Herring Sperm DNA Research Articles

Microcalorimetric and Spectroscopic Investigation of the Antibacterial Properties of Cationic Ytterbium(III)–Porphyrin Complexes Lacking Charged Peripheral Groups

The antibacterial activities towards Escherichia coli of two cationic Yb(III)-monoporphyrin complexes, [Yb(III)(TMP)(H2O)3]Cl (1) and [Yb(III)(TTP)(H2O)3]Cl (2), were investigated at the cellular and sub-cellular levels. The biological effects of the complexes on the growth of E. coli were evaluated by microcalorimetry and by analysis of the resulting metabolic thermogenic curves, from which IC50 values and metabolic parameters such as growth rate and generation time were derived. At the subcellular level, DNA-binding experiments were performed by means of UV/VIS- and fluorescence-titration experiments, as well as by near-infrared (NIR) emission, which revealed that 1 and 2 strongly bind to herring-sperm DNA (HS-DNA), though by different binding modes.

The Farnesyl-diphosphate/Geranylgeranyl-diphosphate Synthase of Toxoplasma gondii Is a Bifunctional Enzyme and a Molecular Target of Bisphosphonates

Farnesyl-diphosphate synthase (FPPS) catalyzes the synthesis of farnesyl diphosphate, an important precursor of sterols, dolichols, ubiquinones, and prenylated proteins. We report the cloning and characterization of two Toxoplasma gondii farnesyl-diphosphate synthase (TgFPPS) homologs. A single genetic locus produces two transcripts, TgFPPS and TgFPPSi, by alternative splicing. Both isoforms were heterologously expressed in Escherichia coli, but only TgFPPS was active. The protein products predicted from the nucleotide sequences have 646 and 605 amino acids and apparent molecular masses of 69.5 and 64.5 kDa, respectively. Several conserved sequence motifs found in other prenyl-diphosphate synthases are present in both TgFPPSs. TgFPPS was also expressed in the baculovirus system and was biochemically characterized. In contrast to the FPPS of other eukaryotic organisms, TgFPPS is bifunctional, catalyzing the formation of both farnesyl diphosphate and geranylgeranyl diphosphate. TgFPPS localizes to the mitochondria, as determined by the co-localisation of the affinity-purified antibodies against the protein with MitoTracker, and in accord with the presence of an N-terminal mitochondria-targeting signal in the protein. This enzyme is an attractive target for drug development, because the order of inhibition of the enzyme by a number of bisphosphonates is the same as that for inhibition of parasite growth. In summary, we report the first bifunctional farnesyl-diphosphate/geranylgeranyl-diphosphate synthase identified in eukaryotes, which, together with previous results, establishes this enzyme as a valid target for the chemotherapy of toxoplasmosis.

A two-dimensional copper(II) polymer with bridging μ- trans-oxamidate and μ 2-picrate ligands: Synthesis, crystal structure and DNA binding studies

A two-dimensional copper(II) polymer with formula of [Cu 2(dmapox)(pic) 2] n · nCH 3OH, where dmapox is the dianion of N, N′-bis[3-(dimethylamino)propyl]oxamide and pic is picrate, was synthesized and characterized by elemental analysis, conductivity measurement, IR and electronic spectra studies. The crystal structure of the complex has been determined by single-crystal X-ray diffraction. It crystallizes in monoclinic, space group P2 1/ c with crystallographic data: a = 14.076(7) Å, b = 13.896(7) Å, c = 9.278(5) Å, β = 106.909(6)° and Z = 2. The structure consists of uncoordinated methanol molecules and two-dimensional copper(II) polymeric coordination network constructed by the bis-tridentate trans-dmapox and tridentate picrate ligands. The environment around the copper(II) atom can be described as a distorted octahedron and the Cu⋯Cu separations through μ- trans-oxamidate and μ 2-picrate bridges are 5.227 Å and 8.359 Å, respectively. The copper(II) complex presents as a polymer in solid state, whereas in solution it presents as discrete neutral binuclear copper(II) species [Cu 2(dmapox)(pic) 2] due to the weak interactions between the copper(II) atoms and the para-nitro oxygens of the adjacent picrate ligands. The fluorescence titration and the ethidium bromide (EB) fluorescence displacement experiments reveal that the binding mode between the binuclear copper(II) complex [Cu 2(dmapox)(pic) 2] and Herring Sperm DNA might be intercalation.

