Chromatographic studies of nucleic acids. 4. The nucleic acid of the turnip yellow mosaic virus including a note on the nucleic acid of the tomato bushy stunt virus.
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Nucleic Acids↗
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[Cytochemical study of free-living flagellates of suborder Bodonina. I. Morphology and nucleic acids].
Nucleic acids (DNA and RNA) have been discovered in the kinetoplast of free-living Bodonina: Bodo caudatus, Pleuromonas jaculans, Rhynchomonas nasuta--by means of cytochemical methods. The kinetoplast has variable contents of nucleic acids whose chemoarchitectonics is due to their non-homogeneous distribution within the kinetoplast. The Feulgen reaction in the kinetoplast is more intensive than in the nucleus. Kinetoplast is closely connected with the cytoplasmic RNA metabolism. Many individuals of R. nasuta were found to have two kinetoplasts, no other signs of cell division being observed. P. jaculans has up to 45% of dyskinetoplastic forms.
Animals↗
Are there structural analogies between amino acids and nucleic acids?
Space-filling molecular models have been used to examine structural analogies between amino acids and nucleic acids. The three-dimensional structures of amino acid R groups appear to be stereochemically related to cavities formed by removal of single bases in double helical nucleic acids. The common L amino acids may thus be complementary to their codons.
Adenine↗
Free amino acids and nucleic acid content of cell nuclei isolated by a modification of Behrens' technique.
1. Nuclei were prepared from frozen rat liver by a modification of the technique of Behrens, and were studied with regard to the content of free amino acids and nucleic acid. 2. Under rigorously controlled conditions, preparations of nuclei are obtained by the Behrens' method which form a gel in the presence of 5 or 10 per cent NaCl or of water plus a small amount of dilute alkali; whereas when conditions are less rigorously controlled, nuclei are obtained which form no such gel. The property of forming gels with alkali is probably characteristic of all cell nuclei which have not undergone autolysis. 3. Nuclei prepared by the Behrens' technique contain the enzymes arginase, catalase, and esterase in very appreciable concentrations. 4. The free amino acids of the isolated cell nuclei, as well as of other liver cell fractions, have been investigated using the technique of paper chromatography. 5. The chromatographic patterns of the free amino acids of whole cells, ground cytoplasm, and isolated cell nuclei were very similar or identical. A feature of interest in these chromatograms was the faintness or absence of the spots due to a number of the essential amino acids, as compared to the intensities of the spots due to glycine, alanine, and glutamic acid. Glutathione was present in the isolated nuclei as well as in the whole cells. 6. Chromatograms made from hydrolysates of nuclei showed high concentrations of the essential amino acids and were similar to chromatograms of hydrolysates of typical proteins.
Amino Acids↗
A code relating sequence to structure in nucleic acids.
Nucleic acids are elucidated in configuration space. An algorithm relating sequence to stability in A and B helical secondary structures, is stated to incorporate NMR conformational and optical melting data. This made possible a classification of elementary sequences in terms of configuration forces driving between A and B states, a finding useful in prediction of structural behavior of different sequences of DNA, RNA and their hybrids.
Algorithms↗
Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid.
Nucleic acid hairpins provide a powerful model system for understanding macromolecular folding, with free-energy landscapes that can be readily manipulated by changing the hairpin sequence. The full shapes of energy landscapes for the reversible folding of DNA hairpins under controlled loads exerted by an optical force clamp were obtained by deconvolution from high-resolution, single-molecule trajectories. The locations and heights of the energy barriers for hairpin folding could be tuned by adjusting the number and location of G:C base pairs, and the presence and position of folding intermediates were controlled by introducing single-nucleotide mismatches.
Base Pair Mismatch↗
Preventing disease transmission by deceased tissue donors by testing blood for viral nucleic acid.
Nucleic acid testing (NAT) has reduced the risk of transmitting infectious disease through blood transfusion. Currently NAT for HIV-1 and HCV are FDA licensed and performed by nearly all blood collection facilities, but HBV NAT is performed under an investigational study protocol. Residual risk estimates indicate that NAT could potentially reduce disease transmission through transplanted tissue. However, tissue donor samples obtained post-mortem have the potential to produce an invalid NAT result due to inhibition of amplification reactions by hemolysis and other factors. The studies reported here summarize the development of protocols to allow NAT of deceased donor samples with reduced rates of invalid results. Using these protocols, inventories from two tissue centers were tested with greater than 99% of samples producing a valid test result.
Blood Specimen Collection↗
Breaking action of reductones related to ascorbic acid on nucleic acids.
