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At least 109 records · Page 6Linked to original sources

E-cadherin expression: a counterbalance for cancer cell invasion.

Invasion, eventually leading to metastasis, is presented as the result of a balance between the activation of 2 sets of genes, coined i+ (invasion promotor) and i- (invasion suppressor) genes. Experiments in vitro have indicated that the homotypic homophilic epithelial cell--cell adhesion molecule E-cadherin (L-CAM; uvomorulin; cell CAM 120/80; Arc-1; rrl antigen) is an i- gene product. In several cell families, manipulation of E-cadherin at the level of the protein by antibody-mediated inactivation, at the level of the mRNA by antisense DNA transfection, and at the level of the genome by sense DNA transfection respectively resulted in induction and suppression of invasiveness. Nude mouse tumors from non-invasive homogeneously E-cadherin-positive cell populations were found to be invasive and metastatic. These tumors expressed E-cadherin in a heterogeneous manner, the undifferentiated cells being negative; but tumor-derived cells in culture were again E-cadherin-positive, indicating downregulation of this protein by host factors. Several types of human cancers showed a similar heterogeneity suggesting a relationship between downregulation of E-cadherin and invasion. Our current research focus is on the factors responsible for E-cadherin downregulation in experimental and human cancers.

Animals↗

DNA and protein polymorphism: application to anthropology and human genetics.

In this paper, the author analyses the different approaches of the DNA polymorphism. Mitochondrial DNA, RFLP haplotypes associated with serum protein polymorphism, variability of some small regions of the genome detected by minisatellite probes are now well developed and often adapted to population analysis. The data gathered are used to build phylogenic or genealogic trees. Despite the limited number sampled in these investigations, it is obvious that they were obtained to establish a beginning of geographical map distribution of the DNA polymorphisms and to answer basic questions in Anthropology. In this sense, DNA polymorphism is a new way to obtain a large amount of information not available through the different polymorphisms previously performed. Today, the interpretation of the data on DNA polymorphism is based on archeological and prehistorical hypotheses. It is highly probable that for a long time, no phylogenic analysis will be able to determine the step of speciation, the period of emergence of primitive man and of his geographical origins. In some fields of anthropological investigations, studies on the DNA structure and organisation may bring new information on the genetic of skin pigmentation, eye and hair colours, body size, etc. But the essential aim of studies on humans cannot exist out of multidisciplinary follow up including sociology, biology, linguistics, behaviour and economy. Molecular biology of DNA is an additional method from which we can learn a lot about human genetic heterogeneity but man is a group, a society, a population, a tribe and not a certain amount of allele frequencies.

Anthropology, Physical↗

Replication protein A-mediated recruitment and activation of Rad17 complexes.

The human Rad17-Rfc2-5 and Rad9-Rad1-Hus1 complexes play crucial roles in the activation of the ATR-mediated DNA damage and DNA replication stress response pathways. In response to DNA damage, Rad9 is recruited to chromatin in a Rad17-dependent manner in human cells. However, the DNA structures recognized by the Rad17-Rfc2-5 complex during the damage response have not been defined. Here, we show that replication protein A (RPA) stimulates the binding of the Rad17-Rfc2-5 complex to single-stranded DNA (ssDNA), primed ssDNA, and a gapped DNA structure. Furthermore, RPA facilitates the recruitment of the Rad9-Rad1-Hus1 complex by the Rad17-Rfc2-5 complex to primed and gapped DNA structures in vitro. These findings suggest that RPA-coated ssDNA is an important part of the structures recognized by the Rad17-Rfc2-5 complex. Unlike replication factor C (RFC), which uses the 3' primer/template junction to recruit proliferating cell nuclear antigen (PCNA), the Rad17-Rfc2-5 complex can use both the 5' and the 3' primer/template junctions to recruit the Rad9-Rad1-Hus1 complex, and it shows a preference for gapped DNA structures. These results explain how the Rad17-Rfc2-5 complex senses DNA damage and DNA replication stress to initiate checkpoint signaling.

Cell Cycle Proteins↗

DNA polymerase epsilon may be dispensable for SV40- but not cellular-DNA replication.

The contributions of DNA polymerases alpha, delta, and epsilon to SV40 and nuclear DNA syntheses were evaluated. Proteins were UV-crosslinked to nascent DNA within replicating chromosomes and the photolabelled polymerases were immunopurified. Only DNA polymerases alpha and delta were detectably photolabelled by nascent SV40 DNA, whether synthesized in soluble viral chromatin or within nuclei isolated from SV40-infected cells. In contrast, all three enzymes were photolabelled by the nascent cellular DNA. Mitogenic stimulation enhanced the photolabelling of the polymerases in the alpha>delta>epsilon order of preference. The data agree with the notion that DNA polymerases alpha and delta catalyse the principal DNA polymerisation reactions at the replication fork of SV40 and, perhaps, also of nuclear chromosomes. DNA polymerase epsilon, implicated by others as a cell-cycle checkpoint regulator sensing DNA replication lesions, may be dispensable for replication of the small, fast propagating virus that subverts cell cycle controls.

