Development of a sensitive and rapid nucleic acid assay with tetraphenyl porphyrinatoiron chloride by a resonance light scattering technique.

Based on the interaction between nucleic acids and tetraphenyl porphyrinatoiron chloride (FeTPPCl), a novel method for the determination of nucleic acids at the nanogram level has been developed. Under the optimum conditions, the weak resonance light scattering (RLS) intensity of FeTPPCl was greatly enhanced by nucleic acids and the enhanced RLS intensity was proportional to the concentration of nucleic acids in the range 0.02-2.8 microg/mL for calf thymus DNA, 0.05-3.3 microg/mL for fish sperm DNA and 0.07-4.5 microg/mL for yeast RNA. The detection limits (3sigma) were 2.9 ng/mL for calf thymus DNA, 3.9 ng/mL for fish sperm DNA and 5.2 ng/mL for yeast RNA. Almost no interference could be observed from proteins, nucleosides and most of the metal ions. The proposed method showed good reliability, sensitivity, rapidity and reproducibility when applied to the determination of nucleic acids in synthetic and biochemical samples. The time savings make this method suitable for large routine analyses.     

Differential thermographic features of some crystalline biopolymers

Crystalline proteins, nucleic acids, nucleotides, and nucleosides have been examined by differential thermal analysis. Characteristic thermograms are illustrated for globular, serum, and blood plasma proteins, calf thymus DNA, sodium triticonucleate, sodium thymonucleate, sperm DNA, yeast RNA, adenosine-3′-phosphate, adenosine-5′-phosphate, disodium adenosine triphosphate, adenosine, and deoxyadenosine. A pronounced effect of moisture on the differential thermal properties of DNA has been observed. It is suggested that solid-state denaturation is one of the prominent thermal effects recorded by the differential thermal analysis of proteins and nucleic acids.     

Levels of acid-soluble polyphosphate in growing cultures of Saccharomyces cerevisiae.

Short-chain acid-soluble polyphosphates were extracted from growing cultures of Saccharomyces cerevisiae, and the changes in the levels of these compounds were determined. The production of acid-soluble polyphosphates correlated with the mitochondrial activities since it occurred in two bursts in respiration-competent yeast cells and in only one burst in respiration-deficient yeast cells. The possible role of these compounds is discussed.     

Effect of castration on purine biosynthesis in the rat liver and kidney

With the present study, the effects of testosterone deficiency on the biosynthesis of purine nucleotides and nucleic acids in rat liver and kidney has been investigated. 20% homogenates were prepared in 1 N HCl04, centrifuged and the nucleic acid were extracted from the precipitate with 0.7 N PCA (15 min at 90 degrees C): the acid-soluble purines were precipitated with 1 M AgNO3 from the supernatant of the centrifuged homogenate, then extracted with 1 M HC1. An increase of the specific activity of the liver (A, +49%; G, +47%) and of the kidney (A, +54%; G, +34%) has been observed (P less than 0.05), while no variation of the specific activity of nucleic acids was evident after castration.     

Nucleic acid of flacherie viruses of the silkworm, Bombyx mori

It was reported previously that two spherical flacherie viruses of silkworm, FVS I and FVS II, had been isolated from flacherie silkworm larvae and the nucleic acid of FVS II was RNA as suggested by the experiments of incorporation of [³H]-uracil. In this paper, it has been confirmed by biochemical methods that the nucleic acid of FVS I and FVS II is RNA. FVS I and FVS II were labeled with ³²P in flacherie silkworms, and the viruses were analyzed by sucrose density gradient centrifugation. When the ³²P-labeled compound in the viruses was treated with 0.5 n KOH, the acid-insoluble ³²P-labeled compound changed to acid-soluble compounds. It was determined by paper chromatography and ion-exchange column chromatography that the alkali-decomposed compounds included four ribonucleotides. Therefore, the viral nucleic acid of FVS I and FVS II was determined to be RNA. The correlations between FVS I and FVS II particles were discussed, and it was suggested that FVS I and FVS II might be closely related or were the same viral species.     

Reaction mechanisms of riboflavin triplet state with nucleic acid bases.

ESR and laser flash photolysis studies have determined a reasonable order of reactivity of nucleotides with triplet riboflavin (3Rb*) for the first time. ESR detection of triplet state reactivity of Rb with nucleoside, polynucleotide and DNA has been obtained simultaneously. In addition, ESR spin elimination measurement of the reactivity of 3Rb* with nucleotides in good accord with laser flash photolysis determination of the corresponding rate constants offers a simple and reliable method to detect the reactivities of nucleic acids and its components with photoexcited flavins. Kinetic, ESR and thermodynamic studies have demonstrated that Rb should be a strong endogenous photosensitizer capable of oxidizing all nucleic acid bases, and preferentially two purine nucleotides with high rate constants.     

Determination and characterization of long-chain fatty acyl-CoA thioesters from yeast and mammalian liver

The long-chain fatty acyl-CoA content of various biological materials, i.e., baker's yeast and mammalian liver, has been determined under standard and several other metabolic conditions, using optimized methods for cell disruption, separating acid-soluble and acid-insoluble CoA from each other, and assaying. After studying the optimization of the extraction of long-chain acyl-CoA compounds and the purification of the extracts, acyl-CoA fractions from several biological sources have been isolated and characterized on behalf of their fatty acid residues by gas-liquid chromatography of the methyl ester derivatives.     

