A rapid colorimetric assay for the estimation of microgram quantities of DNA

The thiobarbituric acid assay, routinely employed for the quantification of sialic acids, has been modified for the estimation of DNA in the range 0.5–500 μg. Neither RNA nor protein interfere in this procedure. The assay, as described, is more sensitive and less time consuming than the diphenylamine reaction.     

MOLECULES AT THE EXTERNAL NUCLEAR SURFACE : Sialic Acid of Nuclear Membranes and Electrophoretic Mobility of Isolated Nuclei and Nucleoli

The molecules occurring as terminal residues on the external surfaces of nuclei prepared from rat liver by either sucrose-CaCl₂ or citric acid methods and nucleoli derived from the sucrose-CaCl₂ nuclei were studied chemically and electrokinetically. In 0.0145 M NaCl, 4.5% sorbitol, and 0.6 mM NaHCO₃ with pH 7.2 ± 0.1 at 25°C, the sucrose-CaCl₂ nuclei had an electrophoretic mobility of -1.92 µm/s/V/cm, the citric acid nuclei, -1.63 µm/s/V/cm, and the nucleoli, -2.53 µm/s/V/cm. The citric acid nuclei and the nucleoli contained no measurable sialic acid. The sucrose-CaCl₂ nuclei contained 0.7 nmol of sialic acid/mg nuclear protein; this was essentially located in the nuclear envelope. Treatment of these nuclei with 50 µg neuraminidase/mg protein resulted in release of 0.63 nmol of sialic acid/mg nuclear protein; treatment with 1 % trypsin caused release of 0.39 nmol of the sialic acid/mg nuclear protein. The pH-mobility curves for the particles indicated the sucrose-CaCl₂ nuclei surface had an acid-dissociable group of pK. ~2.7 while the pK for the nucleoli was considerably lower. Nucleoli treated with 50 µg neuraminidase/mg particle protein had a mobility of -2.53 µm/s/V/cm while sucrose-CaCl₂ nuclei similarly treated had a mobility of -1.41 µm/s/V/cm. Hyaluronidase at 50 µg/mg protein had no effect on nucleoli mobility but decreased the sucrose-CaCl₂ nuclei mobility to -1.79 µm/s/V/cm. Trypsin at 1 % elevated the electrophoretic mobility of the sucrose-CaCl₂ nuclei slightly but decreased the mobility of the nucleoli to -2.09 µm/s/V/cm. DNase at 50 µg/mg protein had no effect on the mobility of the isolated sucrose-CaCl₂ nuclei but decreased the electrophoretic mobility of the nucleoli to -1.21 µm/s/V/cm. RNase at 50 µg/mg protein also had no effect on the electrophoretic mobility of the sucrose-CaCl₂ nuclei but decreased the nucleoli mobility to -2.10 µm/s/V/cm. Concanavalin A at 50 µg/mg protein did not alter the nucleoli electrophoretic mobility but decreased the sucrose-CaCl₂ nuclei electrophoretic mobility to -1.64 µm/s/V/cm. The results are interpreted to mean that the sucrose-CaCl₂ nuclear external surface contains terminal sialic acid residues in trypsin-sensitive glycoproteins, contains small amounts of hyaluronic acid, is completely devoid of nucleic acids, and binds concanavalin A. The nucleolus surface is interpreted to contain a complex made up of protein, RNA, and primarily DNA, to be devoid of sialic acid and hyaluronic acid, and not to bind concanavalin A.     