Animals↗

Base mutation analysis by a ferrocenyl naphthalene diimide derivative.

An electrochemical DNA sensing technique was developed by using ferrocenyl naphthalene diimide coupled with a probe DNA-immobilized electrode. This technique enabled detection of target DNA quickly and with high sensitivity. Applicability of this technique for single nucleotide polymorphisms (SNPs) analysis was demonstrated by successful analysis of a DNA mismatch on the cancer repression gene p53 with high precision.

DNA↗

Antisense targeting of p-glycoprotein expression in tissue culture.

UNLABELLED: Radiolabeled DNA and other oligomers are now under investigation for antisense targeting of a variety of messenger RNA (mRNA). Multidrug resistance (MDR) is detectable as P-glycoprotein (Pgp) expression in most cells and is often elevated in tumor cells, especially those exposed to chemotherapeutic drugs. Radiolabeled antisense DNA has not previously been considered for the targeting of mdr1 mRNA, the product of the mdr1 gene controlling Pgp expression of MDR. METHODS: A 20-mer uniform phosphorothioate DNA, described elsewhere as targeting the AUG start codon of mdr1 mRNA, was used naked along with the sense phosphorothioate DNA control. The 3 cell lines were KB-G2, an epidermal carcinoma cell line that had been transfected to overexpress mdr1 mRNA (i.e., Pgp++) compared with its parent (Pgp+) KB-31, and TCO-1, a thyroid carcinoma cell line also reported to be Pgp++. The relative expression of mdr1 mRNA in these 3 cell lines was confirmed elsewhere by reverse transcriptase polymerase chain reaction. As a marker of Pgp expression, the uptake of (99m)Tc-sestamibi was measured in the 3 cell lines after 20 h of incubation with different concentrations of both antisense and sense DNA. Both DNAs were radiolabeled with (99m)Tc via mercaptoacetyltriglycine, and cellular uptake was measured after 24 h of incubation. RESULTS: In the case of the sense DNA, the ratio of sestamibi uptake in cells incubated with the DNA to those not exposed to the DNA was unaffected regardless of cell line and regardless of DNA concentration. In contrast, this ratio was significantly higher in both the KB-G2 and TCO-1 cells when incubated with antisense DNA at concentrations greater than about 25 nmol/L (i.e., 150 ng/mL). Only in the KB-31 cells was the sestamibi accumulation unaffected by incubation with the antisense DNA. Thus, the antisense DNA was interfering with Pgp expression to a measurable extent in both Pgp++ cells, but not the Pgp+ cells. This behavior is almost certainly due to antisense targeting of mdr1 mRNA by the antisense DNA since the sense control DNA had no effect. A significant increased accumulation of (99m)Tc-antisense versus (99m)Tc-sense DNA was observed in all 3 cell lines. In all cases, this difference was greatest at the lowest DNA concentrations and decreased with increasing concentration as expected for specific binding. In the KB-G2 cells, cellular accumulation of (99m)Tc-antisense DNA was strikingly high at the lowest concentration at 54%, compared with 22% for (99m)Tc-sense DNA. These accumulations therefore probably reflect the higher mRNA target concentration in the MDR++ cells than in the MDR+ cells and the higher specific binding of (99m)Tc-antisense DNA than nonspecific binding of (99m)Tc-sense DNA. CONCLUSION: Further evidence was obtained suggesting that an antisense mechanism is responsible for the accumulation of (99m)Tc-oligomers in cells in culture. Finally, whereas evidence of in vitro targeting is not necessarily evidence of in vivo targeting, our results do suggest that radiolabeled antisense DNA against the mdr1 mRNA may potentially be useful for antisense imaging of MDR in cancer.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Mutation analysis of the DNA-damage checkpoint gene CHK2 in myelodysplastic syndromes and acute myeloid leukemias.