The action of two types of ascorbate-related reductones on nucleic acids was investigated by comparison with that of ascorbic acid (AsA). Amino reductone (ScA) and thiol reductone (MHC) caused strandscissions in nucleic acids. This was confirmed by the fact that reductones lowered the viscosity of DNA solution and shifted the peaks of DNA and RNA to the low molecular side in centrifugal profile. Cu2+ strengthened their action as in the case of enediol reductones. The braking activity of thiol reductone is relatively wesk compared with those of amino and enediol reductones. The preferential degradation of spurinic acid was caused with amino and thiol reductones, suggesting that pyrimidine clusters in nucleic acids were susceptible to breakage.
4-Hydroxycoumarins↗
Locked nucleic acid: a potent nucleic acid analog in therapeutics and biotechnology.
Locked nucleic acid (LNA) is a class of nucleic acid analogs possessing very high affinity and excellent specificity toward complementary DNA and RNA, and LNA oligonucleotides have been applied as antisense molecules both in vitro and in vivo. In this review, we briefly describe the basic physiochemical properties of LNA and some of the difficulties that may be encountered when applying LNA technology. The central part of the review focuses on the use of LNA molecules in regulation of gene expression, including delivery to cells, stability, unspecific effects, toxicity, pharmacokinetics, and design of LNA oligonucleotides. The last part evaluates LNA as a diagnostic tool in genotyping.
Animals↗
X-ray crystallographic studies of nucleic acids and nucleic acid-drug complexes.
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Intercalating Agents↗
Antibiotics from basidiomycetes. XVII. The effect of marasmic acid on nucleic acid metabolism.
From submerged cultures of Lachnella villosa, Lachnella sp. 541, and Peniophora laeta we isolated marasmic acid (1), a metabolite first described from surface cultures of Marasmius conigenus. The sesquiterpenoid exhibits potent antimicrobial and cytotoxic properties. In cells of the ascitic form of Ehrlich carcinoma RNA and DNA syntheses are preferentially inhibited. Marasmic acid inhibits RNA synthesis in isolated nuclei, but does not interfere with the transport of nucleoside precursors into the cells. RNA polymerase II and capping enzyme (mRNA guanylyltransferase), two enzymes of nucleic acid metabolism, are markedly affected after preincubation with marasmic acid. We assume that marasmic acid acts on nucleic acid syntheses by direct inhibition of some of the enzymes involved. This mode of action would also explain its mutagenic properties. The preparation and testing of two derivatives, 2 and 3, revealed that the alpha,beta-unsaturated aldehyde is essential for the antimicrobial and cytotoxic activity of marasmic acid.
Animals↗
Cytofluorometry of lymphocytes infected with Epstein-Barr virus: effect of phosphonoacetic acid on nucleic acid.
DNA synthesis in Epstein-Barr virus (EBV)-infected lymphocytes was inhibited by phosphonoacetic acid (PAA) as measured by [3H]thymidine incorporation. PAA, at a concentration of 200 microgram/ml, inhibited [3H]thymidine incorporation by human umbilical cord lymphocytes infected with EBV strain P94 but had little effect on DNA synthesis in mitogen-stimulated cells. Transformed cell lines did not develop from infected cord cell cultures treated with 100 microgram of PAA per ml. Cytofluorometric analysis showed marked increases in cellular nucleic acid content (RNA plus DNA) as early as 9 days after infection of cord cells in the absence of PAA and before significant enhancement of [3H]thymidine incorporation became apparent. Moreover, EBV led to increases in cellular nucleic acid even when 200 microgram of PAA per ml was added to cell cultures before infection. The apparent discrepancy between results obtained by [3H]thymidine incorporation and cytofluorometry is explained either by significant inhibition of cellular DNA polymerases by PAA or by a block at the G2 + M phase of the cell cycle. The data suggest that EBV initiates alterations in cellular nucleic acid synthesis or cell division without prior replication of viral DNA by virus-induced DNA polymerases.
Cell Transformation, Viral↗
Watersoluble synthetic nucleic acid analogs--polyethyleneimine derivatives containing nucleic acid bases--conformation and interactionwith nucleic acids.
Water soluble polyethyleneimine derivatives containing nucleic acid bases were found to interact with polynucleotides, DNA, RNA. The conformational change by formation of complex was observed by CD spectra and was discussed with the hypochromicity in UV spectra. The rates of interactions between nucleic acid bases in polymers were slow as shown by UV spectra, but the conformational changes of the polynucleotides were fast as shown by CD spectra. In the case of the uracil derivative (PEI-Hse-Ura), high value of CD spectra [theta] 2.80 = -8.0 x 10(-4) for the complex with DNA might be caused by psi type conformation of DNA.
Circular Dichroism↗
Affinity chromatography of nucleosides and nucleic acid base derivatives with nucleic acid bases or nitrobenzeneboronic acid substituted silicas.
