Effect Of Nucleic Acids Research Articles

A tRNA-derived fragment of ginseng protects heart against ischemia/reperfusion injury via targeting the lncRNA MIAT/VEGFA pathway

Traditional Chinese medicines (TCMs) have been widely used for treating ischemic heart disease (IHD), and secondary metabolites are generally regarded as their pharmacologically active components. However, the effects of nucleic acids in TCMs remain unclear. We reported for the first time that a 22-mer double-strand RNA consisting of HC83 (a tRNA-derived fragment [tRF] from the 3′ end of tRNAGln(UUG) of ginseng) and its complementary sequence significantly promoted H9c2 cell survival after hypoxia/reoxygenation (H/R) in vitro. HC83_mimic could also significantly improve cardiac function by maintaining both cytoskeleton integrity and mitochondrial function of cardiomyocytes. Further in vivo investigations revealed that HC83_mimic is more potent than metoprolol by >500-fold against myocardial ischemia/reperfusion (MI/R) injury. In-depth studies revealed that HC83 directly downregulated a lncRNA known as myocardial infarction-associated transcript (MIAT) that led to a subsequent upregulation of VEGFA expression. These findings provided the first evidence that TCM-derived tRFs can exert miRNA-like functions in mammalian systems, therefore supporting the idea that TCM-derived tRFs are promising RNA drug candidates shown to have extraordinarily potent effects. In summary, this study provides a novel strategy not only for discovering pharmacologically active tRFs from TCMs but also for efficiently exploring new therapeutic targets for various diseases.

Recent Advances in Nucleic Acid Modulation for Functional Nanozyme

Nanozymes have the potential to replace natural enzymes, so they are widely used in energy conversion technologies such as biosensors and signal transduction (converting biological signals of a target into optical, electrical, or metabolic signals). The participation of nucleic acids leads nanozymes to produce richer interface effects and gives energy conversion events more attractive characteristics, creating what are called “functional nanozymes”. Since different nanozymes have different internal structures and external morphological characteristics, functional modulation needs to be compatible with these properties, and attention needs to be paid to the influence of nucleic acids on nanozyme activity. In this review, “functional nanozymes” are divided into three categories, (nanozyme precursor ion)/ (nucleic acid) self-assembly, nanozyme-nucleic acid irreversible binding, and nanozyme-nucleic acid reversible binding, and the effects of nucleic acids on modulation principles are summarized. Then, the latest developments of nucleic acid-modulated nanozymes are reviewed in terms of their use in energy conversion technology, and their conversion mechanisms are critically discussed. Finally, we outline the advantages and limitations of “functional nanozymes” and discuss the future development prospects and challenges in this field.

Effect of Nucleic Acids on the Quality Indicators of Functional Fish Products

There have been proposed rational technology of combined fish-grain and fish-vegetable masses for functional nutrition. As the objects of research were selected minced raw fish fillet, minced boiled fish fillet and industrial frozen minced fillet from horse mackerel (Trachurus Trachurus L.). The studies have been carried out in accordance with the experimental design, in which the variable factors were the heat treatment time (10–15 minutes) and the temperature of treatment (82–98 ° C). It was found that the organoleptic characteristics of boiled mince from raw fillet of horse mackerel are significantly inferior to the organoleptic characteristics of minced meat from boiled fillet of horse mackerel. When comparing the data for ice cream and freshly prepared minced horse mackerel, it was found that the loss of nucleic acids in industrial minced meat is 4.6–13.1% higher (T = 82 ± 2 and 98 ± 2 ° C), the loss of dry matter is higher by 11, 3–5.8%, mass - by 8.4–14.6%. The content of the total amount of nucleic acids in industrial minced meat is 11.1% lower than in freshly prepared minced meat. Obviously, in the process of preparing products for dietary nutrition, it is preferable to use minced meat from boiled fish fillets.

