gel this DNA has permitted specific hybridization of the rDNA sequences with a radioactive rRNA probe.Abbreviations Kbp kilobasepairs - Kb kilobases     

Single copy gene detection requiring minimal cell numbers

There has been an increasing application of molecular DNA probes to evaluate a variety of clinical conditions. Frequently, the amount of tissue or number of cells available limits analysis by conventional DNA extraction and Southern blot hybridization. Moreover, DNA amplification techniques cannot be used in all cases. We have applied a modification of the DNA extraction-Southern blot hybridization technique to clinical samples which provides essentially quantitative recovery and analysis of DNA from minimal numbers of cells. DNA was obtained from cells which were immobilized in agarose blocks for lysis, deproteinization and restriction enzyme digestion. The DNA was then run directly into agarose gels to size fractionate for Southern blot analysis. Cells can be suspended in agarose blocks for over one year and frozen cells can be thawed and suspended in agarose. A variety of restriction enzymes can be used. Single copy sequences can be detected from as few as 5 x 10(4) cells. We have employed this method to examine immunoglobulin gene rearrangements in PBL from leukemia patients as well as bone marrow from myeloma patients. In addition, we have used the technique to accurately assess bone marrow engraftment after transplant. These results demonstrate a diagnostic application of this technique in a variety of clinical samples where there may be limited availability of cells.     

Genetic analyses of restriction fragment length polymorphisms using high molecular weight DNA from sperm or lymphocytes embedded in agarose

A simple and efficient method for determining restriction fragment length polymorphism types on large numbers of individuals using small samples of peripheral blood or sperm cells is described. Whole cells embedded in low gelling/melting temperature agarose were treated with a series of enzyme, detergent, and washing steps to release high molecular weight DNA that was then digested with standard restriction enzymes such as EcoRI and PstI, electrophoresed, blotted, and probed as in normal Southern analyses. The technique should be readily adaptable to any application requiring DNA from small numbers of cells for Southern analyses or pulsed field gel electrophoresis.     

Access of proteinase K to partially translocated nascent polypeptides in intact and detergent-solubilized membranes

We have used proteinase K as a probe to detect cytoplasmically and luminally exposed segments of nascent polypeptides undergoing transport across mammalian microsomal membranes. A series of translocation intermediates consisting of discrete-sized nascent chains was prepared by including microsomal membranes in cell-free translations of mRNAs lacking termination codons. The truncated mRNAs were derived from preprolactin and the G protein of vesicular stomatitis virus and encoded nascent chains ranging between 64 and 200 amino acid residues long. Partially translocated nascent chains of 100 amino acid residues or less were insensitive to protease digestion from the external surface of the membrane while longer nascent chains were susceptible to digestion by externally added protease. We conclude that the increased protease sensitivity of larger nascent chains is due to the exposure of a segment of the nascent polypeptide on the cytoplasmic face of the membrane. In contrast, low molecular weight nascent chains were remarkably resistant to protease digestion even after detergent solubilization of the membrane. The protease resistant behaviour of detergent solubilized nascent chains could be abolished by release of the polypeptide from the ribosome or by the addition of protein denaturants. We propose that the protease resistance of partially translocated nascent chains can be ascribed to components of the translocation apparatus that remain bound to the nascent chain after detergent solubilization of the membrane.     

Glycosaminoglycan content of glomerular and tubular basement membranes of various mammalian species

A spectrophotometric assay was applied for quantitation of sulfated glycosaminoglycans in digested renal basement membranes of six mammalian species. The conditions of digestion and the accuracy of the assay were evaluated. Papain digestion and alkaline treatment appeared to be most effective for solubilization. Basement membrane preparations obtained by sonication contained more glycosaminoglycans than those isolated by detergent treatment. Glomerular basement membranes had generally a higher glycosaminoglycan content than tubular basement membranes.     

Mammalian expression cloning of nucleic acid binding proteins by agarose thin-layer gelshift clone selection

Here we report a functional screening technique to identify cDNAs encoding mammalian nucleic acid binding proteins. We have combined cDNA expression cloning with the agarose thin-layer gelshift assay technique to detect specific nucleic acid binding proteins from a mammalian expression library. We divided this cDNA expression library into multiple pools and transfected mammalian cells with the individual pools. Following transfection, we tested the expressed proteins for DNA-binding activity by agarose thin-layer electrophoretic gelshift assay. After we identified a single expression poolfor the presence of a DNA-binding protein, the corresponding cDNA pool was further divided into smaller aliquots. Then, the cDNA expression and gelshift clone selection was repeated until a single clone was isolated In contrast to traditional polyacrylamide gels, the agarose thin-layer is significantly faster and resolves larger DNA-protein complexes. This method can be widely used for the cDNA cloning of DNA- and RNA-binding proteins from various mammalian host cells.     

Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA

Analysis of mammalian mtDNA by two-dimensional agarose gel electrophoresis revealed two classes of replication intermediate. One was resistant to single-strand nuclease digestion and displayed the mobility properties of coupled leading- and lagging- strand replication products. Intermediates of coupled, unidirectional mtDNA replication were found in mouse liver and human placenta and were the predominant species in cultured cells recovering from transient mtDNA replication. Replication intermediates sensitive to single-strand nuclease were most abundant in untreated cultured cells. These are presumed to derive from the orthodox, strand-asynchronous mode of mtDNA replication. These findings indicate that two modes of mtDNA replication operate in mammalian cells and that changes in mtDNA copy number involve an alteration in the mode of mtDNA replication.     

Protoporphyrinogen oxidation, an enzymatic step in heme and chlorophyll synthesis: partial characterization of the reaction in plant organelles and comparison with mammalian and bacterial systems

High rates of oxidation of protoporphyrinogen to protoporphyrin were demonstrable in etioplasts, chloroplasts, and mitochondria from young barley shoots. Much lower rates were observed in chloroplasts from older barley or mature spinach, in mitochondria from potatoes or rat liver, and in membranes from the bacteria Escherichia coli and Rhodopseudomonas spheroides. The presence of high activity in cells capable of rapid synthesis of large amounts of chlorophyll suggests a role for this activity in chlorophyll synthesis. Characteristics of the plant protoporphyrinogen-oxidizing activity were compared to the activity in rat liver mitochondria. The activity in spinach chloroplasts exhibited a pH optimum of 7, which was lower than that of the mammalian enzyme. The plant activity was more sensitive to inhibition by glutathione or excess detergent, and was more readily inactivated at room temperature. The plant activity exhibited less specificity toward porphyrinogen substrates, oxidizing mesoporphyrinogen as rapidly as protoporphyrinogen. The mammalian enzyme oxidized mesoporphyrinogen slowly, and neither system oxidized coproporphyrinogen or uroporphyrinogen. Both the plant and the mammalian activity were bound to organelle membranes, but could be extracted with detergents. In contrast, activity from membranes of the bacteria E. coli and R. spheroides was inactivated by detergent treatment. The plant extracts could be fractionated with ammonium sulfate and retained activity after dialysis or Sephadex G-25 treatment, suggesting no readily dissociable cofactor. The activity extracted from spinach chloroplasts was mostly inactivated by trypsin digestion, which was additional evidence for the protein nature of the plant activity.     

Preparation of target antigens specifically recognized by human natural killer cells

In an attempt to identify target cell membrane molecules recognized by natural killer (NK) cells, artificial membranes were prepared from detergent-solubilized plasma membranes of NK target cells and synthetic lipids. Such reconstituted membranes from human and rat NK target cells were shown to inhibit both human and rat NK-target cell conjugates in a species-specific fashion; these reconstituted membranes failed to inhibit NK cytotoxicity. The detergent-solubilized material from the human NK target K562 was subjected to various procedures prior to reconstitution and the conjugate inhibition assay. Conjugate inhibitory activity was lost upon trypsin digestion and incubation at 65 degrees C. This inhibition activity was absorbed to concanavalin A agarose and could subsequently be eluted with alpha-methylmannoside, resulting in approximately 20-fold purification. Gel filtration of this material on an AcA-34 column in detergent gave a broad activity peak with maximal activity in the molecular weight range of 30,000-165,000. Gel electrophoresis of purified membranes demonstrated multiple molecular weight bands in lipid membranes. The K562 membrane material, purified by concanavalin A agarose and gel filtration, inhibited conjugates between human NK cells and any of four human target cells, but not of conjugates with (1) human large granular lymphocytes and antibody-coated mouse tumor cells nor (2) rat NK cells and their target cells. Thus the purified glycoproteins from K562 retain the property of specific inhibition of human NK-target conjugates.     

Carboxyl-coated magnetic nanoparticles for mRNA isolation and extraction of supercoiled plasmid DNA

Carboxyl-coated magnetic nanoparticles (MNPs) were used to demonstrate dual functionality: isolation of messenger RNA (mRNA) from mammalian cells and extraction of the supercoiled (sc) form of plasmid DNA (pDNA) from agarose gel. These MNPs were attached with 5′-NH₂-tagged oligo-(dT)₂₅ primer and were used to isolate mRNA from breast cancer cells. The isolated mRNA was used for amplification of β-actin to confirm the compatibility. These MNPs were also used to extract the sc form of pDNA from agarose gel. The compatibility of the pDNA was demonstrated by restriction digestion. Both of these methodologies are simple, inexpensive (compared with existing kits), and efficient.     