Nucleic acid bases such as adenine and uracil, and nitrobenzeneboronic acid substituted silicas were prepared by the reaction of chloromethylbenzene substituted silica with adenine sodium salt and trimethylsilylated uracil, and nitration of benzeneboronic acid substituted silica, respectively. From the results of HPLC of nucleosides and N-ethyl derivatives of nucleic acid bases using modified silicas, hydrophobic base stacking interaction, selective hydrogen bonding interaction between purine and pyrimidine bases, and reversible cyclic boronate ester formation between diols of nucleosides with boronic acid were effective for the separation of nucleic acid related compounds. Moreover, association constants for hydrogen bonding formation of nucleic acid bases were estimated.
Boronic Acids↗
Incorporation of glycine-2-C14 into purines of pentose nucleic acid and desoxyribose nucleic acid.
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Fabaceae↗
Prions and nucleic acids: search for "residual" nucleic acids and screening for mutations in the PrP-gene.
Studies on prions involve nucleic acid chemistry under two headings: i) do infectious prion particles contain nucleic acids? ii) is it possible by a simple procedure to screen the prion protein (PrP)-gene for mutations? The return refocusing gel electrophoresis technique was developed to detect by sensitive silver staining homogeneous and heterogeneous nucleic acids extracted from highly purified scrapie prion preparations. With this method all kinds of nucleic acids from a length of 13 nucleotides up to several thousand could be recovered and detected with a yield over 90%. Despite extensive nuclease digestion some small polynucleotides remained. The results define clear restrictions for a hypothetical scrapie-specific nucleic acid. If homogeneous in size, such a molecule would be smaller than 80 nucleotides in length at a particle-to-infectivity ratio near unity; if heterogeneous, scrapie-specific nucleic acids would have to include molecules smaller than 240 nucleotides. To detect mutations in the PrP-gene, either known mutations from human prion diseases or artificial ones in transgenic animals, or to screen for not yet identified mutations in patients, a method is required which guarantees detection of mutations which might occur in every single position of the whole PrP-ORF. It will be shown that a combination of PCR and temperature-gradient gel electrophoresis fulfils these requirements. By thermodynamic calculations the shift in the gel electrophoresis due to a mutation can be calculated depending on the position of the mutation. The theoretical results were tested with the mutations known so far.
Animals↗
Uric acid, a nucleic acid degradation product, down-regulates dsRNA-triggered arthritis.
Uric acid, the naturally occurring degradation product of purine metabolism, is a danger signal, driving maturation of dendritic cells. It is well known that uric acid crystals display potent proinflammatory properties--the cause of gout--whereas the biological properties of soluble uric acid are less well documented. We have demonstrated previously that nucleic acids of endogenous and exogenous origin display proinflammatory properties. The aim of the present study was to assess the impact of soluble uric acid on in vivo inflammatory responses. Mice were administered with uric acid suspension in saline or saline alone prior to induction of neutrophil-mediated inflammation, delayed-type hypersensitivity, histamin-induced edema (measure of vasodilation capacity), as well as double-stranded (ds)RNA-triggered arthritis. Frequency and severity of arthritis were decreased significantly in mice exposed to dsRNA and simultaneously treated with uric acid as compared with saline-treated controls. Also, granulocyte-mediated inflammatory response and vasodilation capacity were reduced significantly in mice treated with uric acid as compared with their control group. The data suggest that down-regulation of inflammation was mediated by skewing the inflammatory response from the peripheral sites to the peritoneal cavity and down-regulating vasodilatatory capacity and thereby affecting leukocyte migration. In contrast, the T cell-mediated delayed-type hypersensitivity reaction was not affected significantly in mice exposed to uric acid. These findings demonstrate that uric acid displays a potent, distant anti-inflammatory effect in vivo. This property seems to be mediated by down-regulation of neutrophil influx to the site of inflammatory insult.
Animals↗
Determination of three-bond 1H3'-31P couplings in nucleic acids and protein-nucleic acid complexes by quantitative J correlation spectroscopy.
A new sensitive two-dimensional quantitative J correlation experiment is described for measuring 3JH3'-P couplings in nucleic acids and protein-nucleic acid complexes. The method is based on measuring the change in intensity of the 1H-1H cross peaks in a constant-time 1H-1H COSY experiment which occurs in the presence and absence of 3JH3'-P dephasing during the constant-time evolution period. For protein-nucleic acid complexes where the protein is 13C-labeled but the nucleic acid is not, 12C-filtering is readily achieved by the application of a series of 13C purge pulses during the constant time evolution period without any loss of signal-to-noise of the nucleic acid cross peaks. The method is demonstrated for the Dickerson DNA dodecamer and a 19 kDa complex of the transcription factor SRY with a 14mer DNA duplex. The same approach should be equally applicable to numerous other problems, including the measurement of JH-Cd couplings in cadmium-ligated proteins, or 3JCH couplings in other selectively enriched compounds.
Base Sequence↗