Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “DNA sensing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 433 records · Page 24Linked to original sources
PubMed2006

The role of ATM in breast cancer development.

Complete or partial inability to sense and repair DNA damage increases the risk of developing cancer. The ataxia telangiectasia mutated (ATM) protein kinase has a crucial role in response to DNA double-strand breaks. Hereditary mutations in the ATM gene are the cause of a rare genomic instability syndrome ataxia telangiectasia (AT) characterized, among others, by elevated cancer risk. Although clear in homozygotes, numerous studies have failed to find a link between heterozygotes and cancer. However, there is increasing evidence that ATM heterozygotes have an increased risk of developing breast cancer. First, epidemiological studies conferred an increased risk of breast cancer among AT relatives. Second, in vitro studies of heterozygous cells provide strong evidence of hyperradiosensitivity. Third, some clinical studies found an increased frequency of ATM mutations among high-risk breast cancer families.

Ataxia Telangiectasia↗
PubMed1983

A weak upstream promoter gives rise to long human beta-globin RNA molecules.

The 5' ends of most normal human beta globin mRNA molecules correspond to a single transcription initiation site, often referred to as the "CAP" site (1-4). Using S1 nuclease mapping and primer extension techniques, we have determined that a minority of beta globin gene transcripts are longer at the 5' ends. These longer molecules comprise about 10% of total beta globin RNA molecules in normal human bone marrow cells and in peripheral blood reticulocytes. The long molecules are transcribed only from the sense strand of DNA and are probably spliced correctly. A DNA segment that includes imperfect "CCAAT" and "TATA" promoter-like sequences begins approximately 150 base pairs (bp) upstream from the normal beta globin gene promoter; this "pseudo-promoter" may function in the initiation of the long globin RNA molecules.

Bone Marrow↗
PubMed1994

A single temperature amplification technique applied to the detection of citrus tristeza viral RNA in plant nucleic acid extracts.

A procedure for the successful detection of citrus tristeza virus (CTV) RNA in total crude nucleic acid extracts of infected citrus whole leaves and bark is described. The method requires the isolation and precipitation of total nucleic acids from either infected whole leaf or bark tissue. The CTV viral RNA is then specifically amplified using a single temperature RNA Self-Sustained Sequence Replication technique (3SR) performed at 42 degrees C for 60 minutes. The amplified negative-sense viral RNA product can subsequently be detected by fixing a portion of the reaction mixture onto a nylon membrane and hybridizing with positive sense tristeza specific DNA oligonucleotide probes. Central California isolates of CTV were readily detected by this method. Denatured viral specific dsRNA was also a suitable template for the specific detection of CTV.

Base Sequence↗
PubMedDate not supplied

Searching for promoter activity in RIME/Ingi retrotransposons from Trypanosoma brucei: binding of a nuclear protein to their 5' extremity.

In Trypanosoma brucei only two promoters for protein-encoding genes have been characterized so far. The RIME and Ingi elements of T. brucei are similar in structure to the non-long terminal repeat retrotransposons. Internal promoters usually located at their 5' end drive transcription of several of the latter elements. During a search for promoter activity within RIME and Ingi we focused on a region at the 5' end of both elements, which we termed rime5. A 50 kDa nuclear protein was found to specifically bind to the double strand and single strand sense of rime5 DNA. However, constructs containing several rime5 fragments inserted upstream of a chloramphenicol acetyltransferase (CAT) reporter gene failed to promote both transcription and expression of this gene in transient transfection assays. Finally, we have analyzed the expression of the Ingi elements and despite the high level of transcripts detectable in the cytoplasm, antibodies raised against two different domains of the single open reading frame did not detect any component in total extracts from T. brucei, suggesting that few Ingi copies, if any, are actually active.

Animals↗
PubMed1988

Self-assembly of porphyrins on nucleic acid templates.

The cis and trans isomers of dicationic bis(4-N-methylpyridyl)diphenylporphine show a much greater tendency to aggregate than similar tetracationic porphyrins. Upon binding to nucleic acids these aggregating dicationic porphyrins form long-range structures on the polymer template giving intense circular dichroism signals whose profile reports the helical sense of the DNA.

