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Nuclease
Kinds of Nuclease Terms modified by Nuclease Selected AbstractsNovel method for genomic analysis of PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease,HUMAN MUTATION, Issue 2 2009Ying-Cai Tan Abstract Genetic testing of PKD1 and PKD2 is useful for diagnosis and prognosis of autosomal dominant polycystic kidney disease (ADPKD), particularly in asymptomatic individuals or those without a family history. PKD1 testing is complicated by the large transcript size, complexity of the gene region, and the extent of gene variations. A molecular assay was developed using Transgenomic's SURVEYOR Nuclease and WAVE Nucleic Acid High Sensitivity Fragment Analysis System to screen for PKD1 and PKD2 variants, followed by sequencing of variant gene segments, thereby reducing the sequencing reactions by 80%. This method was compared to complete DNA sequencing performed by a reference laboratory for 25 ADPKD patients from 22 families. The pathogenic potential of gene variations of unknown significance was examined by evolutionary comparison, effects of amino acid substitutions on protein structure, and effects of splice-site alterations. A total of 90 variations were identified, including all 82 reported by the reference laboratory (100% sensitivity). A total of 76 variations (84.4%) were in PKD1 and 14 (15.6%) in PKD2. Definite pathogenic mutations (seven nonsense, four truncation, and three splicing defects) were detected in 64% (14/22) of families. The remaining 76 variants included 26 missense, 33 silent, and 17 intronic changes. Two heterozygous nonsense mutations were incorrectly determined by the reference laboratory as homozygous. "Probably pathogenic" mutations were identified in an additional five families (overall detection rate 86%). In conclusion, the SURVEYOR nuclease method was comparable to direct sequencing for detecting ADPKD mutations, achieving high sensitivity with lower cost, providing an important tool for genetic analysis of complex genes. Hum Mutat 0, 1,10, 2008. © 2008 Wiley-Liss, Inc. [source] Use of Short Duplexes for the Analysis of the Sequence-Dependent Cleavage of DNA by a Chemical Nuclease, a Manganese PorphyrinCHEMBIOCHEM, Issue 12 2005Sophie Mourgues Abstract A manganese porphyrin, manganese(III)-bis(aqua)- meso -tetrakis(4- N -methylpyridiniumyl)porphyrin, in the presence of KHSO5 is able to perform deoxyribose or guanine oxidation depending on its mode of interaction with DNA. These two reactions involve an oxygen-atom transfer or an electron transfer, respectively. The oxidative reactivity of the manganese-oxo porphyrin was compared on short oligonucleotide duplexes of different sequences. The major mechanism of DNA damage is due to deoxyribose hydroxylation at a site of strong interaction, an (A,T)3 sequence. Guanine oxidation by electron transfer was found not to be competitive with this major mechanism. It was found that a single intrastrand guanine was three orders of magnitude less reactive than an (A,T)3 sequence. The reactivity of a 5,-GG sequence was found to be intermediate and was estimated to be two orders of magnitude less than that of an (A,T)3 site. Short oligonucleotide duplexes, as double-stranded-DNA models, proved to be convenient tools for the study of the comparative reactivity of this reagent toward different sequences of DNA. However, they showed a particular reactivity at their terminal base pairs (the "end effect") that biased their modeling capacity for double-helix-DNA models. [source] Aptamer-Conjugated Nanoparticles Efficiently Control the Activity of ThrombinADVANCED FUNCTIONAL MATERIALS, Issue 18 2010Yen-Chun Shiang Abstract Thrombin-binding aptamer-conjugated gold nanoparticles (TBA-Au NPs) for highly effective control of thrombin activity towards fibrinogen are demonstrated. While a 29-base long oligonucleotide (TBA29) has known no enzymatic inhibitory functions for thrombin-mediated coagulation, the ultrahigh anticoagulant potency of TBA29 -Au NPs can be demonstrated via the steric blocking effect, at two orders of magnitude higher than that of free TBA29. The surface aptamer density on the Au NPs is important in determining their enzymatic inhibition of thrombin and their stability in the presence of nuclease. The practicality of 100TBA29 -Au NPs (100 TBA29 molecules per Au NP) for controlling thrombin-mediated coagulation in plasma is found, and the 100TBA29 -Au NPs has an ultra binding affinity towards thrombin (Kd = 2.7 × 10,11M) due to their high ligand density. The anticoagulant activity of TBA29 -Au NPs is found to be suppressed by TBA29 complementary sequence (cTBA29) modified Au NPs (cTBA29 -Au NPs), with a suppression rate 4.6-fold higher than that of cTBA29. The easily prepared and low-cost TBA29 -Au NPs and cTBA29 -Au NPs show their potential in biomedical applications for treating various diseases related to blood clotting disorders. In principle, this study opens the possibility of regulation of molecule binding, protein recognizing, and enzyme activity by using aptamer-functionalized nanomaterials. [source] Re-oxygenation of hypoxic simian virus 40 (SV40)-infected CV1 cells causes distinct changes of SV40 minichromosome-associated replication proteinsFEBS JOURNAL, Issue 9 2002Hans-Jörg Riedinger Hypoxia interrupts the initiation of simian virus 40 (SV40) replication in vivo at a stage situated before unwinding of the,origin region. After re-oxygenation, unwinding followed by a synchronous round of viral replication takes place. To,further characterize the hypoxia-induced inhibition of unwinding, we analysed the binding of several replication proteins to the viral minichromosome before and after re-oxygenation. T antigen, the 34-kDa subunit of replication protein A (RPA), topoisomerase I, the 48-kDa subunit of primase, the 125-kDa subunit of polymerase ,, and the 37-kDa subunit of replication factor C (RFC) were present at the viral chromatin