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At least 631 records · Page 35Linked to original sources
PubMed1994

Inhibition of the synthesis of a cytochrome-c-oxidase subunit isoform by antisense RNA.

To investigate the role of subunit VIIe, an oxygen-regulated subunit isoform of Dictyostelium discoideum cytochrome-c oxidase, the full-length cDNA was inserted into an expression vector under the control of an actin promoter in the sense and antisense orientation. The DNA constructs were used for stable transformation of the slime mold amoebae. In most of the 28 antisense clones tested, the concentration of cytochrome-c oxidase was lowered compared to the wild type, while no significant changes were found in the sense mutants. Antisense RNA was abundantly expressed, leading to a drastic reduction of the steady-state level of the endogenous subunit VIIe mRNA, which was decreased up to 20-30% the level observed in parent cells. In these transformants, the amount of the target polypeptide and cytochrome c oxidase was 40-50% and 60-70% of control, respectively. A similar decrease was found in the level of the remaining nuclear and mitochondrial subunits. Unexpectedly, these changes affected neither basal nor uncoupled cell respiration suggesting an increase of the enzyme specific activity. Hypoxia completely relieved the cytochrome-c-oxidase deficit. These results indicate that subunit VII is needed for an efficient assembly of the protein complex and provide evidence for its involvement in the modulation of the enzyme activity.

Animals↗
PubMed2006

Voltammetric detection of single base-pair mismatches and quantification of label-free target ssDNA using a competitive binding assay.

The application of electrochemical techniques for DNA detection is motivated by their potential to detect hybridisation events in a more rapid, simplistic and cost-effective manner compared to conventional optical assays. Here, we present an electrochemical DNA sensor for the specific and quantitative detection of single-stranded DNA (ssDNA). Probe oligonucleotides were immobilised onto thin gold film electrodes by a 5'-thiol-linker. Hybridisation was detected by means of the electroactive redox-marker methylene blue (MB) covalently attached to the 5'-end of the target ssDNA and voltammetric techniques. MB-labeled target ssDNA was recognised down to 30 pmol. By application of a competitive binding assay, non-labeled ssDNA was detected down to 3 pmol. In addition, the DNA-modified electrodes were capable of sensing single base-pair mismatches at different positions within the sequence of the hybridised double-stranded DNA (dsDNA).

Base Pair Mismatch↗
PubMed1991

Actinomycin D induced DNase I hypersensitivity and asymmetric structure transmission in a DNA hexadecamer.

DNase I cleavage rates and nmr chemical shifts are shown to change for DNA sequences distal to an intercalated actinomycin D molecule in a duplex hexadecamer upon drug binding. Both sets of observations suggest that the source of these changes is a DNA-mediated structural response. The nmr results imply the response is transmitted preferentially in a 5'-to-3' direction from the drug binding site. An inequivalent response of the two strands to a ligand-induced conformational change immediately suggests a mechanism for distinguishing the sense and antisense strands of DNA.

Base Sequence↗
PubMed1983

Significance of electrophilic reactivity and especially DNA alkylation in carcinogenesis and mutagenesis.

Alkylating agents have proved useful as models, especially for low molecular weight mutagens and carcinogens, to probe molecular mechanisms of genotoxicity. Results of many studies have indicated that not all DNA substitutions cause mutagenic or carcinogenic responses. Often, quantitatively minor alkylation products are responsible for initiating these biological processes. The factors that influence the distribution of DNA substitution products include: the SN1 reactivity of the electrophilic species; the nucleophilicity and steric accessability of the DNA site; van der Waals or electrostatic interactions that attract the agent to specific DNA sites; and post-alkylation rearrangements. With low molecular weight alkylating agents, a primary determinant of product distribution in DNA, and of genotoxic potential, is the electrophilic reactivity. Agents with high SN1 reactivity (low Swain -Scott s factors) generally have high mutagenic and carcinogenic activity, at equal levels of total DNA alkylkation . This appears to be due to the ability of such agents to cause relatively more alkylation at oxygen sites in DNA, especially at O6 of guanine and at O4 of thymine. Alkylation of DNA alone is insufficient to induce cancer or mutations. Post-alkylation factors such as DNA repair, rate of cell turnover, or presence of tumor promoters can have a profound effect on the biological response to DNA damage (1,5,6,24,42). In this sense, the persistence of a specific miscoding of altered DNA base is significant in carcinogenesis or mutagenesis only to the extent that it remains in DNA long enough to be fixed into the code. This concept necessarily assumes that the altered base has promutagenic potential. Persistence of an alkylated DNA constituent does not, by itself, indicate that the alkylated constituent has biological significance.