THE LYSOSOME PERIPHERY: BIOCHEMICAL AND ELECTROKINETIC PROPERTIES OF THE TRITOSOME SURFACE

Normal rat liver lysosomes were isolated by the technique of loading with Triton WR-1339. Purity of the preparation was monitored with marker enzymes; a high enrichment in acid hydrolases was obtained in the tritosome fraction. In 0.0145 M NaCl, 4.5% sorbitol, 0.6 mM NaHCO₃, pH 7.2 at 25°C the tritosomes had an electrophoretic mobility of -1.77 ± 0.02 µm/s/V/cm, a zeta potential of 23.2 mV, a surface charge of 1970 esu/cm², and 33,000 electrons per particle surface assuming a tritosome diameter of 5 x 10^-7 m. Treatment of the tritosomes with 50 µg neuraminidase/mg tritosome protein lowered the electrophoretic mobility of the tritosome to -1.23 ± 0.02 µm/s/V/cm under the same conditions and caused the release of 2.01 µg sialic acid/mg tritosome protein. Treatment of the tritosomes with hyaluronidase did not affect their electrophoretic mobility, while trypsin treatment elevated the net negative electrophoretic mobility of the tritosomes. Tritosome electrophoretic mobilities indicated a homogeneous tritosome population and varied greatly with ionic strength of the suspending media. pH vs. electrophoretic mobility curves indicated the tritosome periphery to contain an acid-dissociable group which likely represents the carboxyl group of N-acetylneuraminic acid; this was not conclusively proven, however, since the tritosomes lysed below a pH of 4 in the present system. Total tritosome carbohydrate (anthrone-positive material as glucose equivalents) was 0.19 mg/mg tritosome protein while total sialic acid was 3.8 µg (11.4 nmol)/mg tritosome protein. A tritosome "membrane" fraction was prepared by osmotic shock, homogenization, and sedimentation. Approximately 25% of the total tritosome protein was present in this fraction. Analysis by gas-liquid chromatography and amino acid analyzer showed the following carbohydrate composition of the tritosome membrane fraction (in microgram per milligram tritosome membrane protein): N-acetylneuraminic acid, 14.8 ± 3; glucosamine, 24 ± 3; galactosamine, 10 ± 2; glucose, 21 ± 2; galactose, 26 ± 2; mannose, 31 ± 5; fucose, 7 ± 1; xylose, 0; and arabinose, 0. The results indicate that the tritosome periphery is characterized by external terminal sialic acid residues and an extensive complement of glycoconjugates. Essentially all the tritosome N-acetylneuraminic acid is located in the membrane and about 53% of it is neuraminidase susceptible.     

Interactions between glycosaminoglycans and proteins, with particular reference to a new technique for isolating serum glycoproteins

1. Chondroitin sulphate–serum protein complexes (A, B and C), successively precipitated by adding chondroitin sulphate to serum at three arbitrary descending pH values (5·2, 4·3 and 3·1), were dissociated at pH 6·7 and chromatographed on DEAE-Sephadex, when the liberated serum proteins were simultaneously freed of chondroitin sulphate and separated into five fractions. Evidence that serum proteins were precipitated as a result of electrostatic interactions with dissociated carboxylate groups on the glycosaminoglycan is presented. 2. Serum proteins (fraction G), unable to form complexes with chondroitin sulphate, contained 4·4% of sialic acid and accounted for 4 and 26% of the total protein and protein-bound sialic acid in serum respectively. This fraction interacted electrostatically with chondroitin sulphate only when rendered more basic by removal of sialic acid residues with neuraminidase. The heat stability, solubility properties and high carbohydrate content of fraction G classified it as a seromucoid fraction. 3. Fraction G contained several glycoprotein and hexuronic acid-containing fractions, including a hitherto undetected brown-pigmented high-molecular-weight serum component, which migrated in starch gel between the origin and Sα₂-globulin and contained 3·1 and 4·1% of sialic acid and hexuronic acid respectively. 4. Glycosaminoglycan–protein interactions are discussed in relation to protein fractionation. By prior removal of less acidic proteins by these interactions, a new technique is available for isolating serum seromucoids in higher yields and under milder conditions than existing methods.     

Proton magnetic resonance studies of ultraviolet-irradiated apurinic acid

In apurinic acid, a single-stranded polydeoxyribonucleotide easily obtained upon depurination of DNA, the proton resonances arising from thymine and cytosine are readily observable in aqueous solution of 25°C. Two methyl thymine resonances, centered at 1.88 ppm and separated by 0.045 ppm, are observed. We attribute the downfield methyl resonance to thymines with no pyrimidine nearest neighbors and the upfield methyl resonance to thymines having pyrimidine neighbors in the 3′ and/or 5′ positions. Upon ultraviolet irradiation, the upfield methyl and thymine H-6 resonances decrease in amplitude and two methyl resoances appear at 1.63 and 1.52 ppm, corresponding, respectively, to cytosine-thymine and thymine-thymine cyclobutane dimers. Photoreversal eliminates these two minor methyl resonances from the pmr spectrum. We conclude that apurinic acid provides a suitable model system for pmr studies of chemically modified pyrimidine bases in DNA.     