Chemical Phenomena↗
PubMed2003

Anionic polyethyleneglycol lipids added to cationic lipoplexes increase their plasmatic circulation time.

Cationic liposomes have been widely sensed as good DNA compacting delivery agents. Although their use generally met with encouraging results in vitro, the results in vivo were rather disappointing, as they strongly interact with the blood components before they can reach the therapeutic target. Polyethyleneglycol (PEG) shielding has been proposed as a way to alleviate this effect, but was still found unsatisfactory in most instances for systemic administration. We demonstrate here that the insertion of anionic functions between the lipid part and the PEG, at a correct distance to favor electrostatic interactions with the outer cationic layer of the lipoplexes, provides not only a decrease in the mean peripheral charge of the lipoplex (zeta potential), but also a greater colloidal stability of the particles in the presence of serum. Transfection in the lung is also decreased with negatively charged PEG shielding, although no significant changes are observed in the tumor. This encouraging new approach should consequently be combined with active extra-cellular receptor targeting to achieve the desired delivery of the therapeutic DNA to tumor tissues.

Animals↗
PubMed2006

Inorganic nanotubes: a novel platform for nanofluidics.

Templating approaches are being developed for the synthesis of inorganic nanotubes, a novel platform for nanofluidics. Single crystalline semiconductor GaN nanotubes have been synthesized using an epitaxial casting method. The partial thermal oxidation of silicon nanowires leads to the synthesis of silica nanotubes. The dimension of these nanotubes can be precisely controlled during the templating process. These inorganic nanotubes can be integrated into metal-oxide solution field effect transistors (MOSolFETs), which exhibit rapid field effect modulation of ionic conductance. These nanofluidic devices have been further demonstrated to be useful for single-molecule sensing, as single DNA molecules can be readily detected either by charge effect or by geometry effect. These inorganic nanotubes will have great implications in subfemtoliter analytical technology and large-scale nanofluidic integration.

Chemistry, Inorganic↗
PubMed1976

On the association of reverse transcriptase with polynucleotide templates during catalysis.

The association of avian myeloblastosis virus (AMV) DNA polymerase with polynucleotide templates during catalysis has been studied. During the course of polymerization, different template-primer complexes were added and the ability of the enzyme to switch from one polynucleotide template to another was determined. At 37 degrees C as well as at 4 degrees C, the polymerase is able to switch from certain template-primer complexes to others. For example, the addition of poly(A)-oligo(dT) during the course of synthesis with poly(C)-oligo(dG) results in the immediate cessation of dGMP polymerization and the start of dTMP polymerization without any lag. Early during the course of polymerization, the size of the product, as determined by alkaline sucrose gradient centrifugation, is, in part, a function of the ratio of the template-primer complex to the enzyme. These cumulative experiments indicate that catalysis on polynucleotide templates with avian myeloblastosis virus DNA polymerase under the conditions tested is not processive in a classical sense. Similar to cellular DNA polymerases the enzyme can shift from one template-primer to another. Using autoradiography after gel electrophoresis to estimate the product size, it can be calculated that the enzyme switches from one template to another within 0.25 min at 37 degrees C which corresponds to the incorporation of greater than 25 nucleotides. At 4 degrees C, switching can be calculated to occur in less than three nucleotide addition steps. Thus, with certain homopolymers, conditions can be found by which AMV DNA polymerase can switch from one template-primer complex to another, perhaps after each nucleotide addition step.

Avian Leukosis Virus↗
PubMed2006

Biochemical and structural domain analysis of xeroderma pigmentosum complementation group C protein.