Alkylating Agents↗
PubMed2005

Towards a label-free optical porous silicon DNA sensor.

We report on the fabrication of an optical silicon-based label-free DNA sensor. n-Type crystalline silicon wafers have been electrochemically etched to form porous silicon layers and characterized in terms of porosity, pore distribution, surface composition and photoluminescence. Samples (0.25 cm(2)) have been cut and properly derivatized using trimethoxy-3-bromoacetamidopropylsilane in order to link single strand DNA (ss-DNA). Such a molecule is not commercially available and has been ad-hoc prepared by reacting hydrobromic acid and 3-aminopropyltrimethoxysilane in presence of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide as coupling agent. Trimethoxy-3-bromoacetamidopropylsilane acts as a bridge anchored to the porous silicon surface through the silane group while immobilizing ss-DNA by means of the bromoacetamido moiety. We have found that derivatized samples exhibit a photoluminescence that is stable in time and is not modified after exposure to non-complementary DNA strand. On the other hand, a sensible enhancement of the light emission has been observed when the derivatized samples react with the complementary strand, showing that the specific ss-DNA/complementary DNA (c-DNA) interaction can be optically sensed without using further labeling steps. This strongly strengthens the possible role of silicon as a material for biosensors.

Biosensing Techniques↗
PubMed2006

Resistive-pulse DNA detection with a conical nanopore sensor.

In this paper, we describe resistive-pulse sensing of two large DNAs, a single-stranded phage DNA (7250 bases) and a double-stranded plasmid DNA (6600 base pairs), using a conically shaped nanopore in a track-etched polycarbonate membrane as the sensing element. The conically shaped nanopore had a small-diameter (tip) opening of 40 nm and a large-diameter (base) opening of 1.5 microm. The DNAs were detected using the resistive-pulse, sometimes called stochastic sensing, method. This entails applying a transmembrane potential difference and monitoring the resulting ion current flowing through the nanopore. The phage DNA was driven electrophoretically through the nanopore (from tip to base), and these translocation events were observed as transient blocks in the ion current. We found that the frequency of these current-block events scales linearly with the concentration of the DNA and with the magnitude of the applied transmembrane potential. Increasing the applied transmembrane potential also led to a decrease in the duration of the current-block events. We also analyzed current-block events for the double-stranded plasmid DNA. However, because this DNA is too large to enter the tip opening of the nanopore, it could not translocate the pore. As a result, much shorter duration current-block events were observed, which we postulate are associated with bumping of the double-stranded DNA against the tip opening.

DNA↗
PubMed2003

Antiangiogenic effect of KR-31372 by apoptosis via mediation of mitochondrial KATP channel opening and the phosphatase and tensin homolog deleted from chromosome 10 phosphorylation.