Study of Physical Properties of Cadmium Oxide (CdO) and CdO/DNA/RNA Nanostructures Thin Layers Produced by Spray Pyrolysis Technique for Manufacturing Cadmium Oxide (CdO) Nanoparticles and Evaluation of the Effect of DNA/RNA Doping on Their Optical Characteristics

In the current research, Cadmium Oxide (CdO) nanoparticles are produced by ultrasonic waves and the effect of nucleic acids (DNA/RNA) doping on their optical and structural characteristics are investigated. X-ray Diffraction (XRD) analysis confirms extension of peaks and formation of Cadmium Oxide (CdO) nanoparticles. Absorption spectra for the produced samples are shown that addition of DNA/RNA affects the spectrum and absorption edge shifts towards blue region which is due to reduction of nanoparticle size and it confirms by SEM images. In addition, SEM images show the formation of approximately single size ellipsoidal nanostructures for pure Cadmium Oxide (CdO). However, the size, form and distribution of nanoparticles are varied after doping. On the other hand, in the current paper, Cadmium Oxide (CdO) and DNA/RNA/Cadmium Oxide (CdO) nanostructures thin layers are produced using spray pyrolysis technique over a glassy substrate. Annealing of CdO thin layer for half an hour in the air leads to improvement of crystalline structure. Optical characteristics and crystalline structure of samples are studied through X-ray Diffraction (XRD) and UV-Visible spectroscopy. The results of the current study were shown that CdO thin layers are of hexagonal structure. Further, optical gaff of CdO/DNA/RNA/glass thin layer is increased compared to CdO/glass layer.

Effect of Nucleic Acids on Oxidation and Photoluminescence of Porous Silicon

Effect of Nucleic Acids on Oxidation and Photoluminescence of Porous Silicon

O006 Role of nucleic acid-binding polymers in TLR activation and autoimmune disease development

Introduction Toll-like receptors (TLRs) play a critical role in innate and adaptive immune responses by responding to pathogenic nucleic acids. Moreover, they have recently been shown to play a role in the pathogenesis of autoimmune disorders such as systemic lupus erythematosus (SLE) due to their ability to recognize self-antigens. There has been growing evidence suggesting that blocking of nucleic acid-sending TLRs such as TLR7 and 9 results in ameliorated disease. Although effective in blocking autoimmune disease progression, TLR inhibitors are not ideal given that they interfere with normal responses to pathogens. Our goal is to create compounds that bind nucleic acids prior to their entry into the cell and engagement of TLRs. Here we determined the role of nucleic acid-binding cationic polymers in neutralizing the proinflammatory effects of nucleic acids on a variety of immune cells implicated in autoimmune disease development. Methods B cells and dendritic cells (DCs) of wild type and lupus prone mice were exposed to TLR7 and 9 synthetic agonists. Supernatants were subsequently assessed for nucleic acid-driven proinflammatory cytokine release, plasma cell differentiation and antibody production. Cells were also assessed for their ability to respond to encapsulated viral particles in the presence of nucleic-acid binding cationic polymers. Results Nucleic acid-binding polymers inhibit TLR activation and subsequent cytokine production by both dendritic cells (DCs) and B cells of wild type and lupus prone mice. They also block nucleic acid-driven plasma cell differentiation and antibody production. Additionally, they modulate co-stimulatory cell surface marker expression (CD80, CD86) in stimulated DCs and B cells. Stimulation of immune cells by encapsulated viral particles is unaffected in the presence of polymers. Conclusion These findings provide a new avenue in drug development as nucleic acid-binding agents can potentially be utilized to block overt autoimmune disorders while allowing normal immune responses to occur.

Nucleic Acids in Protein Samples Interfere with Phosphopeptide Identification by Immobilized-Metal-Ion Affinity Chromatography and Mass Spectrometry

Immobilized-metal-ion affinity chromatography (IMAC) is used extensively for phosphopeptide enrichment in phosphoproteomics. However, the effect of nucleic acids in protein samples on phosphopeptide enrichment by IMAC has not yet been well clarified. In this study, we demonstrate that IMAC beads possess a strong adsorption of nucleic acids, especially single-stranded or single-stranded-region-containing nucleic acids, leading to approximately 50% loss of phosphopeptides during the process of IMAC enrichment. Therefore, nucleic acids must be removed from protein samples prior to IMAC. Acetonitrile (ACN) precipitation, a simple and efficient procedure, was established to remove nucleic acids from the protein samples. We showed that ACN precipitation approximately doubled the phosphopeptide number identified by IMAC and mass spectrometry, indicating that nucleic acid removal significantly improves the identification of phosphopeptides.