Molecular and Biochemical Analysis of the Plastidic ADP-glucose Transporter (ZmBT1) from Zea mays

Physiological studies on the Brittle1 maize mutant have provided circumstantial evidence that ZmBT1 (Zea mays Brittle1 protein) is involved in the ADP-Glc transport into maize endosperm plastids, but up to now, no direct ADP-Glc transport mediated by ZmBT1 has ever been shown. The heterologous synthesis of ZmBT1 in Escherichia coli cells leads to the functional integration of ZmBT1 into the bacterial cytoplasmic membrane. ZmBT1 transports ADP-Glc in counterexchange with ADP with apparent affinities of about 850 and 465 mum, respectively. Recently, a complete ferredoxin/thioredoxin system has been identified in cereal amyloplasts and BT1 has been proposed as a potential Trx target protein (Balmer, Y., Vensel, W. H., Cai, N., Manieri, W., Schurmann, P., Hurkman, W. J., and Buchanan, B. B. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 2988-2993). Interestingly, we revealed that the transport activity of ZmBT1 is reversibly regulated by redox reagents such as diamide and dithiothreitol. The expression of ZmBT1 is restricted to endosperm tissues during starch synthesis, whereas a recently identified BT1 maize homologue, the ZmBT1-2, exhibits a ubiquitous expression pattern in hetero- and autotrophic tissues indicating different physiological roles for both maize BT1 isoforms. BT1 homologues are present in both mono- and dicotyledonous plants. Phylogenetic analyses classify the BT1 family into two phylogenetically and biochemically distinct groups. The first group comprises BT1 orthologues restricted to cereals where they mediate the ADP-Glc transport into cereal endosperm storage plastids during starch synthesis. The second group occurs in mono- and dicotyledonous plants and is most probably involved in the export of adenine nucleotides synthesized inside plastids.

Novel ebselen–porphyrin conjugates: Synthesis and nucleic acid interaction study

Novel porphyrins bearing ebselen (2-phenyl-1,2-benzisoselenazol-3[2H]-one) moiety were synthesized and characterized. Their interactions with herring sperm DNA were studied by means of UV–visible, fluorescence, circular dichroism spectroscopy, and gel electrophoresis.

Determination of Nucleic Acids Sensitized by Emulsifier OP‐micelle Using Ethyl Rhodamine B as a Resonance Light‐Scattering Probe

The resonance light scattering (RLS) spectra of ethyl rhodamine B with nucleic acid (calf thymus DNA and herring sperm DNA) have been studied. The effective factors and the optimum conditions have been studied, and the enhanced intensity of RLS is in proportion to the concentration of nucleic acids in the range 0∼5.00 µg mL−1 for calf thymus DNA (ctDNA) and 0∼3.50 µg mL−1 for herring sperm DNA (hsDNA). The limits of detection are 3.42 and 3.14 ng mL−1, respectively. Based on this, a RLS method for the determination of nucleic acids sensitized by emulsifier OP‐micelle was accordingly established. The binding mode concerning the interactions of ethyl rhodamine B with nucleic acids was also studied, and this method has good selectivity and high sensitivity and it has been applied to the determination of DNA in synthetic samples and real samples with satisfactory results.