Antiangiogenic action of (2R,3R,4S)-N"-cyano-N-(6-nitro-3,4-dihydro-hydroxy-2-methyl-2-dimethoxymethyl-2H-1-benzopyran-4yl)-N'-benzyl guanidine (KR-31372) was examined with its proapoptotic action in human umbilical vein endothelial cells (HUVECs) compared with diazoxide. KR-31372 as well as diazoxide significantly suppressed the neovascularization in mice induced by the Matrigel-containing recombinant human vascular endothelial growth factor (VEGF)165 in vivo and the basal tube formation of HUVECs in vitro with suppression of proliferation of HUVECs stimulated by VEGF165. KR-31372 and diazoxide enhanced DNA fragmentation associated with increase in phosphatase and tensin homolog deleted from chromosome 10 (PTEN) and decrease in serine/threonine kinase phosphorylation, which were accompanied by augmented Bax and cytochrome c release, and suppressed Bcl-2 in HUVECs. In the U87-MG cells, when transfected with expression vectors for sense PTEN, KR-31372 enhanced DNA fragmentation, but not in naive U87-MG cells. The suppression by KR-31372 and diazoxide of these variables was significantly antagonized by 5-hydroxydecanoic acid, a mitochondrial KATP channel blocker. Taken together, KR-31372 strongly inhibited angiogenesis in HUVECs by proapoptotic mechanism via mediation of 5-hydroxydecanoic acid-inhibitable mitochondrial KATP channel opening and PTEN phosphorylation.

Angiogenesis Inhibitors↗
PubMedDate not supplied

A mouse locus at which transcription from both DNA strands produces mRNAs complementary at their 3' ends.

The organization and large size of the mammalian cell genome allows spatial separation of different transcription units. In those cases where more than one species of messenger are synthesized from the same cellular DNA sequence, they have been found to be generated from transcription proceeding in the same direction. These mRNAs always share regions of homology and can differ from one another as a result of differential processing (splicing and/or polyadenylation) or alternative initiation. In contrast, complementary mRNAs transcribed from opposite strands of the same cellular DNA sequence have not previously been observed. Here we have identified a region of mouse DNA at which processed mRNAs from two adjacent convergent transcription units overlap by 133 base pairs (bp) at their 3'-untranslated ends. One of the transcription units appears to encode a second mRNA which does not contain this overlapping region. This represents the first description of the natural occurrence of processed mammalian cell mRNAs transcribed from opposite strands of the same DNA sequence. The implications of these complementary regions in normal gene regulation are discussed in the context of the finding that the artificial introduction into cells of DNA constructs synthesizing anti-sense RNAs complementary to regions of mRNA transcribed from a chromosomal gene, can inhibit the gene's activity, presumably by the formation of double-stranded RNA.

Animals↗
PubMed2001

Kinetic proofreading can explain the supression of supercoiling of circular DNA molecules by type-II topoisomerases.

The enzymes that pass DNA through DNA so as to remove entanglements, adenosine-triphosphate-hydrolyzing type-II topoisomerases, are able to suppress the probability of self-entanglements (knots) and mutual entanglements (links) between approximately 10 kb plasmids, well below the levels expected, given the assumption that the topoisomerases pass DNA segments at random by thermal motion. This implies that a 10-nm type-II topoisomerase can somehow sense the topology of a large DNA. We previously introduced a "kinetic proofreading" model which supposes the enzyme to require two successive collisions in order to allow exchange of DNA segments, and we showed how it could quantitatively explain the reduction in knotting and linking complexity. Here we show how the same model quantitatively explains the reduced variance of the double-helix linking number (supercoiling) distribution observed experimentally.

Binding Sites↗
PubMed2006

DNA-dependent protein kinase catalytic subunit is not required for dysfunctional telomere fusion and checkpoint response in the telomerase-deficient mouse.