An improved method of plant megabase DNA isolation in agarose microbeads suitable for physical mapping and YAC cloning

The isolation of high quality megabase DNA from plant cells that is susceptible to a variety of molecular reagents is a critical first step in the physical analysis of complex genomes. A method for the isolation of such DNA by encapsulating plant protoplasts in agarose microbeads is presented. In comparison with the conventional agarose plug method, microbeads provide a dramatic increase in the surface area yielding megabase DNA that can be treated essentially as an aqueous DNA solution. Examples of the utility of DNA prepared by this technique for physical mapping, partial restriction enzyme digestion and cloning of large inserts as YACs are presented.     

Efficient extraction of RNA from mammalian tissue

RNA extraction from mammalian tissue has been compared using the different deproteinizing agents: a) guanidine-HCl, b) guanidinium-thiocyanate, c) buffer-saturated phenol, or d) buffer-saturated phenol followed by a proteinase K digestion of the aqueous phase. Both solid tissues (first, second, and third trimester fetal bovine pancreas), and human white blood cell populations were studied. Degradation, as seen in citric acid-urea agarose gels, and the ability to serve as templates for cell-free protein synthesis were used as criteria to assess the efficiency of the different methods. We conclude that employing buffer-saturated phenol with proteinase K digestion is a superior method for consistent extraction of relatively undegraded RNA in quantitative amounts from mammalian tissue.     

APols-Aided Protein Precipitation: A Rapid Method for Concentrating Proteins for Proteomic Analysis

Amphipols (APols) are a newly designed and milder class of detergent. They have been used primarily in protein structure analysis for membrane protein trapping and stabilization. We have recently demonstrated that APols can be used as an alternative detergent for proteome extraction and digestion, to achieve a “One-stop” single-tube workflow for proteomics. In this workflow, APols are removed by precipitation after protein digestion without depleting the digested peptides. Here, we took further advantage of this precipitation characteristic of APols to concentrate proteins from diluted samples. In contrast with tryptic peptides, a decrease in pH leads to the unbiased co-precipitation of APols with proteins, including globular hydrophilic proteins. We demonstrated that this precipitation is a combined effect of acid precipitation and the APols’ protein interactions. Also, we have been able to demonstrate that APols-aided protein precipitation works well on diluted samples, such as secretome sample, and provides a rapid method for protein concentration.     

Two-dimensional electrophoretic display of restriction fragments from genomic DNA

We have developed a procedure for the resolution of restriction enzyme digests of mammalian genomic DNA in two dimensions. Fragments from a first digestion are separated on a column of purified agarose containing a second restriction enzyme in the absence of the divalent cation required for enzyme activity. After enzyme activation and digestion, the fragments are resolved on an agarose slab gel. We have digested rat genomic DNA and found in the ethidium-stained pattern a variety of features which have not been described previously.     

Isolation of high-molecular-weight plant DNA for DNA damage quantitation: relative effects of solar 297 nm UVB and 365 nm radiation

Quantitation of UV-induced DNA damages in nanogram quantities of non-radiactive DNA from irradiated plants by gel electrophoresis requires a prompt, efficient, high-yield method of isolating DNA yielding high-molecular-weight, enzymatically digestible DNA. To meet these criteria we devised a high-yield method for isolating from plant tissue, DNA whose single-strand molecular length is greater than about 170 kb. Leaf tissue is embedded in agarose plugs, digested with Proteinase K in the presence of detergent, and treated with phenylmethylsulfonyl fluoride (PMSF). The agarose plugs are then soaked with buffer appropriate to the desired enzyme treatment. Evaluation of the DNA on neutral and alkaline gels indicates its high molecular length and low frequency of single-strand breaks. The DNA can be digested with damage-specific and other endonucleases. The method is especially suitable for DNA damage quantitation, as tissue processing is carried out immediately after harvesting (allowing DNA lesion measurement at precisely known times after irradiation), and many samples can be easily handled at once. It should also be useful for molecular analysis of large numbers of plant samples available only in small quantities. We here use this method to quantitate DNA damage induced by 297 and 365 nm radiation, and calculate the relative damaging effects of these wavebands in today's solar spectrum.     

Analysis of cellular integration sites in avian sarcoma virus infected duck embryo cells.