Nucleic acid-phospholipid recognition: Fourier transform infrared spectrometric characterization of ternary phospho-lipid-inorganic cation-dna complex and its relevance to chemicopharmaceutical design of nanometric liposome based gene delivery formulations

The present work is a continuation of our previous microscopic, spectroscopic and microcalorimetric measurements of liposomes and poly(ribo)nucleotides and their ternary complexes with inorganic cations as an alternative formulation employing zwitterionic phospholipids instead of cytotoxic cationic lipids. Current report describes Fourier transform infrared spectrometric study as employed to follow structural transitions of newly proposed ternary solid neutral lipid-Mg(2+)-DNA complexes as promising gene delivery formulation. Spectra of the unbound components are compared with those obtained after their complexation as binary and ternary mixtures. Results are described at the levels of carbonyl, phosphate, choline and CH groups and discussed as effects of nucleic acid and phosphatidylcholine moiety on each other in the absence and in the presence of Mg(2+). The infrared spectra of DNA-lipid phases are dominated by the lipid specific absorption bands, with a very little contribution of DNA. Data suggest that upon recognition of DNA with lipids, the DNA undergoes helical transition. Mg(2+) effects are interpreted as dehydrations of phosphates and H-bonding inducing effects on carbonyl groups. The role of residual and surface water on these associations, as well as on chain packing is also discussed followed by possible implications of the ternary complex formation for further gene transfer designs.

A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays

The high affinity of certain cellular polyanions for many proteins (polyanion-binding proteins (PABPs)) has been demonstrated previously. It has been hypothesized that such polyanions may be involved in protein structure stabilization, stimulation of folding through chaperone-like activity, and intra- and extracellular protein transport as well as intracellular organization. The purpose of the proteomics studies reported here was to seek evidence for the idea that the nonspecific but high affinity interactions of PABPs with polyanions have a functional role in intracellular processes. Utilizing yeast protein arrays and five biotinylated cellular polyanion probes (actin, tubulin, heparin, heparan sulfate, and DNA), we identified proteins that interact with these probes and analyzed their structural and amino acid sequence requirements as well as their predicted functions in the yeast proteome. We also provide evidence for the existence of a network-like system for PABPs and their potential roles as critical hubs in intracellular behavior. This investigation takes a first step toward achieving a better understanding of the nature of polyanion-protein interactions within cells and introduces an alternative way of thinking about intracellular organization.

The effect of nucleic acids on growth, ureagenesis and nitrogen excretion of gilthead sea bream Sparus aurata juveniles

The aim of this trial was to evaluate the effect of dietary nucleic acids on ureagenesis and nitrogen balance in gilthead sea bream juveniles. For that purpose, 5 isonitrogenous (7.25% N) diets were formulated based on fish meal as protein source (FM-control diet) and to partially replace the fish meal nitrogen with two levels of nucleic acids (diets RNA1 and RNA2) or brewers yeast (diets BY1 and BY2). Each diet was fed for 10 weeks, to apparent visual satiety, to triplicate groups of 50 fish each with an average body weight of 12.7 g. Inclusion of nucleic acid N either as brewers yeast or RNA led to significant improvement of feed intake and growth, except for fish fed diet RNA2. There were no differences in final weight between groups fed the yeast- and the RNA-containing diets. Although there was an improvement of growth rate of fish fed the RNA or yeast containing diets, dietary nucleic acid supplementation did not have a clear N sparing effect. At the end of the trial there were no significant differences in whole body composition among groups, except for the lipid content which was significantly higher in fish fed the Y2 diet. Hepatic glutamate dehydrogenase activity levels did not differ among groups. Ornithine carbamyl transferase activities were very low in all groups, but appear to be induced by high levels of dietary RNA. Fish fed the yeast diets exhibited the highest arginase activity of all groups. No increase of uricase activities was observed in fish fed the RNA supplemented diets. Ammonia and urea excretion of fish fed the RNA-including diets was higher or significantly higher than in the other groups. Plasma urea levels were higher in fish fed the RNA diets than in the other groups confirming excretion data in that dietary nucleic acid influenced urea excretion through uricolysis. In conclusion, substitution of N supplied by fish meal by that supplied by brewers yeast had a positive effect on growth performance of sea bream, while dietary nucleic acid supplementation did not have a clear N sparing effect. At a dietary level of 11.5% of RNA extract, there was no improvement of fish performance compared to the control, possibly due to an insufficient capacity of fish to degrade high levels of nucleic acid. Data on excretion and plasma metabolites strongly suggest that purinolysis contributes also to ureogenesis in gilthead sea bream.