already under hypoxia. The 70-kDa subunit of RPA, the 180-kDa subunit of polymerase ,, and proliferating cell nuclear antigen (PCNA) were barely detectable at the SV40 chromatin under hypoxia and significantly increased after re-oxygenation. Immunoprecipitation of minichromosomes with T antigen-specific antibody and subsequent digestion with micrococcus nuclease revealed that most of the minichromosome-bound T antigen was associated with the viral origin in hypoxic and in re-oxygenated cells. T antigen-catalysed unwinding of the SV40 origin occurred, however, only after re-oxygenation as indicated by (a) increased sensitivity of re-oxygenated minichromosomes against digestion with single-stranded DNA-specific nuclease P1; (b) stabilization of RPA-34 binding at the SV40 minichromosome; and (c) additional phosphorylations of RPA-34 after re-oxygenation, probably catalysed by DNA-dependent protein kinase. The results presented suggest that the subunits of the proteins necessary for unwinding, primer synthesis and primer elongation first assemble at the SV40 origin in form of stable, active complexes directly before they start to work. [source] Extensive deproteinization of Dictyostelium discoideum RNase P reveals a new catalytic activityFEBS JOURNAL, Issue 7 2001Constantinos Stathopoulos Nuclear Dictyostelium discoideum RNase P was subjected to vigorous deproteinization procedures. After treatment with proteinase K followed by phenol extraction of samples containing D. discoideum RNase P activity, a new enzymatic activity was recovered. The proteinase K/phenol/SDS treated enzyme cleaves Schizossacharomyces pombe tRNAser (supS1), D. discoideum tRNASer and tRNALeu precursors several nucleotides upstream of the cleavage site of RNase P, liberating products with 5,-hydroxyl ends. This activity seems to be associated with one or two RNA molecules copurifying with D. discoideum RNase P activity as judged by its inhibition in the presence of micrococcal nuclease, which is in contrast to its resistance to proteinase K/phenol/SDS treatment. [source] Purification and characterization of the single-strand-specific and guanylic-acid-preferential deoxyribonuclease activity of the extracellular nuclease from Basidiobolus haptosporusFEBS JOURNAL, Issue 16 2000Neelam A. Desai An extracellular nuclease from Basidiobolus haptosporus (designated as nuclease Bh1) was purified to homogeneity by ammonium sulfate precipitation, heat treatment, negative adsorption on DEAE-cellulose, and chromatography on phenyl-Sepharose followed by FPLC on phenyl-Superose. The overall yield was 26%. The Mr of the purified enzyme, determined by gel filtration, was 41 000 whereas by SDS/PAGE (after deglycosylation) it was 30 000. It is a glycoprotein with a pI of 6.8. The optimum pH and temperature for DNA hydrolysis were 8.5 and 60 °C, respectively. Nuclease Bh1 is a metalloprotein but has no obligate requirement for metal ions to be active, nor is its activity stimulated in the presence of metal ions. The enzyme was inhibited by Zn2+, Ag2+, Hg2+, Fe3+ and Al3+, inorganic phosphate, pyrophosphate, dithiothreitol, 2-mercaptoethanol, NaCl and KCl. It was stable to high concentrations of organic solvents and urea but susceptible to low concentrations of SDS and guanidine hydrochloride. Nuclease Bh1 is a multifunctional enzyme and its substrate specificity is in the order of ssDNA , 3,AMP , RNA > dsDNA. Studies on its mode of action showed that it cleaved supercoiled pUC 18 DNA and phage M13 DNA, endonucleolytically, generating single base nicks. The enzyme hydrolyzed DNA with preferential liberation of 5,dGMP, suggesting it to be a guanylic acid preferential endoexonuclease. 5,dGMP, the end product of hydrolysis, was a competitive inhibitor of the enzyme. The absence of 5,dCMP as a hydrolytic product, coupled with the resistance of (dC)10 and deoxyribodinucleoside monophosphates having cytosine either at the 3, or the 5, end, indicates that C-linkages are resistant to cleavage by nuclease Bh1. [source] Genetic diversity and distribution of periphytic Synechococcus spp. in biofilms and picoplankton of Lake ConstanceFEMS MICROBIOLOGY ECOLOGY, Issue 2 2004Sven Becker Abstract In various water depths of the littoral zone of Lake Constance (Bodensee) cyanobacteria of the Synechococcus -type were isolated from biofilms (periphyton) on three natural substrates and an artificial one (unglazed tiles). From one tile three strains of phycoerythrin (PE)-rich Synechococcus spp. were isolated, the first examples of these organisms in the epibenthos. Phylogenetic inference based on the 16S,23S rRNA intergenic spacer (ITS-1) assigned all periphytic isolates to two clusters of the picophytoplankton clade (evolutionary lineage VI of cyanobacteria). The sequence divergence in the ITS-1 was used to design specific PCR primers to allow direct, culture-independent detection and quantification of isolated Synechococcus strains in natural periphytic and pelagic samples. Denaturing gradient gel electrophoresis (DGGE) analysis revealed depth-related differences of Synechococcus spp. distribution on tiles placed in the littoral zone. Synechococcus genotypes were observed which occurred in both the periphyton (on tiles) and in the pelagic picoplankton. A strain with one of these genotypes, Synechococcus sp. BO 8805, was isolated from the pelagic zone in 1988. Its genotype was found on tiles that had been exposed at different water depths in the littoral zone in spring and autumn of the year 2000. Quantitative analysis with a genotype-specific TaqMan probe and real-time Taq nuclease assays (TNA) confirmed its presence in the pelagic zone, although appearance of this and related genotypes was highly irregular and exhibited strong differences between consecutive years. Our results show that the ability to form significant subpopulations in pelagic and periphytic communities exists in three out of four phylogenetic clusters of Synechococcus spp. in