Purification of rabbit kidney cytokinase and a comparison of its properties with human urokinase

1. The cytokinase (tissue activator of plasminogen) content of several mammalian tissues was evaluated by a quantitative casein hydrolysis method. 2. An alkaline (pH10·5) extraction of cytokinase from rabbit kidney lysosome–microsome fraction, followed by chromatography on DEAE-cellulose at pH7·6 with stepwise or linear increase in concentration of phosphate buffer, gave an 86-fold purification of the enzyme. The purified material was non-proteolytic against casein and heated fibrin and was freeze-dried without significant loss of activity or solubility. 3. Cytokinase is a protein with E^0·1%_1cm.=0·87 at 280mμ, and does not possess sufficient hexose or sialic acid to be classified as a glycoprotein. It has S_20,w 2·9–3·1s and molecular weight 50000 when measured on a calibrated Sephadex G-100 column. It has an isoelectric point between pH8 and pH9, and is maximally active and stable at pH8·5. It is inactivated by heat at 78°. 4. Cytokinase and human urokinase have the same K_m value and are inhibited in a partially competitive manner by -aminohexanoic acid and aminomethylcyclohexanecarboxylic acid. They are also inhibited by cysteine and arginine, but are unaffected by iodoacetamide and p-chloromercuribenzoate. 5. On the basis of this and other evidence it is suggested that rabbit kidney cytokinase and human urokinase are similar, if not identical, enzymes.     

Use of diphenylamine as a colorimetric reagent for ribonucleic acid

RNA has been demonstrated to react with diphenylamine when acid hydrolysis is performed for 1 hour or more at 100°C. This reaction can be used for quantitative analysis of RNA, since there is a linear relationship between RNA concentration and absorbance. The reaction of RNA with diphenylamine can be quanlitatively distinguished from the reaction of DNA: the absorption spectrum of the RNA-diphenylamine reaction product has a maximum at 650 mμ, and a second, smaller peak at 490 mμ, while the DNA-diphenylamine reaction product has a single maximum at 605 mμ. It was found that, when mixtures of DNA and RNA are reacted with diphenylamine, the spectra reflect both the DNA:RNA ratios and the total amounts of nucleic acids. When the two-wavelength method of spectrum analysis was applied to such spectra, good agreement was found between actual and calculated values of nucleic acid concentrations. In this way, diphenylamine can be used for the simultaneous determination of the concentrations of DNA and RNA in mixtures. As is the case for the reaction of DNA with diphenylamine, it was found that the reaction of RNA is not altered by the presence of protein and that it involves primarily the purine nucleotides. The reaction of RNA with diphenylamine is discussed in relation to its possible analytical applications.     

Selective Glutaraldehyde-Mediated Coupling of Proteins to the 3′-Adenine Terminus of Polymerase Chain Reaction Products

Attachment of proteins to the 3′ end of DNA increases stability of the DNA in serum and retards clearance of DNA by major organs, thereby enhancing in vivo half-life and therapeutic potential of DNA. Unfortunately, the length of DNA molecules that can be produced with 3 ′ modifications by solid-phase synthesis for protein attachment is limited to 45–60 nucleotides due to uncertainties about sequence fidelity for longer oligonucleotides. Here we describe selective covalent coupling of proteins or other molecules to the 3′-adenine overhang of unlabeled and fluorophore-labeled double-stranded polymerase chain reaction products putatively at the N⁶ position of adenine using 2.5% glutaraldehyde at pH 6.0 and 4°C for at least 16 h. Gel mobility shift analyses and fluorescence analyses of the shifted bands supported conjugate formation between double-stranded polymerase chain reaction products and β2-microglobulin. In addition, blunt-ended DNA ladder fragments treated with glutaraldehyde at 4°C showed no evidence of DNA–DNA or DNA–protein conjugate formation. With the present cold glutaraldehyde technique, longer DNA–3′-protein conjugates might be easily mass-produced. The protein portion of a DNA–3′-protein conjugate could possess functionality as well, such as receptor binding for cell entry, cytotoxicity, or opsonization.     