Effects of nucleic acids and polyanions on dimer formation and DNA binding by bZIP and bHLHZip transcription factors

A large fraction of known transcription factors form 2:1 complexes with DNA. In our studies of the assembly of such ternary (protein–protein–DNA) complexes formed by bZIP and bHLHZip proteins, we found that the proteins recognize DNA as monomers. Here we show that protein monomer–DNA complexes are favored at high DNA concentrations. Further, we show that, due to fast rates of association with protein monomers, DNA and other polyanions accelerate the rate of protein dimer formation. Finally, we find that DNA-assisted formation of protein dimers provides a mechanism by which dimeric transcription factors can rapidly discriminate between specific and nonspecific sites.

Dietary nucleic acids promote a shift in Th1/Th2 balance toward Th1-dominant immunity.

Dietary sources of nucleic acids and their relative components are known to affect host immune function; however, it has not yet been clarified whether such dietary nucleic acids influence the pathogenesis of allergic reaction. The purpose of this study is to elucidate the effect of dietary nucleic acids on Th1/Th2 balance. Both human flora-associated and specific pathogen-free BALB/c mice were maintained on either nucleic acid-free, or -supplemented diets. The effects of nucleic acids on both in vivo antibody levels and in vitro splenocyte cytokine production were compared using these mice. Supplementation of nucleic acids caused a reduction in the serum antibody levels of total IgM, IgG, IgG1, and IgE in the human flora-associated mice without affecting the composition of intestinal flora. In contrast, there was no significant difference of the serum IgG2a levels between nucleic acid-free and -supplemented mice. Such a phenomenon as that, the supplementation of dietary nucleic acids reduces the serum IgE or IgG1 levels, but not the IgG2a level, was also seen in the specific pathogen free mice. Moreover, when the mice were systematically challenged with ovalbumin, the supplementation of nucleic acids also suppressed the serum ovalbumin-specific IgE and IgG1 antibody levels as well as in vitro IL-4 and IL-10 secretion, while enhancing both the serum ovalbumin-specific IgG2a antibody levels and in vitro IFN gamma secretion. These results suggested that dietary nucleic acids may play an important role in promoting a shift in Th1/Th2 balance toward Th1-dominant immunity.

The effects of nucleic acids on the casein kinase II catalyzed phosphorylation of a 34 kDa ribonucleoprotein purified from spinach chloroplasts.

To understand biological significance of a 34kDa ribonucleoprotein (p34) in the chloroplast gene expression, effects of DNAs and RNAs on the phosphorylation of p34 by CK-II were analyzed biochemically. CK-II catalyzed phosphorylation of p34 was stimulated about 12-fold by dsDNA and 4.2-fold by poly (rG), respectively. The analysis of CD spectra revealed that DNA and RNA induced conformational change of p34. These results suggest that the conformational modification of p34 by nucleic acids results in enhancement of the affinity between the protein and CK-II. Based on the experimental results and findings of previous reports, a possible model for post-transcriptional regulation through phosphorylation of p34 by CK-II in chloroplast gene expression is proposed.

Nucleic acids induce the formation of a carcinogen, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in a model system.