Checkpoint genes code for a family of proteins which sense DNA damage in eukaryotic cells. They play an important role in the control of the cell cycle. The human CHK2 is a homolog of the yeast G(2) checkpoint kinases known as CDS1 and RAD53. The CHK2 may be a tumor suppressor gene because it was found to be mutated in some individuals with the Li-Fraumeni syndrome. These cases had a normal, non-mutated p53 gene. We performed a mutational analysis of the CHK2 gene using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) in 41 bone marrow samples from individuals with myelodysplastic syndrome (MDS) and 41 samples of acute myeloid leukemias (AML). We found a novel G to C transversion resulting in a change from Ala to Gly at codon 507 of CHK2 in one MDS sample, but normal cells from this individual did not have the abnormality. In addition, we demonstrated a previously described polymorphism at codon 84 (A to G at nucleotide 252) of exon 1 of CHK2 in three of 41 MDS and three of 41 AML patients. The presence of a CHK2 mutation in MDS highlights the importance of alterations of cell cycle checkpoint genes in this disease.

Acute Disease↗

Molecular aspects of cellular responses to radiotherapy.

Advances have been made in unravelling the molecular chains of cause and effect that determine cellular responses to radiotherapy, including cell cycle arrest, DNA repair and apoptosis. To begin with, cells must have mechanisms that enable them to sense DNA damage. Little was known about this until recently, when a DNA-protein kinase (DNA-PK) system for detecting radiation-induced strand breaks was described. The ataxia telangiectasia (ATM) gene has amino acid sequence similarities to DNA-PK, raising the possibility that the ATM protein also functions in some way as a sensor of DNA damage. However, just knowing the DNA damage is present is not enough. Signals must be transmitted via afferent biochemical pathways to proteins, such as p53, that determine which cellular responses are activated. The responses include cell cycle arrest, apoptosis and DNA repair, all of which relate closely to loss of clonogenic capacity and the outcome of treatment in our patients.

Animals↗

Direct detection of DNA with an electrocatalytic threading intercalator.

Herein we report the synthesis, intercalating properties, and analytical applications of an imidazole-substituted naphthalene diimide, N,N'-bis(3-propylimidazole)-1,4,5,8-naphthalene diimide (PIND), functionalized with electrocatalytic redox moieties. PIND was prepared in a single-step reaction from the corresponding dianhydride. Attachment of the redox moieties to PIND relied upon ligand exchange with one of the liable chloride ligands of an Os(bpy)2Cl2 (bpy = 2,2'-bipyridine) complex. The Os(bpy)2Cl2 complex was grafted onto PIND through coordinative bonds with the two imidazole groups at its termini, forming a PIND-[Os(bpy)2Cl]+ compound (PIND-Os). Gel electrophoretic studies revealed that PIND-Os binds more strongly to double-stranded DNA (ds-DNA) than its parent compound 1,4,5,8-naphthalene diimide. The naphthalene diimide group binds to ds-DNA in a "classical" threading intercalation mode, while the two Os(bpy)2Cl+ pendants interact with DNA via electrostatic interaction, reinforcing the intercalation by "locking up" the naphthalene diimide group in place. An electrochemical biosensor was fabricated using the redox-active and catalytic PIND-Os intercalator. An increase in sensitivity of 2500-fold over direct voltammetry was obtained in electrocatalytic amperometry, making this an interesting system for amperometric DNA sensing. Under optimized experimental conditions, the biosensor allowed the detection of a 50-mer target DNA in the range of 1.0-300 pM with a detection limit of 600 fM (1.5 amol, 23 fg).

Biosensing Techniques↗

Molecular characterization of a distinct begomovirus species and its associated satellite DNA isolated from Malvastrum coromandelianum in China.

A virus isolate Y160 was obtained from Malvastrum coromandelianum showing yellow vein symptoms in Baoshan, Yunnan province of China. The complete nucleotide sequence of DNA-A was determined, it contains 2747 nucleotides and has typical genomic organization of a begomovirus. Comparisons show that the total DNA-A of Y160 has the highest sequence identity (82.2%) with that of Malvastrum yellow vein virus-[Y47] (AJ457824), while less than 77.6% identities are found when compared with the other begomoviruses. The molecular data show that Y160 is a distinct begomovirus species, for which the name Malvastrum yellow vein Yunnan virus (MYVYNV) is proposed. Satellite DNA molecule (Y160beta) was found to be associated with Y160 using the abutting primers beta 0l and beta 02 specific for DNA beta. Y160beta consists of 1350 nucleotides, with a functional ORF (beta C1) in complementary-sense DNA. Y160beta has the highest sequence identity (73.5%) with DNA beta molecule associated with Malvastrum yellow vein virus-[Y47] (AJ421482).

Begomovirus↗

Peroxynitrite-induced cytotoxicity: mechanism and opportunities for intervention.

