Disrupting Protein Expression with Peptide Nucleic Acids Reduces Infection by Obligate Intracellular Rickettsia

Peptide Nucleic Acids (PNAs) are single-stranded synthetic nucleic acids with a pseudopeptide backbone in lieu of the phosphodiester linked sugar and phosphate found in traditional oligos. PNA designed complementary to the bacterial Shine-Dalgarno or start codon regions of mRNA disrupts translation resulting in the transient reduction in protein expression. This study examines the use of PNA technology to interrupt protein expression in obligate intracellular Rickettsia sp. Their historically intractable genetic system limits characterization of protein function. We designed PNA targeting mRNA for rOmpB from Rickettsia typhi and rickA from Rickettsia montanensis, ubiquitous factors important for infection. Using an in vitro translation system and competitive binding assays, we determined that our PNAs bind target regions. Electroporation of R. typhi and R. montanensis with PNA specific to rOmpB and rickA, respectively, reduced the bacteria’s ability to infect host cells. These studies open the possibility of using PNA to suppress protein synthesis in obligate intracellular bacteria.     

绿豆子叶衰老期间核酸代谢的变化

萌发绿豆的子叶自然衰老期间,核酸含量降低,RNA降低的幅度比DNA大。电泳分析结果表明,子叶衰老期间细胞核主带DNA明显降低;而迁移慢的卫星带DNA变化不大。在RNA各组分中,18S rRNA从衰老前期就开始降低;25S rRNA和4～5S小分子RNA到衰老后期才缓慢下降。DNase和RNase活性在子叶整个衰老期间都明显升高,是导致核酸含量下降的主要原因。~3H-核苷掺入试验表明,核酸的合成速率在子叶衰老前期有所上升,到衰老后期又降低。poly(A)~ -mRNA含量在子叶开始衰老时明显上升。     

Intracellular Nucleic Acid Delivery by the Supercharged Dengue Virus Capsid Protein

Supercharged proteins are a recently identified class of proteins that have the ability to efficiently deliver functional macromolecules into mammalian cells. They were first developed as bioengineering products, but were later found in the human proteome. In this work, we show that this class of proteins with unusually high net positive charge is frequently found among viral structural proteins, more specifically among capsid proteins. In particular, the capsid proteins of viruses from the Flaviviridae family have all a very high net charge to molecular weight ratio (> +1.07/kDa), thus qualifying as supercharged proteins. This ubiquity raises the hypothesis that supercharged viral capsid proteins may have biological roles that arise from an intrinsic ability to penetrate cells. Dengue virus capsid protein was selected for a detailed experimental analysis. We showed that this protein is able to deliver functional nucleic acids into mammalian cells. The same result was obtained with two isolated domains of this protein, one of them being able to translocate lipid bilayers independently of endocytic routes. Nucleic acids such as siRNA and plasmids were delivered fully functional into cells. The results raise the possibility that the ability to penetrate cells is part of the native biological functions of some viral capsid proteins.     

Effect of Fluoride on Nucleic Acids and Growth in Germinating Corn Seedling Roots

Corn seeds were treated with 0.01 M sodium fluoride for various time periods. The treated seeds were germinated and grown until the seedling roots reached a standard size of 12±3 mm. Analyses were made for RNA and DNA contents of 3-mm seedling root tips. Determinations also were made for growth rate, rate of cell elongation, cell multiplication, and tissue maturity of 12-mm roots. RNA contents of 3-mm root tips were found to be directly proportional to the growth rates of the entire seedling root of corn seeds treated with sodium fluoride for various periods of time. The RNA content was reduced on a cell basis and was independent of the root tip cell number. The amount of DNA was not related to the growth rate of the intact seedling roots. Since fluoride reduced the number of mitotic figures, it was likely that fluoride inhibited DNA synthesis during the interphase of the mitotic cycle. Growth by cell multiplication was inhibited more than that by cell elongation in the sample treated with fluoride for a shorter period. The two types of growth, however, showed a similar level of growth reduction in the sample treated with fluoride for a longer period. Fluoride seemed to reduce the rates of cellular elongation and multiplication not more than about 40 per cent of the control value in these tissues under present experimental conditions. Fluoride also induced maturity in the seedling roots in proportion to the periods of fluoride treatment.     

Labeling During Cleavage of Nucleic Acids for Their Detection on DNA Chips

Abstract

A new and efficient strategy for labeling of nucleic acids prior to their hybridization on high density DNA chip has been developed. Our approach which combines the fragmentation and the labeling is based on the reactivity of the terminal phosphates of cleaved DNA and RNA fragments with a reporter molecule bearing aryldiazomethane group.     