Impact of Inoculum Preparation and Storage Conditions on the Response of Escherichia coli O157:H7 Populations to Undercooking and Simulated Exposure to Gastric Fluid

This study evaluated the impact of inoculum preparation and storage conditions on the response of Escherichia coli O157:H7 exposed to consumer-induced stresses simulating undercooking and digestion. Lean beef tissue samples were inoculated with E. coli O157:H7 cultures prepared in tryptic soy broth or meat decontamination runoff fluids (WASH) or detached from moist biofilms or dried biofilms formed on stainless steel coupons immersed in inoculated WASH. After inoculation, the samples were left untreated or dipped for 30 s each in hot (75°C) water followed by lactic acid (2%, 55°C), vacuum packaged, stored at 4 (28 days) or 12°C (16 days), and periodically transferred to aerobic storage (7°C for 5 days). During storage, samples were exposed to sequential heat (55°C; 20 min) and simulated gastric fluid (adjusted to pH 1.0 with HCl; 90 min) stresses simulating consumption of undercooked beef. Under the conditions of this study, cells originating from inocula of planktonic cells were, in general, more resistant to heat and acid than cells from cultures grown as biofilms and detached prior to meat inoculation. Heat and acid tolerance of cells on meat stored at 4°C was lower than that of cells on nondecontaminated meat stored at 12°C, where growth occurred during storage. Decontamination of fresh beef resulted in injury that inhibited subsequent growth of surviving cells at 12°C, as well as in decreases in resistance to subsequent heat and acid stresses. The shift of pathogen cells on beef stored under vacuum at 4°C to aerobic storage did not affect cell populations or subsequent survival after sequential exposure to heat and simulated gastric fluid. However, the transfer of meat stored under vacuum at 12°C to aerobic storage resulted in reduction in pathogen counts during aerobic storage and sensitization of survivors to the effects of sequential heat and acid exposure.     

Partial characterization of the sialic acid-free forms of α1-acid glycoprotein from human plasma

Some of the properties of sialic acid-free α₁-acid glycoprotein prepared by mild acid hydrolysis (pH1·6 at 80° for 1hr.) were compared with those of neuraminidasetreated α₁-acid glycoprotein. Chemically, the former contained less fucose (15%) and amide (2%) residues. Physicochemically, it had undergone certain changes primarily pertaining to the secondary structure, so that the specific optical rotation was more negative than that of the latter. A further expression of this change is probably the difference in the pH range of the resolution into two bands on electrophoresis. The resolution of the glycoprotein prepared by mild acid hydrolysis seems to be extended to more acidic pH values both by starch-gel and free moving-boundary electrophoresis. On ultracentrifugation both preparations appeared homogeneous and sedimented with a rate of 3s. Removal of sialyl residues at different pH values, in the range 1–7, showed that 2moles of sialic acid/mole of protein are very strongly bound. The two variants of α₁-acid glycoprotein were isolated from pooled sialic acid-free α₁-acid glycoprotein by preparative starch-gel electrophoresis and from selected blood of normal adults by fractionation by solubility and chromatography. Ultracentrifugal and starch-gel electrophoretic analyses at pH5, with incubation times of 1 or 24hr., demonstrated that no dissociation–association equilibrium (constant sedimentation coefficient and molecular weight) or isomerization (constant apparent electrophoretic mobilities) exist between the two variants. Therefore these variants are not sub-units of native α₁-acid glycoprotein but represent modifications of naturally occurring proteins. Further, it was shown that the difference in the electrophoretic mobilities between the two variants was not due to any difference in amide content. Immunochemically, the two variants share the same determinants.     

