Selective staining of nucleic acids by osmium-ammine complex in thin sections from lowicryl-embedded samples

Osmium-ammine (OA)/SO2 selectively contrasted RNA- and DNA-containing structures in thin sections from Lowicryl-embedded samples. No cell structures were stained after Epon embedding. RNAse and DNAse digestion experiments demonstrated that only RNA and DNA were stained in Lowicryl thin sections. Protease digestion did not modify the staining reaction. The very fine end-reaction produced a very high resolution of the stained structures. The staining reaction was not due to the presence of SO2 but to the low pH of the solution (ranging from 1.5-2.2). OA in glycine buffer, pH 1.5, selectively contrasted nucleic acids. Electrostatic bonds between nucleic acids and OA complex were probably involved in the staining reaction. Increasing the pH value of the staining medium resulted in loss of OA specificity for nucleic acids. The high electrolyte concentration of the staining medium hindered the staining reaction.     

Isolation and Analysis of the Nucleic Acids and Polysaccharides from Clostridium welchii

A method previously described for the use of bentonite in the isolation of the nucleic acids from two gram-positive organisms was applied to the isolation of the nucleic acids from two strains of Clostridium welchii. The nucleic acids were separated from polysaccharides by the fractional precipitation of their cetyltrimethyl-ammonium salts from sodium chloride solution, and the base composition of the nucleic acids was determined. One strain of C. welchii investigated (NCTC 10578) was shown to produce considerable quantities of an acidic and also a weakly acidic or neutral polysaccharide; the other strain (ATCC 10543) gave very small quantities of the latter but none of the former polysaccharide. The monosaccharide composition of these polysaccharides was determined and the acidic polysaccharide was shown to resemble dermatan sulfate.     

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.     

A comparison of some procedures of salt extraction of nucleic acids from pollen. Elimination of interfering substances from extracts

Some methods were studied which use hot 10% NaCl solution for the extraction of both RNA and DNA from pollen. The raw salt extracts were precipitated with perchloric acid, trichloroacetic acid or ethanol and purified according to the described methods. The nucleic acid hydrolysates were obtained in several ways. In all the samples spectra in the UV-region were measured and the nucleic acid contents were determined according to the absorbance at 260 nm. In order to ascertain the extent of contaminants, the contents of phosphorus, saccharides and proteins were determined. It was found that by the methods studied it is possible to remove some impurities from extracts, but that the extractions of nucleic acids from pollen are not quite quantitative. A part of nucleic acids remained unextracted after the salt extraction in pollen, but it was possible to obtain it only by an additional extraction with 1 N perchloric acid at 75°C.     

Tissue culture studies; the relationship of nucleic acid increase to the growth of cells in vitro

The content of ribo- and desoxyribonucleic acids in chick heart cultures at regular intervals after implanting has been determined both with standard culture medium and with Tyrode's solution alone. With an inadequate medium, both nucleic acids dropped in a consistent manner but ribonucleic acid was affected to a much greater extent. When the medium was adequate for growth, both fractions rose smoothly and paralleled each other closely, after an initial drop. The final content of each fraction was markedly higher than the amount present in the original implant. The fundamental definition of growth and the relationship of these data to it are discussed.     

Isolation of nucleic acids from microfungi by treatment with thioglycolic acid

A method for the isolation of nucleic acids from various microfungi by sensitization to the lysis with thioglycolic acid is described.Cells, grown with strong aeration, are suddenly suspended in buffered NaCl-ethylenediaminetetraacetate (EDTA) solution pH 8,5, in the presence of thioglycolic acid for 3—5 hours at 50°C.The method proved to give high per cent of broken cells together with good recovery of nucleic acids.     

Study of the chemical makeup of the mycelium from an active strain of Act. rimosus and from an inactive mutant in relaiton to oxytetracycline biosynthesis]

Chemical composition of the mycelium of the active and inactive mutants of Act. rimosus grown under conditions favourable for oxytetracycline biosynthesis on the starch or maltose medium and under favourable conditions on the glucose medium was studied. It was shown that according to its chemical composition the above strains did not practically differ. When grown on the starch medium the mycelium of both strains contained great amounts of carbohydrates and comparatively small amounts of nucleic acids and nitrogen. Replacement of starch in the medium by glucose or maltose induced significant changes in the mycelium composition: the synthesis of intracellular polysaccharides was markedly suppressed and the synthesis of nucleic acids and nitrogen containing compounds increased. RNA was the main nucleic acid in both strains on starch and glucose media. The content of DNA was low and did not practically change. The mycelium of both strains contained small amounts of lipids which did not significantly change during the process of cultivation and did not correlate with the antibiotic activity.     

The differential precipition of nucleic acids and proteins from aqueous solutions by ethanol.