The cellular sites of integration of avian sarcoma virus (ASV) have been examined in clones of duck embryo cells infected with the Bratislava 77 strain of ASV using restriction endonuclease digestion, agarose gel electrophoresis, Southern blotting, and hybridization with labeled ASV complementary DNA probes. DNA prepared from 11 clones of duck embryo cells infected with the Bratislava 77 strain of ASV was digested with the restriction enzymes HpaI, which cleaves once within the viral genome, and Hind III, which cleaves twice within the viral genome, and the virus-cell DNA juncture fragments were resolved by agarose gel electrophoresis. Analysis of the virus-cell junctures present in individual ASV-infected duck embryo clones revealed that all clones contain at least one copy of nondefective proviral DNA with some clones containing as many as 5 to 6 copies of proviral DNA. A comparison of the virus-cell juncture fragments present in different ASV-infected clones showed that each clone contains a unique set of virus-cell junctures. These data suggest that ASV DNA can integrate at multiple sites within the duck embryo cell genome and that these sites appear to be different as defined by digestion with the restriction enzymes HpaI and HindIII.     

A single buffer that universally serves both restriction digestion and loading

Restriction digestion is routinely performed in a buffer compatible with the restriction enzyme used. To load the samples on agarose gels for electrophoresis it is then necessary to add a loading buffer. A 10X loading buffer is often used, and consists of a dye to track the electrophoresis and a dense solution so that the digestion mixture sinks into the well. We describe a new buffer, which acts as a universal digestion buffer as well as a loading buffer. This avoids double handling of samples, which wastes both time and consumables. Importantly, the efficiency of digestion was found not to be significantly decreased in this new buffer.     

Transformation of mammalian cells with recombinant DNA directly from Seaplaque agarose

Transfection of African green monkey kidney cells directly with recombinant DNA excised from, but still present in, Seaplaque agarose after electrophoresis, is described. Efficiencies of transfection increased by 30% when the gel was present compared with transfection in the absence of the agarose. Extraction of the DNA from the gel was not necessary, thereby obviating a purification step and the concomitant losses. To generate recombinant molecules bacterial plasmid sequences are not necessary, thereby reducing considerably the size of the recombinant molecule and removing extraneous and deleterious sequences, e.g., "poison sequences." Linear or circular DNA molecules could be transfected in the melted and diluted agarose with the same ease as in its absence. Hence linear partial ligation products can be excised from the gel after electrophoresis to generate recombinant DNA molecules directly in mammalian cells.     

Arrangement of Integrated Avian Sarcoma Virus DNA Sequences Within the Cellular Genomes of Transformed and Revertant Mammalian Cells

We have examined the arrangement of integrated avian sarcoma virus (ASV) DNA sequences in several different avian sarcoma virus transformed mammalian cell lines, in independently isolated clones of avian sarcoma virus transformed rat liver cells, and in morphologically normal revertants of avian sarcoma virus transformed rat embryo cells. By using restriction endonuclease digestion, agarose gel electrophoresis, Southern blotting, and hybridization with labeled avian sarcoma virus complementary DNA probes, we have compared the restriction enzyme cleavage maps of integrated viral DNA and adjacent cellular DNA sequences in four different mouse and rat cell lines transformed with either Bratislava 77 or Schmidt-Ruppin strains of avian sarcoma virus. The results of these experiments indicated that the integrated viral DNA resided at a different site within the host cell genome in each transformed cell line. A similar analysis of several independently derived clones of Schmidt-Ruppin transformed rat liver cells also revealed that each clone contained a unique cellular site for the integration of proviral DNA. Examination of several morphologically normal revertants and spontaneous retransformants of Schmidt-Ruppin transformed rat embryo cells revealed that the internal arrangement and cellular integration site of viral DNA sequences was identical with that of the transformed parent cell line. The loss of the transformed phenotype in these revertant cell lines, therefore, does not appear to be the result of rearrangement or deletions either within the viral genome or in adjacent cellular DNA sequences. The data presented support a model for ASV proviral DNA integration in which recombination can occur at multiple sites within the mammalian cell genome. The integration and maintenance of at least one complete copy of the viral genome appear to be required for continuous expression of the transformed phenotype in mammalian cells.     

Formation of unilamellar lipid vesicles of controllable dimensions by detergent dialysis.

Vesicles are formed by solubilizing mixtures of phosphatidylcholine and cholesterol with sodium cholate and removing the detergent by rapid (hollow fiber) dialysis [e.g., Goldin, S. M. (1977) J. Biol. Chem. 252, 5630--5642]. Characterization of the vesicle size distribution by agarose gel filtration, and determination of the intravesicular aqueous compartment, demonstrates that the vesicles are relatively homogeneous in size and are primarily unilamellar. The mean diameter of the vesicles can be varied from 340 to 1280 A by varying the conditions under which they are formed; increasing the mole fraction of cholesterol and lowering the pH of the dialysate tend to produce larger vesicles. The gentle detergent treatment required for vesicle formation and the ability to control vesicle size distribution reproducibly may make this method particularly useful in studies of reconstitution of membrane proteins and in use of vesicles as vehicles for delivery of materials to living cells.