Thiol groups in deoxyribonucleic acid nucleotidyltransferase

1. The inhibitory effects of iodoacetate, iodoacetamide, p-hydroxymercuribenzoate and sarkomycin were studied in a partially purified preparation of deoxyribonucleic acid nucleotidyltransferase from Landschutz ascites-tumour cells. All of these agents inhibited the activity of the enzyme, and it was shown that the inhibition exerted by the last three compounds obeyed non-competitive kinetics. 2. Inclusion of glutathione or 2-mercaptoethanol in the enzyme assays did not prevent the inhibition by iodoacetate or iodoacetamide, but did prevent inhibition by p-hydroxymercuribenzoate. Inhibition by sarkomycin could be partially prevented by glutathione or 2-mercaptoethanol. 3. The enzyme fraction also catalysed incorporation in the presence of only one triphosphate (thymidine 5′-triphosphate), and the limited incorporation observed in these circumstances was more resistant to the inhibitory action of iodoacetamide and p-hydroxy-mercuribenzoate than was the standard nucleotidyltransferase reaction (four triphosphates present). Levels of inhibition imposed on the standard reaction were achieved in the limited incorporation reaction with 2·5-fold higher concentrations of the two inhibitors. 4. The addition of certain bivalent cations to the standard system resulted in severe inhibition of the reaction: Zn²⁺ ions (10μm) gave 50% inhibition; ethylenediaminetetra-acetate (0·4mm) in the reaction mixture gave essentially complete protection against this inhibitory effect of Zn²⁺ ions. 5. Deoxyribonucleic acid-nucleotidyltransferase fractions prepared in the presence of a thiol and ethylenediaminetetra-acetate could be stored without loss of activity for 2 months at 0° or for 1 year at −70°.     

Electrophoretic properties of ovomucoid

1. The nature of the electrophoretic heterogeneity of ovomucoid was investigated. Optimum resolution of the fractions on starch-gel electrophoresis occurred over a narrow range of pH and ionic strength. The pattern was not altered in the presence of 8m-urea but the bands were sharper. Ovomucoid–trypsin complex is stable at pH4·6 but dissociated in 6m-urea. 2. The two major fractions of ovomucoid were eluted from the gels. One of these was virtually free of sialic acid and the other, which contained 0·4mole of sialic acid/mole of protein, split into two components on electrophoresis after neuraminidase treatment. It was concluded that these two components, and likewise the two major fractions of ovomucoid, differ by a unit charge/mol. Differences in sialic acid content account for only part of the electrophoretic heterogeneity of ovomucoid.     

Thermal stability of ribosomal ribonucleic acid from baby hamster kidney cells

1. RNA has been prepared from baby hamster kidney cells by extraction with a phenol–EDTA mixture and further purified by passing through a column of Sephadex G-25 that had been equilibrated with water. 2. Aging of the total RNA extracts at 4° or heating at 95° followed by rapid cooling caused a conversion of 28s RNA into material sedimenting in sucrose gradients at approx. 18s. 3. When heated RNA was re-extracted with phenol the sedimentation profile was not returned to that of the unheated RNA. 4. The 28s and 18s RNA fractions were collected separately from sucrose gradients by precipitation with 2vol. of ethanol and passed through a Sephadex G-25 column equilibrated with water. 5. Heat treatment of purified 28s RNA at 95° caused the sedimentation coefficient to increase to approx. 40s, whereas similar treatment of 18s RNA caused no significant increase. If the RNA was heated before the Sephadex G-25 treatment the sedimentation coefficient of the 28s and 18s RNA decreased to approx. 12s and 8s. 6. Heating mixtures of purified 28s and 18s RNA at 95° caused some aggregation of 18s material with the 28s fraction.     

THE SULFONIUM SALT OF MUSTARD GAS: BIS-β-[BIS(β-HYDROXYETHYL) SULFONIUM] ETHYLSULFIDE DICHLORIDE (H·2TDG)

1. The sulfonium salt H·2TDG is formed when H is mixed with even dilute solutions of TDG. Crystalline H·2TDG was isolated from such a reaction mixture. A simple method of preparation of this salt is outlined. 2. A material which differs from H·2TDG in that it hydrolyzes faster, is formed when H hydrolyzes in water. This material is probably H·1TDG but it was not isolated. Approximately 5 to 8 per cent of the original H is converted to this sulfonium salt. 3. The hydrolysis constant of M/100 H·2TDG has been determined at 20°, 25.5°, 37°, 75°, and 100°C., a temperature coefficient, Q ₁₀, of 3–4 was obtained. The effect of temperature is in agreement with that predicted by the Arrhenius equation. An activation energy of 26,000 calories was calculated.     