Lake Constance. This versatility may be a key feature in the ubiquity of the evolutionary lineage VI of cyanobacteria. [source] DPPA4 modulates chromatin structure via association with DNA and core histone H3 in mouse embryonic stem cellsGENES TO CELLS, Issue 4 2010Hisaharu Masaki Developmental pluripotency associated 4 (DPPA4) is one of the uncharacterized genes that is highly expressed in embryonic stem (ES) cells. DPPA4 is associated with active chromatin and involved in the pluripotency of mouse ES cells. However, the biological function of DPPA4 remains poorly understood. In this study, we performed fluorescence recovery after photobleaching (FRAP) analysis to examine the dynamics of DPPA4 in ES cells. FRAP analysis showed that the mobility of DPPA4 is similar to that of histone H1. In addition, biochemical analysis with purified proteins and immunoprecipitation analysis showed that DPPA4 directly binds to both DNA and core histone H3. The analysis using truncated proteins indicated that DPPA4 is associated with DNA via the N-terminal region and histone H3 via the C-terminal region. In vitro assembled chromatin showed resistance to micrococcal nuclease (MNase) digestion in the presence of DPPA4. Moreover, MNase assay and FRAP analysis with the truncated proteins implies that DPPA4 binding to both DNA and histone H3 is necessary for the chromatin structure resistant to MNase and for the proper localization of DPPA4 in ES cell nuclei. These results suggest that DPPA4 modulates the chromatin structure in association with DNA and histone H3 in ES cells. [source] The MLH1 ,93 G>A promoter polymorphism and genetic and epigenetic alterations in colon cancerGENES, CHROMOSOMES AND CANCER, Issue 10 2008Wade S. Samowitz The MLH1 ,93 G>A promoter polymorphism has been reported to be associated with an increased risk of microsatellite unstable colorectal cancer. Other than microsatellite instability, however, the genetic and most epigenetic changes of tumors associated with this polymorphism have not been studied. We evaluated associations between the ,93 G>A polymorphism and CpG island methylator phenotype (CIMP), BRAF V600E mutations, and MLH1 methylation in tumors from a sample of 1,211 individuals with colon cancer and 1,968 controls from Utah, Northern California, and Minnesota. The ,93 G>A polymorphism was determined by the five prime nuclease assay. CIMP was determined previously by methylation-specific PCR of CpG islands in MLH1, methylated in tumors (MINT)1, MINT2, MINT31, and CDKN2A (p16). The BRAF V600E mutation was determined by sequencing exon 15. The MLH1 ,93 G>A promoter polymorphism was associated with CIMP (odds ratio (OR) 3.44, 95% confidence interval (CI) 1.85, 6.42), MLH1 methylation (OR 4.16, 95%CI 2.20, 7.86), BRAF mutations (OR 4.26, 95%CI 1.83, 9.91), and older age at diagnosis (OR 3.65, 95%CI 2.08, 6.39) in microsatellite unstable tumors. These associations were not observed in stable tumors. Increased age at diagnosis and tumor characteristics of microsatellite unstable tumors associated with MLH1 ,93 G>A suggests the polymorphism is acting at a relatively late stage of colorectal carcinogenesis to drive CIMP+ tumors down the microsatellite instability pathway. © 2008 Wiley-Liss, Inc. [source] Investigation on characterization and transfection of a novel multi-polyplex gene delivery systemJOURNAL OF APPLIED POLYMER SCIENCE, Issue 2 2007Yu Nie Abstract pDNA was condensed by polycationic peptide polylysine (PLL) to form a core, and then encapsulated in biodegradable monomethoxy (poly ethylene glycol)-poly(lactide- co -glycolide)-monomethoxy (poly ethylene glycol) (PELGE) to form core-shell nanoparticles (NPs) as a novel multi-polyplex gene delivery system,PPD(PELGE-PLL-DNA). NPs were prepared by a double emulsification-solvent evaporation technique, using F68 (Pluronic F68, namely Poloxamer 188) as surfactant (not traditional stabilizer PVA), and characterized by morphology, particle size, zeta potential, nuclease, and sonication protection ability, as well as transfection efficiency. Results showed that PPD had a regular spherical shape, with an average diameter of 155 ± 2.97 nm and a zeta potential of ,25.6 ± 1.35 mV. PPD could protect plasmid DNA from nuclease degradation and sonication during preparation, while the transfection efficiencies in HepG2 cells and Hela cells were much higher than that of NPs without PLL. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2007 [source] Single-molecule analysis of chromatin: Changing the view of genomes one molecule at a timeJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 2 2008Santhi Pondugula Abstract Wrapping DNA into chromatin provides a wealth of regulatory mechanisms that ensure normal growth and development in eukaryotes. Our understanding of chromatin structure, including nucleosomes and non-histone protein,DNA interactions, has benefited immensely from nuclease and chemical digestion techniques. DNA-bound proteins, such as histones or site-specific factors, protect DNA against nuclease cleavage and generate large nucleosomal or small regulatory factor footprints. Chromatin subject to distinct modes of regulation often coincides with sites of nuclease hypersensitivity or nucleosome positioning. An inherent limitation of cleavage-based analyses has been the inability to reliably analyze regions of interest when levels of digestion depart from single-hit kinetics. Moreover, cleavage-based techniques provide views that are averaged over all the molecules in a sample population. Therefore, in cases of occupancy of multiple regulatory elements by factors, one cannot define whether the factors are bound to the same or different molecules in the population. The recent development of DNA methyltransferase-based, single-molecule MAP-IT technology overcomes limitations of ensemble approaches and has opened numerous new avenues in chromatin research. Here, we review the strengths, limitations, applications and future prospects of MAP-IT ranging from structural issues to mechanistic questions in eukaryotic chromatin regulation. J. Cell. Biochem. 