Histone Deacetylase Inhibitor Trichostatin A Sustains Sodium Pervanadate-induced NF-κB Activation by Delaying IκBα mRNA Resynthesis

Histone Deacetylase Inhibitor Trichostatin A Sustains Sodium Pervanadate-induced NF-κB Activation by Delaying IκBα mRNA Resynthesis

Study on the interaction of trypsin with some DNAs and their analytical application by resonance Rayleigh scattering spectra

When trypsin reacts with Herring sperm DNA (hsDNA), Salmon sperm DNA (sDNA), and Calf thymus DNA (ctDNA) to form a complex, the resonance Rayleigh scattering (RRS) was remarkably enhanced and new RRS spectra appear. These new spectra have similar characteristics of RRS spectra. The maximum RRS peaks are at 307 nm (hsDNA, sDNA) and 290 nm (ctDNA), and other peaks are at 350 nm. The scattering intensity is proportional to the concentration of DNA or trypsin; so this intereaction can be used to determine trypsin using DNA or DNA using trypsin. In the determination of DNA using trypsin, the linear ranges for hsDNA, sDNA, and ctDNA are 0–2.3, 0–2.5, and 0–1.9 μg·mL−1, and the detection limits are 0.4, 0.7, and 1.1 ng·mL−1, respectively. In the determination of trypsin using hsDNA, the linear range is 0–30.0 μg·mL−1, and the detection limit is 39.0 ng·mL−1. In this paper, the intereaction conditions were optimized. The affecting factors, chemical properties of the complex, and the composition ratio of trypsin with DNA were investigated. Using trypsin as RRS probe, a sensitive method for the determination of trace amounts of DNA was developed.

Interaction of DNA with aromatic hydrocarbons fraction in atmospheric particulates of Xigu District of Lanzhou, China

Abstract Voluminously epidemiological studies show that the relationships exist between the air pollution and human health and cancer. Aromatic hydrocarbons (AHs) in air form a large class of organic pollutants, which are widely in environment and many of them are known to be carcinogenic and/or mutagenic and contribute to ambient air pollution. In the past decades, bioassays mainly have been used to evaluate the toxicity of chemical mixtures in atmospheric particulates or aqueous environment. However, it is well known that the covalent complexes formed by carcinogens with DNA may be exert negative results in bioassay. So the main aim of this paper is to develop an evaluation method of toxicity effects of chemical mixtures in atmospheric particulates from chemical standpoint. In this study, the in vitro interaction of the AHs with DNA was investigated by absorption, fluorescence and resonance light scattering (RLS) spectroscopic techniques. The results showed that the AHs in the atmospheric particulates could combine with calf thymus DNA (ctDNA) and herring sperm DNA (hsDNA) without being activated or metabolized by organism, respectively. Intercalation may be present in the mechanism of interaction. The binding constants of the AHs with ctDNA and hsDNA were 2.5×10 2 and 2.0×103, respectively, which indicated that the interaction of the AHs with hsDNA is stronger than that with ctDNA. In addition, the relationships of dose-effect between the total mole concentration of chemical components and the ability of binding ctDNA and hsDNA were confirmed. This research made it possible to study the toxicity effects of chemical mixtures in atmospheric particulates by chemical method. It is believed that the composition and contents of unknown AHs and the interaction of DNA with AHs in atmospheric particulates of Xigu District of Lanzhou City, China are first reported in the past twenty years.

DNA Interaction of Plant Extracts from Colombian Flora

This study presents the results of DNA interaction of 52 methanol and 51 dichloromethane crude plant extracts with herring sperm DNA evaluated in terms of absorbance reduction of the peak, following the HPLC method described by Pezzuto and his colleagues. The 103 plant extracts belong to the Asteraceae, Euphorbiaceae, Melastomataceae, Rubiaceae, and Solanaceae families and were collected in the Regional Natural Park Ucumarí (RNPU; Colombia). The highest percentages of DNA interaction within the six plant families studied were shown by the methanol extracts of Schistocarpha sinforosi. Cuatrec. (68.30%) Aspilla quinquenervis. Blake (50.74%), and Verbesina nudipes. Blake (43.20%), all members of the Asteraceae family, followed by the methanol extract of Deprea glabra. (Standl.) A.T. Hunziker (41.01%), a species of the Solanaceae family. The dichloromethane plant extracts studied displayed, a low percentage of DNA interaction.