Telomeres are key structural elements for the protection and maintenance of linear chromosomes, and they function to prevent recognition of chromosomal ends as DNA double-stranded breaks. Loss of telomere capping function brought about by telomerase deficiency and gradual erosion of telomere ends or by experimental disruption of higher-order telomere structure culminates in the fusion of defective telomeres and/or the activation of DNA damage checkpoints. Previous work has implicated the nonhomologous end-joining (NHEJ) DNA repair pathway as a critical mediator of these biological processes. Here, employing the telomerase-deficient mouse model, we tested whether the NHEJ component DNA-dependent protein kinase catalytic subunit (DNA-PKcs) was required for fusion of eroded/dysfunctional telomere ends and the telomere checkpoint responses. In late-generation mTerc(-/-) DNA-PKcs(-/-) cells and tissues, chromosomal end-to-end fusions and anaphase bridges were readily evident. Notably, nullizygosity for DNA Ligase4 (Lig4)--an additional crucial NHEJ component--was also permissive for chromosome fusions in mTerc(-/-) cells, indicating that, in contrast to results seen with experimental disruption of telomere structure, telomere dysfunction in the context of gradual telomere erosion can engage additional DNA repair pathways. Furthermore, we found that DNA-PKcs deficiency does not reduce apoptosis, tissue atrophy, or p53 activation in late-generation mTerc(-/-) tissues but rather moderately exacerbates germ cell apoptosis and testicular degeneration. Thus, our studies indicate that the NHEJ components, DNA-PKcs and Lig4, are not required for fusion of critically shortened telomeric ends and that DNA-PKcs is not required for sensing and executing the telomere checkpoint response, findings consistent with the consensus view of the limited role of DNA-PKcs in DNA damage signaling in general.

Animals↗
PubMed2002

Regulation of endothelial cell proliferation and apoptosis by cyclic pressure.

The present study investigated the proliferative and apoptotic responses of human umbilical vein endothelial cells (HUVECs) to well-defined, sinusoidal pressures (60/20, 100/60, and 140/100 mm Hg/mm Hg) at 1 Hz for up to 24 h under Media 199 containing either 1% FBS and 0.04% bovine brain extract (BBE) (low serum/growth factor conditions) or 10% FBS and 0.4% BBE (normal serum/growth factor conditions). Controls were HUVEC maintained under 0.2 mm Hg sustained pressure, but otherwise, similar experimental conditions. Under low serum/growth factor conditions, exposure of HUVEC to 60/20 mm Hg/mm Hg cyclic pressure at 1 Hz for time periods up to 24 h resulted in increases in total cell population density, apoptosis, and DNA synthesis. Under normal serum/growth factor conditions, exposure of HUVEC to either 60/20 or 100/60 mm Hg/mm Hg cyclic pressures resulted in increased DNA synthesis but did not significantly affect cell density or the apoptotic index. A reduced rate of cell death was observed in HUVEC under low serum/growth factor conditions after exposure to 140/100 mm Hg/mm Hg. Under normal serum/growth factor conditions. HUVEC exposed to 140/100 mm Hg/mm Hg cyclic pressure exhibited reduced DNA synthesis. Endothelial cells. therefore, sense and respond to physiologic levels of cyclic pressure by modifying cell proliferation and apoptosis in a mean-pressure-selective manner.

Apoptosis↗
PubMed2005

An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays.

BACKGROUND: DNA microarray is an invaluable tool for gene expression explorations. In the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. To compare a large number of samples, the 'reference design' is widely used, in which all RNA samples are hybridized to a common reference. Genomic DNA is an attractive candidate for use as a universal reference, especially for bacterial systems with a low percentage of non-coding sequences. However, genomic DNA, comprising of both the sense and anti-sense strands, is unlike the single stranded cDNA usually used in microarray hybridizations. The presence of the antisense strand in the 'reference' leads to reactions between complementary labeled strands in solution and may cause the assay result to deviate from true values. RESULTS: We have developed a mathematical model to predict the validity of using genomic DNA as a reference in the microarray assay. The model predicts that the assay can accurately estimate relative concentrations for a wide range of initial cDNA concentrations. Experimental results of DNA microarray assay using genomic DNA as a reference correlated well to those obtained by a direct hybridization between two cDNA samples. The model predicts that the initial concentrations of labeled genomic DNA strands and immobilized strands, and the hybridization time do not significantly affect the assay performance. At low values of the rate constant for hybridization between immobilized and mobile strands, the assay performance varies with the hybridization time and initial cDNA concentrations. For the case where a microarray with immobilized single strands is used, results from hybridizations using genomic DNA as a reference will correspond to true ratios under all conditions. CONCLUSION: Simulation using the mathematical model, and the experimental study presented here show the potential utility of microarray assays using genomic DNA as a reference. We conclude that the use of genomic DNA as reference DNA should greatly facilitate comparative transcriptome analysis.