The addition of an appropriate mixture of ethanol, water and sodium perchlorate to crude extracts of some biological material results in the selective precipitation of nucleic acids. Detergent extracts of tissue-cultured plant cells treated with this reagent yielded as much as 95–100% of the nucleic acid while a similar percentage of the total protein remained in solution.     

"Phantom" structure of solvents and packing of dual-chain nucleic acid molecules in liquid crystal dispersion particles

The properties of mesomorphic dispersions of double-stranded nucleic acids were studied. A comparison of these properties indicates that their diversity cannot be explained unambiguously in terms of the conception of Van-der-Waals interactions in particles of mesomorphic dispersions without regard for the specific properties of the solvent, water, in the vicinity of adjacent nucleic acid molecules. It was assumed that, with small distances between the molecules of nucleic acids, a specific "phantom" structure of the solvent appears in their vicinity, which acts as an elastic medium that modifies the interactions between nucleic acid molecules and as a medium in which a collective tunneling of protons can occur. The combination of the two effects determines the "recognition" of nucliec acid molecules and the stabilization of the cholesteric structure of mesomorphic dispersions of nucleic acids.     

Improved protocol for high-quality Co-extraction of DNA and RNA from rumen digesta

We report an improved method for total nucleic acids extraction from rumen content samples. The method employs bead beating, and phenol-chloroform extraction followed by saline-alcohol precipitation. Total nucleic acids and RNA yield and purity were assessed by spectrophotometric measurements; RNA integrity was estimated using Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer. The method provided total nucleic acids and RNA extracts of good quantity and quality. The extraction is not time consuming and it is valuable for ecological studies of rumen microbial community structure and gene expression.     

The mutagenicity of benzimidazole and benzimidazole derivatives. II. Incorporation of benzimidazole into the nucleic acids of Escherichia coli

The mutagenicity of benzimidazole has been attributed to base substitutions. These were believed to be the result of a small incorporation of benzimidazole—instead of a natural base—into nucleic acids. By using a new indirect method of radioactive labelling it has been possible to prove that benzimidazole is incorporated as such. This method involves growing bacteria in a medium containing radioactive phosphate and sufficient benzimidazole to guarantee optimal incorporation. Upon electrophoretic separation of the nucleotides resulting from the hydrolysis of the nucleic acids an additional phosphorus-containing compound was found and subsequently identified by comparison with an enzymatically synthesized benzimidazole mononucleotide.     

Integrated removal of nucleic acids and recovery of LDH from homogenate of beef heart by affinity precipitation

Lactate dehydrogenase (LDH) was purified from beef heart homogenate by affinity precipitation. The protein purification was integrated with nucleic acid removal and was done by precipitation of nucleic acids by addition of poly(ethylene imine) PEI onto which a ligand, Cibacron blue, had been coupled. The yield of LDH after elution from the precipitate was 63%, the purification factor 6.9 and the nucleic acid content was reduced by 98%. The capacity of the affinity polymer Cibacron blue-PEI is dependent on the nucleic acid concentration in the homogenate. The beef heart homogenate had an unfavourable ratio of nucleic acids to LDH. Precipitation with recirculated Cibacron blue-PEI, already complexed with some nucleic acids, improved the yield of the enzyme to 74%. The loss of Cibacron blue-PEI, when recirculated, was less than 1% after each cycle. This revised version was published online in July 2006 with corrections to the Cover Date.     

Rapid preparation of total nucleic acids from E. coli for multi-purpose applications

Separate protocols are commonly used to prepare plasmid DNA, chromosomal DNA, or total RNA from E. coli cells. Various methods for the rapid preparation of plasmid DNA have been developed previously, but the preparation of the chromosomal DNA and total RNA are usually laborious. We report here a simple, fast, reliable, and cost-effective method to extract total nucleic acids from E. coli by direct lysis of the cells with phenol. Five distinct and sharp bands, which correspond to chromosomal DNA, plasmid DNA, 23S rRNA, 16S rRNA, and a mixture of small RNA, were observed when analyzing the prepared total nucleic acids on a regular 1-2% agarose gel. The simple and high-quality preparation of the total nucleic acids in a single tube allowed us to rapidly screen the recombinant plasmid, as well as to simultaneously monitor the change of the plasmid copy number and rRNA levels during the growth of E. coli in the liquid medium.     

NMR studies of dynamics in RNA and DNA by 13C relaxation

RNA and DNA molecules experience motions on a wide range of time scales, ranging from rapid localized motions to much slower collective motions of entire helical domains. The many functions of RNA in biology very often require this molecule to change its conformation in response to biological signals in the form of small molecules, proteins or other nucleic acids, whereas local motions in DNA may facilitate protein recognition and allow enzymes acting on DNA to access functional groups on the bases that would otherwise be buried in Watson-Crick base pairs. Although these statements make a compelling case to study the sequence dependent dynamics in nucleic acids, there are few residue-specific studies of nucleic acid dynamics. Fortunately, NMR studies of dynamics of nucleic acids and nucleic acids-protein complexes are gaining increased attention. The aim of this review is to provide an update of the recent progress in studies of nucleic acid dynamics by NMR based on the application of solution relaxation techniques.     