Mechanism of endosomal TLR inhibition by antimalarial drugs and imidazoquinolines

Endosomal TLRs play an important role in innate immune response as well as in autoimmune processes. In the therapy of systemic lupus erythematosus, antimalarial drugs chloroquine, hydroxychloroquine, and quinacrine have been used for a long time. Their suppression of endosomal TLR activation has been attributed to the inhibition of endosomal acidification, which is a prerequisite for the activation of these receptors. We discovered that chloroquine inhibits only activation of endosomal TLRs by nucleic acids, whereas it augments activation of TLR8 by a small synthetic compound, R848. We detected direct binding of antimalarials to nucleic acids by spectroscopic experiments and determined their cellular colocalization. Further analysis revealed that other nucleic acid-binding compounds, such as propidium iodide, also inhibited activation of endosomal TLRs and colocalized with nucleic acids to endosomes. We found that imidazoquinolines, which are TLR7/8 agonists, inhibit TLR9 and TLR3 even in the absence of TLR7 or TLR8, and their mechanism of inhibition is similar to the antimalarials. In contrast to bafilomycin, none of the tested antimalarials and imidazoquinolines inhibited endosomal proteolysis or increased the endosomal pH, confirming that inhibition of pH acidification is not the underlying cause of inhibition. We conclude that the direct binding of inhibitors to nucleic acids mask their TLR-binding epitope and may explain the efficiency of those compounds in the treatment of autoimmune diseases.     

Products of the reaction of selenite with intracellular sulfhydryl compounds

The usual first step in the intracellular metabolism of exogenous selenite is its chemical reaction with glutathione to form selenodiglutathione (1). We have investigated whether selenite also reacts intracellularly with other SH compounds. HeLa cells were exposed to [75Se]selenite and lysed with SDS. Cellular proteins and nucleic acids were precipitated with trichloroacetic acid, and the acid-soluble fraction was analyzed by ion-exchange thin-layer chromatography (ion-exchange TLC) and autoradiography. In control cells, the major [75Se]-containing species detected can be identified by its mobility as selenodiglutathione. Two other species were detected, which can be identified as selenodimercaptoethylamine and the mixed selenotrisulfide of mercaptoethylamine and glutathione. In contrast, in cells that were depleted of glutathione (by treatment with buthionine sulfoximine), very little, if any, selenodiglutathione was detected. However, new [75Se]-containing species were detected, which can be identified as selenodicysteine and the mixed selenotrisulfide of cysteine and glutathione. The same species were detected when [75Se]selenite was added to the acid-soluble fraction of a cell extract (as opposed to living cells), confirming that these compounds can be formed by nonenzymatic reactions.     

The reaction of iodobenzene-p-sulphonyl chloride (pipsyl chloride) with certain amino acids and peptides, and with insulin

1. A system of separation using buffered Celite columns is described that enables the pipsyl derivatives of most of the common amino acids to be separated. 2. The reaction of pipsyl chloride with several amino acids not included in previous studies has been investigated. In particular, knowledge of the acid-soluble pipsyl derivatives of arginine, histidine, lysine, tyrosine and cysteic acid has been extended. 3. Reproducible factors have been obtained that enable corrections to be applied for the breakdown of pipsylamino acids on acid hydrolysis. 4. The reaction of pipsyl chloride with peptides has been studied under various conditions. 5. The extent of the reaction between pipsyl chloride and insulin depends on the nature of the solvent–buffer system, and under the best conditions so far found is about 75% complete. 6. In an Appendix, the separation of pipsylamino acids by thin-layer chromatography is described.     

Modulation of the albumin–paraoxon interaction sites by fatty acids: Analysis by the molecular modeling methods

It is known that albumin can break the ester bonds in organophosphorus compounds (OPs). Amino acids responsible for esterase and pseudoesterase activity of albumin towards OPs are still not determined. It is assumed that Sudlow’s site I with residue Tyr150 exhibits the “true” esterase activity; and Sudlow’s site II containing residue Tyr411, a pseudoesterase one. Binding of fatty acids to albumin affects the efficiency of its interaction with xenobiotics; however, the effect of fatty acids on the interaction of albumin with OPs was not studied. The purpose of this work was to study the interaction of OPs with potential sites of albumin enzymatic activity and to examine the effect of fatty acids on the efficiency of such interaction using the molecular modeling methods by the example of paraoxon, a known inhibitor of acetylcholinesterase, and oleic acid. The structures of the protein complexes with paraoxon and oleic acid were determined by the molecular docking procedure; the conformational changes were calculated by the molecular dynamics method. It has been shown that sorption of oleic acid in one of the fatty acid-binding sites leads to the conformational changes in Sudlow’s sites I and II due to a “reversal” of the side chains of Arg410 and Arg257 residues by 90°. It has been found that this change in geometry reduces the affinity of Sudlow’s site I and increases the Sudlow’s site II affinity to paraoxon. The amino acid residue Ser193, which was previously identified as a site of possible albumin esterase activity, is not able to bind paraoxon efficiently. It is assumed that its activity can be affected by the interaction of the oleic acid molecules with other fatty acid-binding sites. It is hypothesized that the lesser toxicity of paraoxon compared to soman may be associated not only with its lower inhibitory activity against cholinesterases, but also with the increased affinity of paraoxon to albumin. It was concluded that albumin may serve as an alternative means of OP detoxification.     