XPC is a 940-residue multidomain protein critical for the sensing of aberrant DNA and initiation of global genome nucleotide excision repair. The C-terminal portion of XPC (residues 492-940; XPC-C) has critical interactions with DNA, RAD23B, CETN2, and TFIIH, whereas functional roles have not yet been assigned to the N-terminal portion (residues 1-491; XPC-N). In order to analyze the molecular basis for XPC function and mutational defects associated with xeroderma pigmentosum (XP) disease, a series of stable bacterially expressed N- and C-terminal fragments were designed on the basis of sequence analysis and produced for biochemical characterization. Limited proteolysis experiments combined with mass spectrometry revealed that the full XPC-C is stable but XPC-N is not. However, a previously unrecognized folded helical structural domain was found within XPC-N, XPC(156-325). Pull-down and protease protection assays demonstrated that XPC(156-325) physically interacts with the DNA repair factor XPA, establishing the first functional role for XPC-N. XPC-C exhibits binding characteristics of the full-length protein, including stimulation of DNA binding by physical interaction with RAD23B and CETN2. Analysis of an XPC missense mutation (Trp690Ser) found in certain patients with XP disease revealed that this mutation is associated with a diminished ability to bind DNA. Evidence of contributions to protein interactions from regions in both XPC-N and XPC-C along with recently recognized homologies to yeast PNGase prompted construction of a structural model of a folded XPC core. This model offers key insights into how domains from the two portions of the protein may cooperate in generating specific XPC functions.

Binding Sites↗
PubMed2001

Heat-shock protein 70 antagonizes apoptosis-inducing factor.

Heat-shock protein 70 (Hsp70) has been reported to block apoptosis by binding apoptosis protease activating factor-1 (Apaf-1), thereby preventing constitution of the apoptosome, the Apaf-1/cytochrome c/caspase-9 activation complex [1,2]. Here we show that overexpression of Hsp70 protects Apaf-1-/- cells against death induced by serum withdrawal, indicating that Apaf-1 is not the only target of the anti-apoptotic action of Hsp70. We investigated the effect of Hsp70 on apoptosis mediated by the caspase-independent death effector apoptosis inducing factor (AIF), which is a mitochondrial intermembrane flavoprotein [3,4]. In a cell-free system, Hsp70 prevented the AIF-induced chromatin condensation of purified nuclei. Hsp70 specifically interacted with AIF, as shown by ligand blots and co-immunoprecipitation. Cells overexpressing Hsp70 were protected against the apoptogenic effects of AIF targeted to the extramitochondrial compartment. In contrast, an anti-sense Hsp70 complementary DNA, which reduced the expression of endogenous Hsp70, increased sensitivity to the lethal effect of AIF. The ATP-binding domain of Hsp70 seemed to be dispensable for inhibiting cell death induced by serum withdrawal, AIF binding and AIF inhibition, although it was required for Apaf-1 binding. Together, our data indicate that Hsp70 can inhibit apoptosis by interfering with target proteins other than Apaf-1, one of which is AIF.

Animals↗
PubMed2003

A comparison of gene repair strategies in cell culture using a lacZ reporter system.

Synthetic oligonucleotides and DNA fragments of less than 1 kilobase (kb) have been shown to cause site-specific genetic alterations in mammalian cells in culture and in vivo. We have used a lacZ reporter gene system to compare the efficiency of episomal and chromosomal gene repair in human embryonic kidney epithelial cells (HEK293), Chinese Hamster Ovary fibroblasts (CHOK1), human bronchial epithelial cells (16HBE), and mouse embryonic stem (ES) cells. The lacZ gene contains a G to A nucleotide change, (Glu to Lys mutation) that abrogates beta-galactosidase activity. We compared the efficiency of different gene repair methods to correct this mutation and restore beta-galactosidase activity. We evaluated PCR-generated double-stranded DNA fragments of 0.52-1.9 kb, single-stranded DNA oligonucleotides of 20, 35, or 80 bases containing internal phosphorothioate links, and a 68 base RNA:DNA oligonucleotide. All of the oligonucleotides and DNA fragments showed some gene repair ability with an episomal plasmid. Short DNA fragments of 0.52 kb or greater gave the highest frequencies of episomal gene repair while single-stranded DNA oligonucleotides gave the highest frequency of chromosomal repair. In the context of a chromosomal target, antisense DNA oligonucleotides gave 5-fold higher frequencies of gene repair than their sense counterparts. The RNA:DNA chimeric oligonucleotide gave little or no gene repair on either a chromosomal or episomal target.

Blotting, Southern↗
PubMed2003

The alpha2 and alpha3 integrins are required for morphologic differentiation of an intestinal epithelial cell line.