105: 330,337, 2008. © 2008 Wiley-Liss, Inc. [source] Mouse spermatozoa contain a nuclease that is activated by pretreatment with EGTA and subsequent calcium incubationJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 5 2008Segal M. Boaz Abstract We demonstrated that mouse spermatozoa cleave their DNA into ,50 kb loop-sized fragments with topoisomerase IIB when treated with MnCl2 and CaCl2 in a process we term sperm chromatin fragmentation (SCF). SCF can be reversed by EDTA. A nuclease then further degrades the DNA in a process we term sperm DNA degradation (SDD). MnCl2 alone could elicit this activity, but CaCl2 had no effect. Here, we demonstrate the existence of a nuclease in the vas deferens that can be activated by ethylene glycol tetraacetic acid (EGTA) to digest the sperm DNA by SDD. Spermatozoa were extracted with salt and dithiothreitol to remove protamines and then incubated with EGTA. Next, the EGTA was removed and divalent cations were added. We found that Mn2+, Ca2+, or Zn2+ could each activate SDD in spermatozoa but Mg2+ could not. When the reaction was slowed by incubation on ice, EGTA pretreatment followed by incubation in Ca2+ elicited the reversible fragmentation of sperm DNA evident in SCF. When the reactions were then incubated at 37°C they progressed to the more complete degradation of DNA by SDD. EDTA could also be used to activate the nuclease, but required a higher concentration than EGTA. This EGTA-activatable nuclease activity was found in each fraction of the vas deferens plasma: in the spermatozoa, in the surrounding fluid, and in the insoluble components in the fluid. These results suggest that this sperm nuclease is regulated by a mechanism that is sensitive to EGTA, possibly by removing inhibition of a calcium binding protein. J. Cell. Biochem. 103: 1636,1645, 2008. © 2007 Wiley-Liss, Inc. [source] Discovery, regulation, and action of the major apoptotic nucleases DFF40/CAD and endonuclease GJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2005Piotr Widlak Abstract Toward the end of the 20th and beginning of the 21st centuries, clever in vitro biochemical complementation experiments and genetic screens from the laboratories of Xiaodong Wang, Shigekazu Nagata, and Ding Xue led to the discovery of two major apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G). Both endonucleases attack chromatin to yield 3,-hydroxyl groups and 5,-phosphate residues, first at the level of 50,300 kb cleavage products and next at the level of internucleosomal DNA fragmentation, but these nucleases possess completely different cellular locations in normal cells and are regulated in vastly different ways. In non-apoptotic cells, DFF exists in the nucleus as a heterodimer, composed of a 45 kD chaperone and inhibitor subunit (DFF45) [also called inhibitor of CAD (ICAD-L)] and a 40 kD latent nuclease subunit (DFF40/CAD). Apoptotic activation of caspase-3 or -7 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease. DFF40's nuclease activity is further activated by specific chromosomal proteins, such as histone H1, HMGB1/2, and topoisomerase II. DFF is regulated by multiple pre- and post-activation fail-safe steps, which include the requirements for DFF45/ICAD, Hsp70, and Hsp40 proteins to mediate appropriate folding during translation to generate a potentially activatable nuclease, and the synthesis in stoichiometric excess of the inhibitors (DFF45/35; ICAD-S/L). By contrast, Endo G resides in the mitochondrial intermembrane space in normal cells, and is released into the nucleus upon apoptotic disruption of mitochondrial membrane permeability in association with co-activators such as apoptosis-inducing factor (AIF). Understanding further regulatory check-points involved in safeguarding non-apoptotic cells against accidental activation of these nucleases remain as future challenges, as well as designing ways to selectively activate these nucleases in tumor cells. © 2005 Wiley-Liss, Inc. [source] The small-angle and wide-angle X-ray scattering set-up at beamline BL9 of DELTAJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2007Christina Krywka The multi-purpose experimental endstation of beamline BL9 at the Dortmund Electron Accelerator (DELTA) is dedicated to diffraction experiments in grazing-incidence geometry, reflectivity and powder diffraction measurements. Moreover, fluorescence analysis and inelastic X-ray scattering experiments can be performed. Recently, a new set-up for small-angle and wide-angle X-ray scattering utilizing detection by means of an image-plate scanner was installed and is described in detail here. First small-angle X-ray scattering experiments on aqueous solutions of lysozyme with different cosolvents and of staphylococcal nuclease are discussed. The application of the set-up for texture analysis is emphasized and a study of the crystallographic texture of natural bio-nanocomposites, using lobster and crab cuticles as model materials, is presented. [source] Exposure to cadmium-contaminated soils increases allergenicity of Poa annua L. pollenALLERGY, Issue 10 2010R. Aina To cite this article: Aina R, Asero R, Ghiani A, Marconi G, Albertini E, Citterio S. Exposure to cadmium-contaminated soils increases allergenicity of Poa annua L. pollen. Allergy 2010; 65: 1313,1321. Abstract Background:, Pollution is considered as one main cause for the increase of allergic diseases. Air pollutants may cause and worsen airway diseases and are probably able to make pollen allergens more aggressive. Previous studies looked at traffic-related air pollution, but no data about the effects of polluted soils on pollen allergens are available. We aimed to assess the effects of plant exposure to cadmium-contaminated soil on allergenicity of the annual blue grass, Poa annua L, pollen. Methods:,Poa plants were grown