Effects of nucleic acids on the formation of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) were studied in a model system. When a mixture of a certain amount of DNA or RNA, creatinine (1 mmol) and phenylalanine (1 mmol) in 10 ml of 50 mM phosphate buffer, pH 7.4, was heated at 60 degrees C for 4 weeks in a screw-capped vial, PhIP was produced, and the yield of PhIP was dependent on the heating time as well as the dose of nucleic acid added to the mixture. However, PhIP was not detectable in the mixtures without the presence of nucleic acids. Both deoxyribonucleotides and ribonucleotides tested induced the formation of PhIP under the presence of phenylalanine and creatinine, although bases of nucleic acids such as adenine and guanine did not induce PhIP formation. Moreover, we confirmed that 2-deoxy-D-ribose as well as D-ribose induced the formation of PhIP in the presence of creatinine and phenylalanine. These results indicate that nucleic acids can induce the formation of PhIP in the presence of creatinine and phenylalanine in the model system. Our data also suggest that pentose in nucleic acids may participate in PhIP forming reactions.

Limited cleavage of eucaryotic elongation factor Tu by trypsin: alignment of the tryptic fragments and effect of nucleic acids on the enzymatic reaction.

Limited cleavage of eucaryotic elongation factor Tu by trypsin: alignment of the tryptic fragments and effect of nucleic acids on the enzymatic reaction.

Studies on saccharases in the roots of sugar beet (Beta vulgaris L.). X. Effect of nucleic acids on the solubility of cell wall-bound saccharase of sugar beet seedlings.

It was found that certain substances which made the bound saccharase insoluble were released together with the enzyme by treating cell wall of sugar beet seedlings with salt. Insolubilization of the enzyme was extremely reduced by pretreatment of the substance with either deoxyribonuclease or hot perchloric acid, but not affected by the substance pretreated with ribonuclease, alkali or Pronase. UV spectrum of the purified substance showed a maximal absorption at 260nm and a minimal at 238nm. The diphenylamine test for deoxyribose and the Fiske-Subbarow test for phosphorus were both positive. These results indicate that the substance causing insolubilization of the enzyme is DNA. Calf thymus DNA and Yeast RNA as well as the purified DNA from sugar beet seedlings were all effective in insolubilization of the enzyme. Association of the enzyme with these nucleic acids depended on the concentration of NaCl. The DNA's from sugar beet seedlings and calf thymus insolebilized the enzyme at NaCl concentrations below 0.16M, while yeast RNA below 0.04M.

Interaction of Aminoacridines with Nucleic Acids

Pulse radiolysis has been used to study the interaction of aminoacridines with nucleic acids. The data confirm that there are two modes of binding. These are: a weak interaction which has a maximum binding ratio of one site per dye; and a strong binding process effected by both electrostatic and Van der Waals interactions. The limit of this latter, strong binding mode is approximately six sites per dye. The radiation-induced transient absorption spectrum of benzoflavine is characterized by a pronounced bleaching at 440 nm, which is quenched by the addition of nucleic acids. Mechanisms have been proposed for the reactions of both eaq-and .OH with benzoflavine which account both for the observed bleaching of benzoflavine solutions and for the protective effect of nucleic acids. It is proposed that eaq-reacts with benzoflavine to form a stable benzoflavine semiquinone radical and that .OH reacts with subsequent formation of a very stable benzoflavine hydroxycyclohexadienyl radical.

Further Studies on the Effect of Nucleic Acids on Shoot and Flower Formation in Citrus Trees

Application of 5-fluorodeoxyuridine together with thymidine during the flower induction period (December-January) increased the percentage of sprouting buds per branch, the number of new laterals per branch and per sprouting bud, and the formation of flowers in February-March The increase in flower formation was mainly due to a large number of mixed laterals (bearing flowers and leaves) which seems to be related to delayed mitotic activity It is suggested that the increase in flower development is related to repression of the synthesis of a flowering inhibitor of a protein nature, which may act either directly or through hormonal balance.

Effect of nucleic acids from immune lymphocytes on rat sarcomata.

Primary rat sarcomata regress, usually temporarily but occasionally completely, after the injection of nucleic acids from lymphocytes of sheep and allogeneic rats which have been immunized with tissues from the tumour to be treated. It is possible that the effect results from the strengthening of an already existing immune reaction and that it is only temporary because it is related to the life span of messenger RNA.

Effect of Nucleic Acid and Its Antimetabolite on Induction of Flowering in Winter Cereals

[in Japanese]