BACKGROUND: The molecular mechanisms controlling intestinal epithelial cell differentiation are poorly defined because of the difficulty of growing normal intestinal cells. We have taken advantage of the ability of the Caco-2 cell line to acquire a glandular phenotype in 3-dimensional (3-D) culture systems to investigate the role of alpha2 and alpha3 integrins in morphologic differentiation. METHODS: Caco-2 cells transfected with sense or antisense DNA constructs of alpha2 or alpha3 integrins were grown in 3-D Matrigel or collagen I in the presence or absence of integrin function-blocking antibodies. We used light and confocal microscopy, BrDU incorporation, TUNEL assay, a fluorometric adhesion assay, FACS analysis, and Western blot analysis to study the effect of extracellular matrix (ECM) and integrins on morphology, polarization, proliferation, apoptosis, cell adhesion, and integrin expression. RESULTS: Compared to collagen I, Caco-2 cells cultured in 3-D Matrigel display cytoskeletal and adherens junction rearrangements and decreased proliferation consistent with cellular differentiation. These changes, which are inhibited by alpha2 and alpha3 blocking monoclonal antibodies and alpha2 and alpha3 antisense DNA transfection, were associated with an increase in alpha3 integrin expression. CONCLUSIONS: We demonstrated that signaling through both constitutively expressed alpha2 integrin and Matrigel-induced alpha3 integrin expression is required to acquire a differentiated phenotype in Caco-2 cells.

Antibodies, Monoclonal↗
PubMed2002

Inhibition of mammalian Gq protein function by local anesthetics.

BACKGROUND: Local anesthetics have been shown to selectively inhibit functioning of Xenopus laevis Gq proteins. It is not known whether a similar interaction exists with mammalian G proteins. The goal of this study was to determine whether mammalian Gq protein is inhibited by local anesthetics. METHODS: In Xenopus oocytes, the authors replaced endogenous Gq protein with mouse Gq (expressed in Sf9 cells using baculovirus vectors). Cells endogenously expressing lysophosphatidic acid or recombinantly expressing muscarinic m3 receptors were injected with phosphorothioate DNA antisense (or sense as control) oligonucleotides against Xenopus Gq. Forty-eight hours later, oocytes were injected with purified mouse Gq (5 x 10(-8) M) or solvent as control. Two hours later, the authors injected either lidocaine, its permanently charged analog QX314 (at IC50, 50 nl), or solvent (KCl 150 mM) as control and measured Ca-activated Cl currents in response to lysophosphatidic acid or methylcholine (one tenth of EC50). RESULTS: Injection of anti-Gq reduced the mean response size elicited by lysophosphatidic acid to 33 +/- 7% of the corresponding control response. In contrast, responses were unchanged (131 +/- 29% of control) in cells in addition injected with mouse Gq protein. Injection of mouse Gq protein "rescued" the inhibitory effect of intracellularly injected QX314: whereas QX314 was without effect on Gq-depleted oocytes, responses to lysophosphatidic acid after QX314 injection were inhibited to 44 +/- 10% of control response in cells in addition injected with mouse Gq protein (5 x 10(-8) M). Similar results were obtained for m3 signaling and intracellularly injected lidocaine. CONCLUSION: Inhibition of Gq function by local anesthetics is not restricted to Xenopus G proteins. Therefore, Gq should be considered as one additional intracellular target site for local anesthetics, especially relevant for those effects not explainable by sodium channel blockade (e.g., antiinflammatory effects).

Anesthetics, Local↗
PubMed2003

Extensive exon reshuffling over evolutionary time coupled to trans-splicing in Drosophila.

The relative position of exons in genes can be altered only after large structural mutations. These mutations are frequently deleterious, impairing transcription, splicing, RNA stability, or protein function, as well as imposing strong inflexibility to protein evolution. Alternative cis- or trans-splicing may overcome the need for genomic structural stability, allowing genes to encode new proteins without the need to maintain a specific exon order. Trans-splicing in the Drosophila melanogaster modifier of mdg4 (mod[mdg4]) gene is the best documented example in which this process plays a major role in the maturation of mRNAs. Comparison of the genomic organization of this locus among several insect species suggests that the divergence between the lineages of the mosquito Anopheles gambiae and D. melanogaster involved an extensive exon rearrangement, requiring >11 breakpoints within the mod(mdg4) gene. The massive reorganization of the locus also included the deletion or addition of a new function as well as exon duplications. Whereas both DNA strands are sense strands in the Drosophila gene, the coding region in mosquito lays in a single strand, suggesting that trans-splicing may have originated in the Drosophila lineage and might have been the triggering factor for such a dramatic reorganization.