Effect of UV-Irradiation on Total Protein and Nucleic Acids in Alternaria alternata and Fusarium solani

UV-A^* irradiation caused increases in total protein in Fusariumsolani, while its effect on Alternaria alternata was variable,and not as clear-cut as in F. solani. On the other hand, UV-Birradiation stimulated protein production in both fungi. UV-Airradiation showed an inhibitory effect on total DNA in bothfungi, while the effect on RNA was stimulatory in F. solanibut had no effect on A. alternata. Short fluences of UV-B inhibitedDNA production to some extent in both fungi, however longerfluences increased DNA content especially in F. solani. Theeffect of UV-B on RNA production was inhibitory in F. solanibut not in A. alternata. A. alternata is much more resistantto UV-irradiation than is F. solani, and increases in proteinin the former after UV-irradiation suggests that protein mayplay a part in protection against the harmful effect of UV-irradiation. UV-A, UV-B, fluence, protein, nucleic acids, Alternaria alternata, Fusarium solani     

Keto Acids in Pollen and Pollen Tubes of Sesbania aegyptica

Pollen and pollen tubes of Sesbania aegyptica Pers. contain α-ketoglutaric acid, oxaloacetic acid and pyruvic acid. Changes in the keto acids have been correlated with their corresponding amino acids during different phases of germination. It is suggested that keto acids were readily turned over during the elongation of pollen tubes.     

Enzyme and Nucleic Acid Formation During Synchronous Growth of Rhodopseudomonas spheroides

The synthesis of various cell components was examined during the anaerobic photosynthetic growth of synchronous populations of Rhodopseudomonas spheroides. Net deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein increased continuously as did the rate of incorporation of radioactive precursors into protein. The rates of incorporation of radioactive precursors into RNA and DNA were marked by abrupt discontinuities. It is not clear whether these discontinuities represent changes in rates of synthesis or fluctuations in precursor pools. Although the synthesis of bacteriochlorophyll occurred in a continuous manner, those enzymes examined which are involved in the synthesis of tetrapyrroles, i.e., succinyl CoA thiokinase, delta-aminolevulinic acid synthetase, and delta-aminolevulinic acid dehydrase, increased discontinuously. Two other enzymes not involved in tetrapyrrole biosynthesis were examined. Alkaline phosphatase increased in a stepwise manner during the division cycle, whereas the synthesis of ornithine transcarbamylase increased rapidly before leveling off for a period of time until synthesis began again. In each instance of discontinuous enzyme synthesis, increases occurred at regular and characteristic times during the division cycle. Ammonium sulfate precipitation was employed to remove low molecular weight end product inhibitors from enzyme preparations. These studies suggested that the stepwise increases in enzyme activity observed in the present investigation were not affected by periodic end product inhibition. A temporal map of enzyme synthesis during the division cycle was constructed. Both delta-aminolevulinic acid synthetase and delta-aminolevulinic acid dehydrase appeared early in the division cycle, whereas alkaline phosphatase and succinyl CoA thiokinase appeared later on.     

Effect of Feeding Millet (Sorghum vulgarie) Protein on Growth,Nucleic Acids and Proteins of Liver and Plasma of Rats

Effect of feeding millet (Sorghum vulgarie) at 5, 10 and 15 per cent protein levels respectively for a period of six weeks to rats on their liver DNA, RNA and proteins of liver, its subcellular fractions and plasma has been studied, and results compared with rats fed casein at 10 per cent level. Both liver DNA and RNA of rats fed millet at 5 per cent protein level were significantly increased. Liver proteins (mg/l00 g body weight) of rats fed millet at 5 and 10 per cent protein level were significantly increased and plasma proteins decreased. Incorporation of leucine-I-¹⁴C into both liver and plasma proteins of rats fed millet was significantly higher than the control.     

Synthesis and Nucleic Acids Binding Properties of Diastereomeric Aminoethylprolyl Peptide Nucleic Acids (aepPNA)

A general synthetic method for Fmoc-protected monomers of all four diastereomeric aminoethyl peptide nucleic acid (aepPNA) has been developed. The key reaction is the coupling of nucleobase-modified proline derivatives and Fmoc-protected aminoacetaldehyde by reductive alkylation. Oligomerization of the aepPNAs up to 10mer was achieved by Fmoc-solid phase peptide synthesis methodology. Preliminary binding studies of these aepPNA oligomers with nucleic acids suggested that the “cis-” homothymine aepPNA decamers with (2′R,4′R) and (2′S,4′S) configurations can bind, albeit with slow kinetics, to their complementary RNA [poly(adenylic acid)] but not to the complementary DNA [poly(deoxyadenylic acid)]. On the other hand, the trans homothymine aepPNA decamers with (2′R,4′S) and (2′S,4′R) configurations failed to form stable hybrid with poly(adenylic acid) and poly(deoxyadenylic acid). No hybrid formation could be observed between a mixed-base (2′R,4′R)-aepPNA decamer with DNA and RNA in both antiparallel and parallel orientations.     

Nucleic Acid and Protein Synthesis During Thymineless Death in Lysogenic and Nonlysogenic Thymine Auxotrophs

Thymine deprivation causes the non-phage-associated component of thymineless death in Escherichia coli 15T(-). Addition of thymine causes the phage-associated component to occur.     

Experimental and Theoretical Volumes of Nucleic Acids

Abstract

Further evidence of the need to incorporate both experimental and theoretical results in estimates of the volumes of molecules is presented. The volumes of a series of alkyllated purines and pyrimidines, with experimentally known volumes, were estimated by van der Waals and Semi-empirical quantum mechanical methods. In all instances, the van der Waals methods failed to reproduce the experimental volumes. The Semi-empircal methods were able to reproduce the experimental volumes consistentally.     

Circuit Topology of Proteins and Nucleic Acids

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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. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.