Proteins involved in binding and cellular uptake of nucleic acids

The study of mechanisms of nucleic acid transport across the cell membrane is valuable both for understanding the biological function of extracellular nucleic acids and the practical use of nucleic acids in gene therapy. It has been clearly demonstrated that cell surface proteins are necessary for transport of nucleic acids into cells. A large amount of data has now been accumulated about the proteins that participate in nucleic acid transport. The methods for revealing and identification of these proteins, possible mechanisms of protein-mediated transport of nucleic acids, and cellular functions of these proteins are described.     

Nucleic acid aptamers and enzymes as sensors

The function of nucleic acids has been an endless source of discovery and invention that has drastically enhanced our appreciation of DNA and RNA as multifaceted polymers. It is now widely known that nucleic acids can act as enzymes (deoxyribozymes and ribozymes) and as receptors (aptamers), and that these functional nucleic acids (FNAs) can either be found in nature or isolated from pools of random nucleic acids. The availability of many natural and artificial FNAs has opened a new horizon for the development of 'smart' molecules for a variety of chemical and biological applications. This review provides a snapshot of recent progress in the application of FNAs as novel sensors for biomolecular detection, drug discovery and nanotechnology.     

Fractionation with ethanol of nucleic acids from viroid-infected plants

A combination of high salt and low ethanol concentration allowed the fractionation of nucleic acids extracted from viroid-infected leaves. By adding 0.4-0.5 vol of ethanol to 1 vol of a solution in 2 M LiCl of nucleic acids (containing mainly DNA, 4S, 5S, 7S, and viroid RNAs), 85% of the DNA and 75% of the 4S RNA remained in solution, from where they could be recovered by increasing the ethanol concentration, whereas almost all 5S, 7S, and viroid RNAs precipitated. When this process was repeated three times a 95% elimination of the initial DNA and 4S RNA was achieved. The method can be of special interest in viroid purification considering that DNA and 4S RNA are the most abundant contaminants in the starting solution of nucleic acids. It is suggested that the highly ordered secondary structure of viroid RNA may be responsible for its particular behavior in the ethanol fractionation of nucleic acids.     

Tracer studies of nitrogen assimilation in yeast

By using N(15) as a tracer the assimilation of ammonia by the yeast, Torulopsis utilis, has been studied. It has been shown that: 1. There was no measurable incorporation of N in the protein or polynucleotide purine of carbon-starved yeast. 2. When ammonia is added to nitrogen-starved yeast there is a long lag period before division begins during which the yeast rapidly synthesizes protein, this process being accompanied by a turnover of polynucleotide purine. There was no significant dilution of the N(15)H(4) (+) of the medium by ordinary NH(4) (+). 3. When yeast containing N(15) is allowed to divide and grow in ordinary ammonia, the total amount of N(15) in the yeast remains constant. The dicarboxylic amino acids are most diluted, while arginine and nucleic acid guanine are not diluted at all.     

Stability of the Nucleic Acids of L Cells After Infection with the Meningopneumonitis Agent

The stability of host nucleic acids in L cells infected with Chlamydia psittaci (strain meningopneumonitis) was studied. The L cells were prelabeled with either (32)P-orthophosphate, (3)H-uridine, or (3)H-thymidine. After infection, the redistribution of each label among the different fractions of host and parasite was quantitatively determined and compared. There were no signs of accelerated degradation of host nucleic acid as the consequence of meningopneumonitis infection. Comparison of the specific activities of the meningopneumonitis nucleic acids with that of the acid-soluble fraction of host cell cytoplasm suggested that the major source of precursors for parasite nucleic acid synthesis was the common cytoplasmic pool of the infected host cell.     

The role of electron donors and acceptors in base stacking in DNA and RNA.

The role of donor-acceptor interactions in base pair stacking in DNA and RNA has been minimized because of the perceived low or negative electron affinities of the purines and pyrimidines. The use of the electron capture detector was among the first methods for measuring electron affinities in the gas phase. Recently, the experimental determination of electron affinities has been extended and improved. Now, there are data for similar compounds in the literature which enable us to estimate electron affinities for purines and pyrimidines. These values are significant, and positive, such that donor-acceptor interactions can, and indeed should play a role in the stacking of bases in nucleic acids.     

Some quantitative changes observed in Philosamia ricini pupal haemolymph during metamorphosis

1. The quantitative variations of the concentrations of uric acid, citrate, nucleic acids and total and acid-soluble phosphorus in the pupal haemolymph of Philosamia ricini during metamorphosis have been studied. 2. The mean value for total nitrogen in the haemolymph and total loss in weight of the insects during metamorphosis have also been recorded.