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

The use of capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing, effectively fueling the genomic revolution. We present an application of this technology for the high-throughput structural analysis of nucleic acids by chemical and enzymatic mapping ('footprinting'). We achieve the throughput and data quality necessary for genomic-scale structural analysis by combining fluorophore labeling of nucleic acids with novel quantitation algorithms. We implemented these algorithms in the CAFA (capillary automated footprinting analysis) open-source software that is downloadable gratis from https://simtk.org/home/cafa. The accuracy, throughput and reproducibility of CAFA analysis are demonstrated using hydroxyl radical footprinting of RNA. The versatility of CAFA is illustrated by dimethyl sulfate mapping of RNA secondary structure and DNase I mapping of a protein binding to a specific sequence of DNA. Our experimental and computational approach facilitates the acquisition of high-throughput chemical probing data for solution structural analysis of nucleic acids.     

Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids

NMR solution structures of nucleic acids are generally less well defined than similar-sized proteins. Most NMR structures of nucleic acids are defined only by short-range interactions, such as intrabase-pair or sequential nuclear Overhauser effects (NOEs), and J-coupling constants, and there are no long-range structural data on the tertiary structure. Residual dipolar couplings represent an extremely valuable source of distance and angle information for macromolecules but they average to zero in isotropic solutions. With the recent advent of general methods for partial alignment of macromolecules in solution, residual dipolar couplings are rapidly becoming indispensable constraints for solution NMR structural studies. These residual dipolar couplings give long-range global structural information and thus complement the strictly local structural data obtained from standard NOE and torsion angle constraints. Such global structural data are especially important in nucleic acids due to the more elongated, less-globular structure of many DNAs and RNAs. Here we review recent progress in application of residual dipolar couplings to structural studies of nucleic acids. We also present results showing how refinement procedures affect the final solution structures of nucleic acids.Copyright 2001 John Wiley & Sons, Inc.     

White and green rust chimneys accumulate RNA in a ferruginous chemical garden

Mechanisms of nucleic acid accumulation were likely critical to life's emergence in the ferruginous oceans of the early Earth. How exactly prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions, is poorly understood. As a possible solution to this concentration problem, we simulated the conditions of prebiotic low-temperature alkaline hydrothermal vents in co-precipitation experiments to investigate the potential of ferruginous chemical gardens to accumulate nucleic acids via sorption. The injection of an alkaline solution into an artificial ferruginous solution under anoxic conditions (O₂ < 0.01% of present atmospheric levels) and at ambient temperatures, caused the precipitation of amakinite (“white rust”), which quickly converted to chloride-containing fougerite (“green rust”). RNA was only extractable from the ferruginous solution in the presence of a phosphate buffer, suggesting RNA in solution was bound to Fe²⁺ ions. During chimney formation, this iron-bound RNA rapidly accumulated in the white and green rust chimney structure from the surrounding ferruginous solution at the fastest rates in the initial white rust phase and correspondingly slower rates in the following green rust phase. This represents a new mechanism for nucleic acid accumulation in the ferruginous oceans of the early Earth, in addition to wet-dry cycles and may have helped to concentrate RNA in a dilute prebiotic ocean.     

The Uptake and Utilization of Bacteria, Amino Acids and Nucleic Acid Components by the Rumen Ciliate Eudiplodinium maggii

Washed suspensions of the rumen ciliate protozoon Eudiplodinium maggii grown in vitro and incubated anaerobically engulfed all the bacteria tested except for Bacteroides ruminicola and Klebsiella aerogenes. There was considerable variation (160–9100 bacteria/h/protozoon at an external concentration of 10¹⁰ bacteria/ml) in the rate at which the bacteria were engulfed, but Eu. maggii showed some preference for bacteria of rumen origin. Some of the bacteria were digested with the release of soluble materials into the medium. Free amino acids were incorporated from an 0.1 mM solution at rates of 0.13 to 0.84 pmol/h/protozoon. Evidence is presented that Eu. maggii could obtain half the amino acids required for growth by the engulfment and digestion of bacteria and half by the uptake of free amino acids. Eudiplodinium maggii incorporated uridine 5' monophosphate and also hydrolysed this to uridine and then to uracil which was reduced to dihydrouracil. These products all appeared in the medium. Ribose was incorporated by the protozoon and appeared as glucose in protozoal and bacterial polysaccharide; none was incorporated as such into protozoal nucleic acid.