in soil contaminated or not contaminated (control) with cadmium. At flowering, mature pollen was analyzed by microscopy, to calculate the percentage of pollen grains releasing cytoplasmic granules, and by proteomic techniques to analyze allergen proteins. Allergens were identified by sera from grass pollen,allergic patients and by mass spectrometry. Results:, Pollen from Cd-exposed plants released a higher amount of allergenic proteins than control plants. Moreover, Cd-exposed pollen released allergens-containing cytoplasmic grains much more promptly than control pollen. Group 1 and 5 allergens, the major grass pollen allergens, were detected both in control and Cd-exposed extracts. These were the only allergens reacting with patient's sera in control pollen, whereas additional proteins strengthening the signal in the gel region reacting with patient's sera were present in Cd-exposed pollen. These included a pectinesterase, a lipase, a nuclease, and a secretory peroxydase. Moreover, a PR3 class I chitinase-like protein was also immunodetected in exposed plants. Conclusion:, Pollen content of plants grown in Cd-contaminated soils is more easily released in the environment and also shows an increased propensity to bind specific IgE. [source] Dopamine Receptor D2 Polymorphism Moderates the Effect of Parental Education on Adolescents' School PerformanceMIND, BRAIN, AND EDUCATION, Issue 2 2008Liisa Keltikangas-Järvinen ABSTRACT, High parental socioeconomic status is known to have a positive effect on students' academic achievement. We examined whether variation in the dopamine receptor gene (DRD2 polymorphism, rs 1800497) modifies the association between parental educational level and school performance in adolescence. The participants were a randomly selected subsample of individuals participating in the Cardiovascular Risk in Young Finns study (921 girls and 742 boys) aged 12,15 years at the time school performance was assessed. The genotyping was performed using TaqMan 5,'-nuclease assay. A significant interaction was found between childhood parental educational level and students' DRD2 polymorphism on academic achievement after adjustment for age, gender, household income, parental occupation, maternal nurturance, hyperactivity, and sociability. Parental educational level was significantly positively associated with school achievement in the A2/A2 (n = 1,061) and the A1/A2 (n = 529) genotype groups, but was negative and statistically insignificant in participants carrying the A1/A1 (n = 73) genotype. It is concluded that the extent to which parental education status affects an individual's academic achievement may be dependent on the individual's genetic constitution. The findings may increase an acceptance of genetic influence in education, and, consequently, may increase accurateness of educational interventions. [source] Nm23-H1 promotes adhesion of CAL 27 cells in vitroMOLECULAR CARCINOGENESIS, Issue 9 2009ica Bago Abstract nm23-H1 was found to diminish metastatic potential of carcinoma cell lines and therefore was placed in the group of metastatic suppressor genes. Its protein product has a function of a nucleoside diphosphate kinase (NDPK) as well as protein kinase and nuclease. Though it was found that Nm23-H1 is involved in many cellular processes, it is still not known how it promotes metastatic suppressor activity. Since the process of metastasis is dependent on adhesion properties of cells, the goal of our work was to describe the adhesion properties of CAL 27 cells (oral squamous cell carcinoma of the tongue) overexpressing FLAG/nm23-H1. In our experiments, cells overexpressing nm23-H1 show reduced migratory and invasive potential. Additionally, cells overexpressing nm23-H1 adhere stronger on substrates (collagen IV and fibronectin) and show more spread morphology than the control cells. Results obtained by EGF induction of migration revealed that the adhesion strength predetermined cell response to chemoattractant and that Nm23-H1, in this cell type, does not interfere with, EGF induced, Ras signaling pathway. These data contribute to the overall knowledge about nm23-H1 and its role in cell adhesion, migration, and invasion, especially in oral squamous cell carcinoma. © 2009 Wiley-Liss, Inc. [source] Effects of denaturants and substitutions of hydrophobic residues on backbone dynamics of denatured staphylococcal nucleasePROTEIN SCIENCE, Issue 7 2003Satoshi Ohnishi NOE, nuclear Overhauser effect; RDC, residual dipolar coupling Abstract Analysis of residual dipolar couplings (RDCs) in the ,131, fragment of staphylococcal nuclease has demonstrated that its ensemble-averaged structure is resistant to perturbations such as high concentrations of urea, low pH, and substitution of hydrophobic residues, suggesting that its residual structure is encoded by local side-chain/backbone interactions. In the present study, the effects of these same perturbations on the backbone dynamics of ,131, were examined through 1H- 15N relaxation methods. Unlike the global structure reported by RDCs, the transverse relaxation rates R2 were quite sensitive to denaturing conditions. At pH 5.2, ,131, exhibits an uneven R2 profile with several characteristic peaks involving hydrophobic chain segments. Protonation of carboxyl side chains by lowering the pH reduces the values of R2 along the entire chain, yet these characteristic peaks remain. In contrast, high concentrations of urea or the substitution of 10 hydrophobic residues eliminates these peaks and reduces the R2 values by a greater amount. The combination of low pH and high urea leads to further decreases in R2. These denaturant-induced increases in backbone mobility are also reflected in decreases in 15N NOEs and in relaxation interference parameters, with the former reporting an increase in fast motions and the latter a decrease in slow motions. Comparison between the changes in chain dynamics and the corresponding changes in Stokes