Determination of Nucleic Acids Using Fluorescence Probe Sensitized by Microemulsion

Because the fluorescence of azur A can be quenched by adding nucleic acid, a sensitive fluorometric method for determination of nucleic acids at nanogram levels was established. Using optimal conditions, the calibration curves were linear in the range of 0-6.0 microg/mL for calf thymus deoxyribonucleic acid (ct DNA) and 0-7.0 microg/mL for herring sperm DNA (hs DNA). The limits of determination were 3.5 and 3.8 ng/mL, respectively, which shows the high sensitivity of this method. Triton X-100 microemulsion was applied as a sensitive media to enhance the sensitivity. The binding mode concerning the interactions of azur A with nucleic acids was also studied and the association constant with different binding numbers was obtained. The method has been applied to the determination of nucleic acid in both synthetic and real samples, such as cauliflower and pork liver, with satisfactory results.

The Wilms Tumor Suppressor Wt1 Promotes Cell Adhesion through Transcriptional Activation of the α4integrin Gene

The Wilms Tumor Suppressor Wt1 Promotes Cell Adhesion through Transcriptional Activation of the α4integrin Gene

An Oligonucleotide Microarray for High-Throughput Sequencing of the Mitochondrial Genome

Previously we developed an oligonucleotide sequencing microarray (MitoChip) as an array-based sequencing platform for rapid and high-throughput analysis of mitochondrial DNA. The first generation MitoChip, however, was not tiled with probes for the noncoding D-loop region, a site frequently mutated in human cancers. Here we report the development of a second-generation MitoChip (v2.0) with oligonucleotide probes to sequence the entire mitochondrial genome. In addition, the MitoChip v2.0 contains redundant tiling of sequences for 500 of the most common haplotypes including single-nucleotide changes, insertions, and deletions. Sequencing results from 14 primary head and neck tumor tissues demonstrated that the v2.0 MitoChips detected a larger number of variants than the original version. Multiple coding region variants detected only in the second generation MitoChips, but not the earlier chip version, were further confirmed with conventional sequencing. Moreover, 31 variations in noncoding region were identified using MitoChips v2.0. Replicate experiments demonstrated >99.99% reproducibility in the second generation MitoChip. In seven head and neck cancer samples with matched lymphocyte DNA, the MitoChip v2.0 detected at least one cancer-associated mitochondrial mutation in four (57%) samples. These results indicate that the second generation MitoChip is a high-throughput platform for identification of mitochondrial DNA mutations in primary tumors.

Protein Kinase Cζ Is Up-regulated in Osteoarthritic Cartilage and Is Required for Activation of NF-κB by Tumor Necrosis Factor and Interleukin-1 in Articular Chondrocytes

Protein kinase Czeta (PKCzeta) is an intracellular serine/threonine protein kinase that has been implicated in the signaling pathways for certain inflammatory cytokines, including interleukin-1 (IL-1) and tumor necrosis factor alpha (TNF-alpha), in some cell types. A study of gene expression in articular chondrocytes from osteoarthritis (OA) patients revealed that PKCzeta is transcriptionally up-regulated in human OA articular cartilage clinical samples. This finding led to the hypothesis that PKCzeta may be an important signaling component of cytokine-mediated cartilage matrix destruction in articular chondrocytes, believed to be an underlying factor in the pathophysiology of OA. IL-1 treatment of chondrocytes in culture resulted in rapidly increased phosphorylation of PKCzeta, implicating PKCzeta activation in the signaling pathway. Chondrocyte cell-based assays were used to evaluate the contribution of PKCzeta activity in NF-kappaB activation and extracellular matrix degradation mediated by IL-1, TNF, or sphingomyelinase. In primary chondrocytes, IL-1 and TNF-alpha caused an increase in NF-kappaB activity resulting in induction of aggrecanase-1 and aggrecanase-2 expression, with consequent increased proteoglycan degradation. This effect was blocked by the pan-specific PKC inhibitors RO 31-8220 and bisindolylmaleimide I, partially blocked by Gö 6976, and was unaffected by the PKCzeta-sparing inhibitor calphostin C. A cell-permeable PKCzeta pseudosubstrate peptide inhibitor was capable of blocking TNFand IL-1-mediated NF-kappaB activation and proteoglycan degradation in chondrocyte pellet cultures. In addition, overexpression of a dominant negative PKCzeta protein effectively prevented cytokine-mediated NF-kappaB activation in primary chondrocytes. These data implicate PKCzeta as a necessary component of the IL-1 and TNF signaling pathways in chondrocytes that result in catabolic destruction of extracellular matrix proteins in osteoarthritic cartilage.