Growth Temperature-Induced Alterations in the Thermotropic Properties of Nerium oleander Membrane Lipids

The temperature boundary for phase separation of membrane lipids extracted from Nerium oleander leaves was determined by analysis of spin label motion using electron spin resonance spectroscopy and by analysis of polarization of fluorescence from the probe, trans-parinaric acid. A discontinuity of the temperature coefficient for spin label motion, and for trans-parinaric acid fluorescence was detected at 7°C and −3°C with membrane lipids from plants grown at 45°C/32°C (day/night) and 20°C/15°C, respectively. This change was associated with a sharp increase in the polarization of fluorescence from trans-parinaric acid indicating that significant domains of solid lipid form below 7°C or −3°C in these preparations but not above these temperatures. In addition, spin label motion indicated that the lipids of plants grown at low temperatures are more fluid than those of plants grown at higher temperatures.

A change in the molecular ordering of lipids was also detected by analysis of the separation of the hyperfine extrema of electron spin resonance spectra. This occurred at 2°C and 33°C with lipids from the high and low temperature grown plants, respectively. According to previous interpretation of spin label data the change at 29°C (or 33°C) would have indicated the temperature for the initiation of the phase separation process, and the change at 7°C (or −3°C) its completion. Because of the present results, however, this interpretation needs to be modified.

Differences in the physical properties of membrane lipids of plants grown at the hot or cool temperatures correlate with differences in the physiological characteristics of plants and with changes in the fatty acid composition of the corresponding membrane lipids. Environmentally induced modification of membrane lipids could thus account, in part, for the apparently beneficial adjustments of physiological properties of this plant when grown in these regimes.

     

Formation of 2'-deoxyoxanosine from 2'-deoxyguanosine and nitrous acid: mechanism and intermediates

The reaction mechanism for the formation of 2′-deoxyoxanosine from 2′-deoxyguanosine by nitrous acid was explored using methyl derivatives of guanosine and an isolated intermediate of the reaction. When 1-methylguanosine was incubated with NaNO₂ under acidic conditions, N⁵-methyloxanosine and 1-methylxanthosine were generated, whereas the same treatment of N²,N²-dimethylguanosine generated no product. In a similar experiment without NO₂^–, participation of a Dimroth rearrangement was ruled out. In the guanosine–HNO₂ reaction system, an intermediate with a half-life of 5.6 min (pH 7.0, 20°C) was isolated and tentatively identified as a diazoate derivative of guanosine. The diazoate intermediate was converted into oxanosine and xanthosine at a molar ratio (oxanosine:xanthosine) of 0.26 at pH 7.0 and 20°C. The ratio was not affected by the incubation pH between 2 and 10, but increased linearly with temperature from 0.22 (0°C) to 0.32 (50°C). The addition of acetone also increased the ratio up to 0.85 (98% acetone). Based on these results, a con-ceivable pathway for the formation of 2′-deoxyoxanosine from 2′-deoxyguanosine by HNO₂ is proposed.     

Fluorescence Properties Indicate that Photosystem II Reaction Centers and Light-Harvesting Complex Are Modified by Low Temperature Growth in Winter Rye

Thylakoids isolated from winter rye (Secale cereale L. cv Puma) grown at 20°C (nonhardened rye, RNH) or 5°C (cold-hardened rye, RH) were characterized using chlorophyll (Chl) fluorescence. Low temperature fluorescence emission spectra of RH thylakoids contained emission bands at 680 and 695 nanometers not present in RNH thylakoids which were interpreted as changes in the association of light-harvesting Chl a/b proteins and photosystem II (PSII) reaction centers. RH thylakoids also exhibited a decrease in the emission ratio of 742/685 nanometers relative to RNH thylakoids.

Room temperature fluorescence induction revealed that a larger proportion of Chl in RH thylakoids was inactive in transferring energy to PSII reaction centers when compared with RNH thylakoids. Fluorescence induction kinetics at 20°C indicated that RNH and RH thylakoids contained the same proportions of fast (α) and slow (β) components of the biphasic induction curve. In RH thylakoids, however, the rate constant for α components increased and the rate constant for β components decreased relative to RNH thylakoids. Thus, energy was transferred more quickly within a PSII reaction center complex in RH thylakoids. In addition, PSII reaction centers in RH thylakoids were less connected, thus reducing energy transfers between reaction center complexes. We concluded that both PSII reaction centers and light-harvesting Chl a/b proteins had been modified during development of rye chloroplasts at 5°C.