radius and the patterns of RDCs suggests that regional variations in backbone dynamics in denatured nuclease arise primarily from local contacts between hydrophobic side chains and local interactions involving charged carboxyl groups. [source] Distance dependence and salt sensitivity of pairwise, coulombic interactions in a proteinPROTEIN SCIENCE, Issue 5 2002Kelly K. Lee Abstract Histidine pKa values were measured in charge-reversal (K78E, K97E, K127E, and K97E/K127E) and charge-neutralization (E10A, E101A, and R35A) mutants of staphylococcal nuclease (SNase) by 1H-NMR spectroscopy. Energies of interaction between pairs of charges (,Gij) were obtained from the shifts in pKa values relative to wild-type values. The data describe the distance dependence and salt sensitivity of pairwise coulombic interactions. Calculations with a continuum electrostatics method captured the experimental ,Gij when static structures were used and when the protein interior was treated empirically with a dielectric constant of 20. The ,Gij when rij , 10 Å were exaggerated slightly in the calculations. Coulomb's law with a dielectric constant near 80 and a Debye-Hückel term to account for screening by the ionic strength reproduced the salt sensitivity and distance dependence of ,Gij as well as the structure-based method. In their interactions with each other, surface charges behave as if immersed in water; the Debye length describes realistically the distance where interactions become negligible at a given ionic strength. On average, charges separated by distances (rij) ,5 Å interacted with ,Gij , 0.6 kcal/mole in 0.01 M KCl, but ,Gij decayed to ,0.10 kcal/mole when rij = 20 Å. In 0.10 M KCl, ,Gij , 0.10 kcal/mole when rij = 10 Å. In 1.5 M KCl, only short-range interactions with rij , 5 Å persisted. Although at physiological ionic strengths the interactions between charges separated by more than 10 Å are extremely weak, in situations where charge imbalance exists many weak interactions can cumulatively produce substantial effects. [source] Crystallization and preliminary X-ray analysis of flap endonuclease 1 (FEN1) from Desulfurococcus amylolyticusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Tomoko Mase Flap endonuclease 1 (FEN1) is a structure-specific nuclease that removes 5,-overhanging flaps in DNA repair and removes the RNA/DNA primer during maturation of the Okazaki fragment in lagging-strand DNA replication. FEN1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus was expressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method with monoammonium dihydrogen phosphate as the precipitant at pH 8.3. X-ray diffraction data were collected to 2.00,Å resolution. The space group of the crystal was determined as the primitive hexagonal space group P321, with unit-cell parameters a = b = 103.76, c = 84.58,Å. The crystal contained one molecule in the asymmetric unit. [source] The effect of the CYP1A2 *1F mutation on CYP1A2 inducibility in pregnant womenBRITISH JOURNAL OF CLINICAL PHARMACOLOGY, Issue 5 2002Anna Nordmark Aims, To investigate the influence of the CYP1A2*1F mutation on CYP1A2 activity in smoking and nonsmoking pregnant women. Methods Pregnant women (n = 904) who served as control subjects in a case-control study of early fetal loss were investigated. They were phenotyped for CYP1A2 using dietary caffeine and the urinary ratio AFMU + 1X + 1 U/1,7 U. An assay for CYP1A2*1F using 5,-nuclease assay (Taqman) was developed to genotype the population. Results, The frequencies of *1 A and *1F alleles among Swedish women were 0.29 and 0.71, respectively. There was no statistically significant difference in CYP1A2 activity between the genotypes, although a trend towards enhanced activity was observed in *1F/*1F (log MRc 0.77) and *1F/*1 A (log MRc 0.82) genotypes compared with the *1 A/*1 A genotype (log MRc 0.71) (anovaP = 0.07). The mean difference between the *1 A homozygotes and the heterozygotes was 0.11 [95% confidence interval of the difference: (,0.21, ,0.01)] and that between the *1 A and *1F homozygotes was 0.05 [95% confidence interval of the difference: (,0.13, 0.03)]. No significant effect (P = 0.22) of the *1F on CYP1A2 activity was observed in smokers, tested using an interaction term (smoking * genotype) in the anova model (*1F/*1F log MRc 0.79, *1F/*1 A log MRc 0.86, and *1 A/*1 A log MRc 0.73). In smokers, there was no difference in ratio between homozygotes for the *1 A and *1F alleles [mean difference ,0.06; 95% confidence interval of the difference: ,0.22, 0.11] or between *1 A/*1 A and *1 A/*1F genotypes [mean difference ,0.13; 95% confidence interval of the difference: ,0.29, 0.04]. Conclusions, The effect of the CYP1A2*1F mutation on CYP1A2 activity in smoking pregnant women could not be confirmed. [source] On the Temperature,Pressure Free-Energy Landscape of ProteinsCHEMPHYSCHEM, Issue 4 2003Revanur Ravindra Dr. Abstract We studied the thermodynamic stability of a small monomeric protein, staphylococcal nuclease (Snase), as a function of both temperature and pressure, and expressed it as a 3D free-energy surface on the p,T -plane using a second-order Taylor expansion of the Gibbs free-energy change ,G upon unfolding. We took advantage of a series of different techniques (small-angle Xray scattering, Fourier-transform infrared spectroscopy, differential thermal analysis, pressure perturbation calorimetry and densitometry) in the evaluation of the conformation of the protein and in evaluating the changes in the thermodynamic parameters upon unfolding, such as the heat capacity, enthalpy, entropy, volume, isothermal compressibility and expansivity. The calculated results of the free-energy landscape of the protein are in good agreement with experimental data of the p,T -stability diagram of the protein over a temperature range from 200 to 400 K and at pressures from ambient pressure to 4000 bar. The results demonstrate that combined temperature,pressure-dependent