Pregnane X Receptor Activators Inhibit Human Hepatic Stellate Cell Transdifferentiation In Vitro

The activated pregnane X receptor is antifibrogenic in rodent chronic liver injury in vivo models. The aim of this study was to determine the effects of human pregnane X receptor activators on human hepatic stellate cell transdifferentiation to a profibrogenic phenotype in vitro. Hepatic stellate cells were isolated from resected human liver and cultured under conditions in which they trans-differentiate into profibrogenic myofibroblasts. The pregnane X receptor was expressed in primary cultures at the level of messenger RNA and protein and was activated by the ligand rifampicin as judged by increases in binding of proteins to the pregnane X receptor ER6 DNA response element and by increases in ER6-dependent reporter gene expression. Short-term treatment of hepatic stellate cells with rifampicin inhibited the expression of selected fibrosis-related genes (transforming growth factor beta1, alpha-smooth muscle actin), proliferation-related genes, and WNT signaling-associated genes. There was also an increase in interleukin-6 secretion and an inhibition in DNA synthesis. Long-term treatment with rifampicin over several weeks reduced the proliferation and transdifferentiation of hepatic stellate cells. Small interfering RNA knockdown of the pregnane X receptor in a hepatic stellate cell line reduced the binding of proteins to the ER6 DNA response element and abrogated pregnane X receptor activator-dependent changes in transforming growth factor beta1 expression, interleukin-6 secretion, and proliferation. The pregnane X receptor is transcriptionally functional in human hepatic stellate cells and activators inhibit transdifferentiation and proliferation. The pregnane X receptor may therefore be an effective target for antifibrotic therapy.

NAB2 Represses Transcription by Interacting with the CHD4 Subunit of the Nucleosome Remodeling and Deacetylase (NuRD) Complex

Early growth response (EGR) transactivators act as critical regulators of several physiological processes, including peripheral nerve myelination and progression of prostate cancer. The NAB1 and NAB2 (NGFI-A/EGR1-binding protein) transcriptional corepressors directly interact with three EGR family members (Egr1/NGFI-A/zif268, Egr2/Krox20, and Egr3) and repress activation of their target promoters. To understand the molecular mechanisms underlying NAB repression, we found that EGR activity is modulated by at least two repression domains within NAB2, one of which uniquely requires interaction with the CHD4 (chromodomain helicase DNA-binding protein 4) subunit of the NuRD (nucleosome remodeling and deacetylase) chromatin remodeling complex. Both NAB proteins can bind either CHD3 or CHD4, indicating that the interaction is conserved among these two protein families. Furthermore, we show that repression of the endogenous Rad gene by NAB2 involves interaction with CHD4 and demonstrate colocalization of NAB2 and CHD4 on the Rad promoter in myelinating Schwann cells. Finally, we show that interaction with CHD4 is regulated by alternative splicing of the NAB2 mRNA.