Amino Acid Sequence↗
PubMed2006

Expression and function of Toll-like receptor 9 in severely injured patients prone to sepsis.

The purpose of this prospective study was to enumerate Toll-like receptor 9 (TLR9)(+) cells and measure their function using synthetic oligonucleotides enriched in CG dinucleotide motifs (CpG)-induced proliferation within 48 h after trauma in severely injured patients prone to sepsis. Sixteen consecutive trauma patients with an injury severity score (ISS) > 21 and 16 blood donors (controls) were included in this study. Using two-colour flow cytometry, TLR9 expression was detectable intracellularly and also on the surface of B lymphocytes. The surface expression of TLR9 of B lymphocytes from whole blood and peripheral blood mononuclear cells (PBMC) stimulated with CpG was significantly increased in B cells of severely injured patients prone to sepsis compared to controls. No significant differences could be observed between CpG-induced proliferation of PBMC of severely injured patients prone to sepsis and controls. As a measure of immunosuppression, human leucocyte antigen (HLA)-DR expression of monocytes of the trauma patients was significantly diminished compared with controls in PBMC and in whole blood. Immunosuppression in the early phase after trauma seems not to be associated with a disturbed sensing of bacterial DNA.

Adult↗
PubMed1994

ANTISENSE oligonucleotides: a new tool in neuroscience.

1. Recent studies have shown that gene expression can be selectively attenuated by administration of short sequences of nucleotides (oligonucleotides) that are complementary to a portion of messenger RNA coding for a particular gene product. 2. This technique is known as ANTISENSE, because the oligonucleotides are complementary to the mRNA which has the same sequence as the SENSE strand of DNA. 3. In the present review we focus, after a brief discussion of gene expression and mechanisms of action of ANTISENSE, on the methodological aspects of ANTISENSE experiments in neuroscience. In particular, we address the advantages, disadvantages and controls for the ANTISENSE technique, as well as the choice, design, mode of delivery, dose and storage of ANTISENSE oligonucleotides.

Animals↗
PubMed1964

RNA CODEWORDS AND PROTEIN SYNTHESIS. THE EFFECT OF TRINUCLEOTIDES UPON THE BINDING OF SRNA TO RIBOSOMES.

A rapid, sensitive method is described for measuring C(14)-aminoacyl-sRNA interactions with ribosomes which are specifically induced by the appropriate RNA codewords prior to peptide-bond formation. Properties of the codeword recognition process and the minimum oligonucleotide chain length required to induce such interactions are presented. The trinucleotides, pUpUpU, pApApA, and pCpCpC, but not dinucleotides, specifically direct the binding to ribosomes of phenylalanine-, lysine-, and proline-sRNA, respectively. Since 5'-terminal, 3'-terminal, and internal codewords differ in chemical structure, three corresponding classes of codewords are proposed. The recognition of each class in this system is described. The template efficiency of trinucleotide codewords is modified greatly by terminal phosphate. Triplets with 5'-terminal phosphate are more active as templates than triplets without terminal phosphate. Triplets with 3'- or 3' (2')-terminal phosphate are markedly less active as templates. These findings are discussed in relation to the probable functions of terminal codewords. The modification of RNA and DNA codewords, converting sense into missense or nonsense codewords, is suggested as a possible regulatory mechanism in protein synthesis.

Adenine Nucleotides↗
PubMed1998

A matter of life and cell death.

In multicellular organisms, mutations in somatic cells affecting critical genes that regulate cell proliferation and survival cause fatal cancers. Repair of the damage is one obvious option, although the relative inconsequence of individual cells in metazoans means that it is often a "safer" strategy to ablate the offending cell. Not surprisingly, corruption of the machinery that senses or implements DNA damage greatly predisposes to cancer. Nonetheless, even when oncogenic mutations do occur, there exist potent mechanisms that limit the expansion of affected cells by suppressing their proliferation or triggering their suicide. Growing understanding of these innate mechanisms is suggesting novel therapeutic strategies for cancer.

Animals↗