DNA↗
PubMed2004

[Inhibition of anti-sense human telomerase reverse transcriptase (hTERT) retroviral vector on lung cancer cells].

BACKGROUND & OBJECTIVE: Inhibition of telomere length can be achieved through suppression of telomerase activity, which may result in the inhibition of immortal cell proliferation. In order to explore the possibility of the telomerase as a target for lung cancer therapy, we investigated the effects of anti-sense human telomerase reverse transcriptase (hTERT) on telomerase activity and cell proliferation of A549 lung cancer cell line. METHODS: The anti-sense hTERT cDNA, an 835 bp in the 5' region of hTERT mRNA was amplified by reverse transcription polymerase chain reaction (RT-PCR), before cloning into pLXSN retroviral vector in sense and anti-sense orientations. A549 cells, a human lung cancer cell line, were infected with recombinant virus obtained after transfection into packaging cell PT67. The expression of hTERT protein was determined by Western blot analysis. The telomerase activity was measured by telomerase repeat amplification protocol (TRAP). The cell proliferation was depicted by cell morphology under inverted microscopy as well as cell growth curve. Apoptosis was analyzed by flow cytometry and DNA electrophoresis. RESULTS: Compared with sense hTERT transduction, hTERT expression and telomerase activity significantly decreased in A549 cells after anti-sense hTERT transduction. The cell proliferation was markedly inhibited with evidence of apoptosis. CONCLUSION: Anti-sense hTERT exhibited significant inhibition of telomerase activity and cell proliferation, in addition to acceleration of apoptosis. This implied the possibility of hTERT as the potential target for gene therapy of lung cancer.

Adenocarcinoma↗
PubMed1983

[Structure of a recombination site in the transducing bacteriophage lambda plac5 DNA].

A recombination site in the transducing bacteriophage lambda plac5 DNA has been structurally elucidated. Comparison of primary structures of E. coli lac-operon (distal end of lacZ gene, Z-Y spacer, and proximal end of lacY gene) described earlier with corresponding segments of bacteriophages lambda CI857 and lambda plac 5-2 DNAs sequenced in this paper showed that the bacterial DNA insert ends immediately after Z-Y spacer, just before the initiating triplet ATG of lacY gene. It thus follows that in contrast to the earlier conception, the insert does not seem to include any part of lacY gene. The recombination sites in both phage and bacterial DNA contain structurally homological segments about 20 b. p. long (crossover region), with two extra basepairs in the bacterial DNA (AT in the sense-strand). We suppose that the very dinucleotide plays a substantial role in initiation of recombinational event: causing formation of a nonperfect heteroduplex structure, it determines the T-A internucleotide bond to be endonucleolytically cut (crossover point) followed by exonucleolytic elimination of the extra links (AT) and reciprocal strand exchange. The second recombination site in lambda plac5 DNA has been localized by us within lacI gene as being close to the HindII site (nucleotides 854 to 859 of the gene). The structures of the two regions of site-specific recombination may shed light upon mechanisms of the phage abnormal excision leading to formation of transducing phages.

Bacteriophage lambda↗
PubMedDate not supplied

[Evolution of the DNA structure: direction, mechanism, rate].