Characterization of DNA degradation using direct current conductivity and dynamic dielectric relaxation techniques

The purpose of this study was to evaluate DNA degradation upon thermal heating using dielectric relaxation and direct current (DC) conductivity methods. Herring sperm DNA, human growth hormone (HgH) plasmid DNA, and secreted alkaline phosphatase (SEAP) plasmid DNA were used as the examples. DNA was heated at 80 degrees C for 1 hour. The dielectric relaxation spectra as a function of the applied field frequency were measured for HgH DNA at 0.5 hours and at 1 hour. The frequency range covered was from 10 kHz to 100 kHz. The DC conductivity measurements were made for all 3 kinds of DNA at 4 time points: 0 hours, 0.5 hours, 0.75 hours, and 1 hour. At each time point the DC conductivity was measured for each sample as a function of concentration via water dilution. The results show that the dielectric relaxation method is less sensitive in characterizing heat-driven DNA degradation. Conversely, DC conductivity is very sensitive. The semiquantitative dependence of the conductivity upon heating suggests that DNA degradation involves more than plasmid DNA nicking. Double strand and single strand breaks may also occur. In addition, herring sperm DNA, HgH DNA, and SEAP DNA, though similar in their DC conductivity functional forms upon dilution, exhibit significant differences in their responses to sustained heating.

Electrochemical and Spectroscopic Studies of the Interaction of Proflavine with DNA

The interaction of proflavine with herring sperm DNA has been investigated by cyclic voltammetry and UV-Vis spectroscopy as well as viscosity measurements. Shifts in the peak potentials in cyclic voltammetry, spectral changes in UV absorption titration, an increase in viscosity of DNA and the results of the effect of ionic strength on the binding constant strongly support the intercalation of proflavine into the DNA double helix. The binding constant for the interaction between proflavine and DNA was K = 2.32 (+/- 0.41) x 10(4) M(-1) and the binding site size was 2.07 (+/- 0.1) base pairs, estimated in voltammetric measurements. The value of the binding site size was determined to be closer to that expected for a planar intercalating agent. The standard Gibbs free-energy change is ca. -24.90 kJ/mol at 25 degrees C, indicating the spontaneity of the binding interaction. The binding constant determined by UV absorption measurements was K = 2.20 (+/- 0.48) x 10(4) M(-1), which is very close to the value determined by cyclic voltammetry assuming that the binding equilibrium is static.

Polyhydroxylated 4-thiaflavans as multipotent antioxidants: Protective effect on oxidative DNA damage in vitro

Hydroxylated 4-thiaflavans, possessing the antioxidant features of catechol containing flavonoids and/or tocopherols, were evaluated as protective agents against oxidation damage induced in herring sperm DNA by cumene hydroperoxide (CumOOH) or by the glutathione/ferric ion (GSH/Fe 3+) system. Our data indicate that the effective protection exerted by some of the tested compounds is overall higher than those provided by catechin and α-tocopherol, which might be attributed both to the scavenging properties and chelation of Fe 2+ ions.

Ribosome-inactivating proteins in edible plants and purification and characterization of a new ribosome-inactivating protein from Cucurbita moschata

The basic protein fraction of tissue extracts from 40 edible plants inhibited cell-free protein synthesis and released adenine from herring sperm DNA, thus having adenine glycosylase activity. This suggested the presence of ribosome-inactivating proteins (RIPs) in the plant extracts. This indication was further strengthened by the presence of the two activities after a partial chromatographic purification of three extracts, including that from Lycopersicon esculentum (tomato), which had very low activity. From the extract of Cucurbita moschata (pumpkin), the most active one, a glycoprotein of 30,665 Da was purified which had the properties of a RIP, in that (i) it inhibited protein synthesis by a rabbit reticulocyte lysate with IC 50 (concentration giving 50% inhibition) 0.035 nM (1.08 ng ml −1) and by HeLa, HT29 and JM cells with IC 50 in the 100 nM range, (ii) deadenylated hsDNA and other polynucleotidic substrates, and (iii) depurinated yeast rRNA at a concentration of 0.1 ng ml −1, all values being comparable to those of other RIPs. The C. moschata RIP gave a weak cross-reaction only with an antiserum against dianthin 32, but not with antisera against other RIPs, and had superoxide dismutase, antifungal and antibacterial activities.