studies can help delineate the free-energy landscape of proteins and hence help elucidate which features and thermodynamic parameters are essential in determining the stability of the native conformational state of proteins. The approach presented may also be used for studying other systems with so-called re-entrant or Tamman loop-shaped phase diagrams. [source] Influence of the SCGE protocol on the amount of basal DNA damage detected in the Mediterranean mussel, Mytilus galloprovincialisENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 8 2006Nicola Machella Abstract Genotoxicity studies using the single cell gel electrophoresis (SCGE) assay indicate that basal levels of DNA strand breaks (SBs) in marine invertebrates are higher and more variable than those in marine vertebrates. This elevated level of DNA damage was attributed to a large number of alkali-labile sites, which are characteristic of the tightly-packaged DNA in invertebrate cells. To investigate if altering the SCGE protocol can artificially modulate high levels of SBs, SCGE experiments were performed on haemocytes from the Mediterranean mussel (Mytilus galloprovincialis) using proteinase K (PK) digestion in combination with assay buffers containing various concentrations of EDTA. In addition, the effects of Trolox® (soluble antioxidant) and aurintricarboxylic acid (ATA; inhibitor of Ca2+/Mg2+ -dependent nucleases) also were tested. The levels of SBs in M. galloprovicialis cells were compared with SBs in cells from a terrestrial mollusk (the snail Helix aspersa), and a teleost fish (the seabass Dicentrarchus labrax). The integrity of M. galloprovincialis DNA isolated with phenol extractions using EDTA, Trolox, and ATA was further assayed by gel electrophoresis. High SBs in mussel cells were reduced by combining EDTA with PK digestion, or using Trolox® or ATA during cell processing for the SCGE assay. Snails and seabass had lower levels of SBs in the SCGE assay, and the levels were not affected by the protocol modifications. Adding EDTA, Trolox®, or ATA to phenol extractions of M. galloprovincialis genomic DNA also reduced the extent of DNA fragmentation. These results suggest that the internal fluids of M. galloprovincialis may increase the basal levels of DNA SBs through oxidative and/or enzyme-mediated pathways. M. galloprovincialis is used extensively as a sentinel species for assessing the genotoxic hazard of marine pollutants. Our data suggest that the SCGE protocol should be carefully considered when assessing DNA damage in these species. Environ. Mol. Mutagen., 2006. © 2006 Wiley-Liss, Inc. [source] Cationic Conjugated Polymer/DNA Complexes for Amplified Fluorescence Assays of Nucleases and Methyltransferases,ADVANCED MATERIALS, Issue 21 2007F. Feng A new method is developed for sensitive, homogeneous, and convenient assays of nucleases and methyltransferases using complexes of cationic conjugated polymers with DNA containing a fluorescein tag at the 5,-terminus (DNA-Fl). The cleavage of DNA by nucleases can be monitored by fluorescence spectra by observing conjugated-polymer or fluorescein emission changes in aqueous solutions. [source] Nuclear aggregates of polyaminesIUBMB LIFE, Issue 2 2006Luciano D'Agostino Abstract Nuclear aggregates of polyamines (NAPs) are cyclic supramolecular compounds made of polyamines and phosphate groups. Three different aggregates, s-NAP, m-NAP and l-NAP, with a molecular weight of 1035, 5175 and 9552 Da, respectively, are described. These molecules interact with genomic DNA. In consequence of this interaction, NAPs not only protect DNA from nucleases with extraordinarily greater efficiency than single polyamines (spermine, spermidine and putrescine), but also induce noticeable changes in DNA condensation status, as shown by temperature-dependent modifications of DNA electrophoretic properties. The biochemical characterization of these compounds has allowed the definition of a structural model for each NAP. According to this model, five s-NAPs assemble together to form a m-NAP unit. We hypothesize that the complexation of s-NAP into m-NAP favours the transition to Z-DNA through the progressive widening of DNA strands and the exposure of bases. We propose that NAPs, by wrapping the DNA helixes, form supramolecular tunnel-like structures that confer efficient protection without affecting DNA elasticity. iubmb Life, 58: 75-82, 2006 [source] Discovery, regulation, and action of the major apoptotic nucleases DFF40/CAD and endonuclease GJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2005Piotr Widlak Abstract Toward the end of the 20th and beginning of the 21st centuries, clever in vitro biochemical complementation experiments and genetic screens from the laboratories of Xiaodong Wang, Shigekazu Nagata, and Ding Xue led to the discovery of two major apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G). Both endonucleases attack chromatin to yield 3,-hydroxyl groups and 5,-phosphate residues, first at the level of 50,300 kb cleavage products and next at the level of internucleosomal DNA fragmentation, but these nucleases possess completely different cellular locations in normal cells and are regulated in vastly different ways. In non-apoptotic cells, DFF exists in the nucleus as a heterodimer, composed of a 45 kD chaperone and inhibitor subunit (DFF45) [also called inhibitor of CAD (ICAD-L)] and a 40 kD latent nuclease subunit (DFF40/CAD). Apoptotic activation of caspase-3 or -7 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease. DFF40's nuclease activity is further activated by specific chromosomal proteins, such as histone H1, HMGB1/2, and topoisomerase II. DFF is regulated by multiple pre- and post-activation fail-safe steps, which include the requirements for DFF45/ICAD, Hsp70, and Hsp40 proteins to mediate appropriate folding during translation to generate a potentially activatable nuclease, and the synthesis in stoichiometric excess of the inhibitors (DFF45/35; ICAD-S/L). By contrast, Endo G resides in the mitochondrial intermembrane space in normal cells, and is released into the nucleus upon apoptotic disruption of mitochondrial membrane permeability in association with co-activators such as apoptosis-inducing factor (AIF). Understanding further regulatory check-points involved in safeguarding non-apoptotic cells against accidental activation of these nucleases remain as future challenges, as well as designing ways to selectively activate these nucleases in tumor cells. © 2005 Wiley-Liss, Inc. [source] Mitochondria, the killer organelles and their weaponsJOURNAL OF CELLULAR PHYSIOLOGY, Issue 2 2002Luigi Ravagnan Apoptosis is a cell-autonomous mode of death that is activated to eradicate superfluous, damaged, mutated, or aged cells. In addition to their role as the cell's powerhouse, mitochondria play a central role in the control of apoptosis. Thus, numerous pro-apoptotic molecules act on mitochondria and provoke the permeabilization of mitochondrial membranes. Soluble proteins contained in the mitochondrial intermembrane space are released through the outer membrane and participate in the organized destruction of the cell. Several among these lethal proteins can activate caspases, a class of cysteine proteases specifically activated in apoptosis, whereas others act in a caspase-independent fashion, by acting as nucleases (e.g., endonuclease G), nuclease activators (e.g., apoptosis-inducing factor), or serine proteases (e.g., Omi/HtrA2). In addition, mitochondria can generate reactive oxygen species, following uncoupling and/or inhibition of the respiratory chain. The diversity of mitochondrial factors participating in apoptosis emphasizes the central role of these organelles in apoptosis control and unravels novel mechanisms of cell death execution. © 2002 Wiley-Liss, Inc. [source] Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteriaJOURNAL OF PHYCOLOGY, Issue 1 2000Daniel Tillett The isolation of high-quality nucleic acids from cyanobacterial strains, in particular environmental isolates, has proven far from trivial. We present novel techniques for the extraction of high molecular weight DNA and RNA from a range of cultured and environmental cyanobacteria, including stains belonging to the genera Microcystis, Lyngbya, Pseudanabaena, Aphanizomenon, Nodularia, Anabaena, and Nostoc, based on the use of the nontoxic polysaccharide solubilizing compound xanthogenate. These methods are rapid, require no enzymatic or mechanical cell disruption, and have been used to isolate both DNA and RNA free of enzyme inhibitors or nucleases. In addition, these procedures have proven critical in the molecular analysis of bloom-forming and other environmental cyanobacterial isolates. Finally, these techniques are of general microbiological utility for a diverse range of noncyanobacterial microorganisms, including Gram-positive and Gram-negative bacteria and the Archea. [source] Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coliMOLECULAR MICROBIOLOGY, Issue 4 2000Bijoy K. Mohanty Poly(A) tails in Escherichia coli are hypothesized to provide unstructured single-stranded substrates that facilitate the degradation of mRNAs by ribonucleases. Here, we have investigated the role that such nucleases play in modulating polyadenylation in vivo by measuring total poly(A) levels, polyadenylation of specific transcripts, growth rates and cell viabilities in strains containing various amounts of poly(A) polymerase I (PAP I), polynucleotide phosphorylase (PNPase), RNase II and RNase E. The results demonstrate that both PNPase and RNase II are directly involved in regulating total in vivo poly(A) levels. RNase II is primarily responsible for degrading poly(A) tails associated with 23S rRNA, whereas PNPase is more effective in modulating the polyadenylation of the lpp and 16S rRNA transcripts. In contrast, RNase E appears to affect poly(A) levels indirectly through the generation of new 3, termini that serve as substrates for PAP I. In addition, whereas excess PNPase suppresses polyadenylation by more than 70%, the toxicity associated with increased poly(A) levels is not reduced. Conversely, toxicity is significantly reduced in the presence of excess RNase II. Overproduction of RNase E leads to increased polyadenylation and no reduction in toxicity. [source] Specific localization of transcription factors in the chromatin of mouse mature spermatozoaMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 1 2001Carmine Pittoggi Abstract We previously characterized a nuclease-hypersensitive fraction of mouse sperm chromatin, which is organized in a typical nucleosomal structure. A partial genomic library was constructed with the DNA from the nuclease-hypersensitive chromatin, which revealed a high content in retroposon/retroviral DNA sequences. Here we report that the cloned nuclease-hypersensitive DNA also contains clusters of potential sites for transcription factors: among those, binding sites for Oct-1, Oct-4, TBP, Ets-1, and C/EBP are most abundant. This observation prompted us to ask whether mature spermatozoa contain the corresponding protein factors. Indirect immunofluorescence experiments show that all analyzed factors are indeed present in the sperm heads. Moreover, transcription factors are associated with the nuclease-hypersensitive chromatin of spermatozoa, as endogenous nucleases that degrade the hypersensitive fraction also cause the concomitant release of transcription factors from sperm cells into the medium. Band-shift assays with proteins extracted from the supernatant, and immunofluorescence analysis of sperm pellets, indicate that transcription factors are largely recovered in the supernatant while being absent or poorly retained in spermatozoa. The possible involvement of these factors in early embryogenesis is discussed. Mol. Reprod. Dev. 60: 97,106, 2001. © 2001 Wiley-Liss, Inc. [source] | ||||||||||||||||||||||||||||||||||