On the basis of the analysis of frequencies of occurence of pyrimidines of different length, the degree of clustering of DNA of a hundred species belonging to different taxons has been determined. A tendency towards increase in the index of DNA clustering was revealed in the sequence: bacteria, invertebrates, fishes, amphibians, reptiles, birds, mammals. A mechanism is postulated, according to which an increase in the degree of clustering of DNA in the process of progressive evolution of species may be due to accumulation of mutations, Pyr in equilibrium Pur transversions, resulting in an increase in the degree of asymmetry of the complementary chains of DNA. That this mechanism does exist is proved by a positive correlation between the degree of clustering of DNA and the degree of asymmetry of natural DNA chains. The mean frequency of mutation of vertebrates is about 4,6-10(-8) substitutions per nucleotide per year. Evolution of different groups of organisms may be accompanied with an increase in the rate of evolution of DNA structure. With the help of a special computer program, proceeding from the amino acid sequence of cytochromes c in 40 species belonging to different taxons, the degree of clustering of pyrimidines and the degree of asymmetry of complementary chains of DNA cistrons coding for cytochrome c was determined. A general tendency towards an increase in the mean values of the corresponding parametres of structure was found in the following: bacteria, invertebrates, fishes, amphibians, reptiles, birds and mammals. Thus, it was established that "neutral" amino acid substitutions in cytochromes are based on the selection of mutations leading to accumulation of pyrimidines in sense H-chain of DNA, and purines--in the corresponding mRNA. The frequency of mutation in cytochrome c of chordates is about 5,2-10(-8) of amino acid residues per year. It is assumed that the evolution modification of DNA structure may be due to increase in the disturbance stability of translation.

Amino Acids↗
PubMed1999

Activation of systemic acquired silencing by localised introduction of DNA.

BACKGROUND: In plants, post-transcriptional gene silencing results in RNA degradation after transcription. Among tobacco transformants carrying a nitrate reductase (Nia) construct under the control of the cauliflower mosaic virus 35S promoter (35S-Nia2), one class of transformants spontaneously triggers Nia post-transcriptional gene silencing (class II) whereas another class does not (class I). Non-silenced plants of both classes become silenced when grafted onto silenced stocks, indicating the existence of a systemic silencing signal. Graft-transmitted silencing is maintained in class II but not in class I plants when removed from silenced stocks, indicating similar requirements for spontaneous triggering and maintenance. RESULTS: Introduction of 35S-Nia2 DNA by the gene transfer method called biolistics led to localised acquired silencing (LAS) in bombarded leaves of wild-type, class I and class II plants, and to systemic acquired silencing (SAS) in class II plants. SAS occurred even if the targeted leaf was removed 2 days after bombardment, indicating that the systemic signal is produced, transmitted and amplified rapidly. SAS was activated by sense, antisense and promoterless Nia2 DNA constructs, indicating that transcription is not required although it does stimulate SAS. CONCLUSIONS: SAS was activated by biolistic introduction of promoterless constructs, indicating that the DNA itself is a potent activator of post-transcriptional gene silencing. The systemic silencing signal invaded the whole plant by cell-to-cell and long-distance propagation, and reamplification of the signal.

Base Sequence↗
PubMed1999

Peptide nucleic acids targeted to the neurotensin receptor and administered i.p. cross the blood-brain barrier and specifically reduce gene expression.

Intraperitoneal injection of an unmodified antisense peptide nucleic acid (PNA) complementary to mRNA of the rat neurotensin (NT) receptor (NTR1) was demonstrated by a gel shift assay to be present in brain, thus indicating that the PNA had in fact crossed the blood-brain barrier. An i.p. injection of this antisense PNA specifically inhibited the hypothermic and antinociceptive activities of NT microinjected into brain. These results were associated with a reduction in binding sites for NT both in brain and the small intestine. Additionally, the sense-NTR1 PNA, targeted to DNA, microinjected directly into the brain specifically reduced mRNA levels by 50% and caused a loss of response to NT. To demonstrate the specificity of changes in behavioral, binding, and mRNA studies, animals treated with NTR1 PNA were tested for behavioral responses to morphine and their mu receptor levels were determined. Both were found to be unaffected in these NTR1 PNA-treated animals. The effects of both the antisense and sense PNAs were completely reversible. This work provides evidence that any antisense strategy targeted to brain proteins can work through i. p. delivery by crossing the normal blood-brain barrier. Equally important was that an antigene strategy, the sense PNA, was shown in vivo to be a potentially effective therapeutic treatment.

Animals↗