Peroxynitrite is formed in biological systems when superoxide and nitric oxide are produced at near equimolar ratio. Although not a free radical by chemical nature (as it has no unpaired electron), peroxynitrite is a powerful oxidant exhibiting a wide array of tissue damaging effects ranging from lipid peroxidation, inactivation of enzymes and ion channels via protein oxidation and nitration to inhibition of mitochondrial respiration. Low concentrations of peroxynitrite trigger apoptotic death, whereas higher concentrations induce necrosis with cellular energetics (ATP and NAD) serving as switch between the two modes of cell death. Peroxynitrite also damages DNA and thus triggers the activation of DNA repair systems. A DNA nick sensor enzyme, poly(ADP-ribose) polymerase-1 (PARP-1) also becomes activated upon sensing DNA breakage. Activated PARP-1 cleaves NAD(+) into nicotinamide and ADP-ribose and polymerizes the latter on nuclear acceptor proteins. Peroxynitrite-induced overactivation of PARP consumes NAD(+) and consequently ATP culminating in cell dysfunction, apoptosis or necrosis. This cellular suicide mechanism has been implicated among others in the pathomechanism of stroke, myocardial ischemia, diabetes and diabetes-associated cardiovascular dysfunction. Here, we review the cytotoxic effects (apoptosis and necrosis) of peroxynitrite focusing on the role of accelerated ADP-ribose turnover. Regulatory mechanisms of peroxynitrite-induced cytotoxicity such as antioxidant status, calcium signalling, NFkappaB activation, protein phosphorylation, cellular adaptation are also discussed.

Animals↗

BTG gene expression in the p53-dependent and -independent cellular response to DNA damage.

Exposure of mammalian cells to genotoxic agents evokes a complex cellular response. An ordered series of molecular events is necessary to sense DNA damage, transduce the signal, and ultimately delay the cell cycle or trigger apoptosis. Recently, we have shown that BTG2/TIS21 gene expression was induced in response to DNA damage through a p53-dependent pathway. This gene belongs to a newly identified family of structurally related genes whose other known human members are BTG1, BTG3, and Tob. To define the respective involvement of these four related genes in the cellular response to DNA damage, we studied their expression in human cell lines after a variety of genotoxic treatments. Our results demonstrated that were BTG1, BTG2/TIS21, and Tob genes the DNA damage--inducible genes. However, BTG2/TIS21 appeared to be the only p53-transcriptional target gene. We speculate that BTG proteins may play a coordinate role in a general transduction pathway that is induced in response to DNA damage. It has been previously described that recombinant BTG1 and BTG2/TIS21 can physically interact with PRMT1, an arginine methyl transferase, suggesting that BTG1 and BTG2/TIS21 induction may lead to posttranslational modifications of cellular proteins. In support of this hypothesis, we showed that the endogenous induction of BTG1 and BTG2 after genotoxic treatment was correlated with a modulation of protein methylation.

Animals↗

The DNA damage response: sensing and signaling.

The protein kinases ATM and ATR are central components of the checkpoint mechanisms that signal the presence of damaged DNA and stalled replication forks. Recent studies have provided important new insights into how these kinases work together with their regulatory subunits, DNA repair proteins and adaptor proteins to sense abnormal DNA structures and implement the appropriate DNA damage response. These advances have provided a more detailed understanding of the interface between damaged DNA and the checkpoint sensor proteins.

Animals↗

Ku protein stimulates DNA end joining by mammalian DNA ligases: a direct role for Ku in repair of DNA double-strand breaks.

Ku protein binds to DNA ends and is a cofactor for the DNA-dependent protein kinase. Both of these components are involved in DNA double-strand break repair, but it has not been clear if they function indirectly, by sensing DNA damage and activating other factors, or if they are more directly involved in the processing and rejoining of DNA breaks. We demonstrate that intermolecular ligation of DNA fragments is highly dependent on Ku under conditions designed to mimic those existing in the cell. This effect of Ku is specific to eukaryotic DNA ligases. Ku protein, therefore, has an activity consistent with a direct role in rejoining DNA breaks and independent of DNA-dependent protein kinase.

Antigens, Nuclear↗

Development of a novel sensing probe using DNA aptamer inhibiting enzymatic activity.

A novel sensing probe for adenosine has been developed using the thrombin-inhibiting DNA aptamer fused with the adenosine-binding DNA aptamer. The adenosine aptamer was inserted into the G-quartet structure of the thrombin aptamer to change its inhibitory activity to thrombin upon binding of the adenosine aptamer part to adenosine. This designed aptamer had lower inhibitory activity than that of the original thrombin aptamer, and it was increased in the presence of adenosine. CD spectra of this designed aptamer indicated that its structure was changed by its binding to adenosine. Using this designed aptamer, we were able to detect adenosine by measuring thrombin activity in homogeneous assay.

Adenosine↗

Evidence for a bidirectional promoter complex within the X gene of woodchuck hepatitis virus.

The genetic organization of hepadnaviruses is unusual in that all cis-acting regulatory sequences are located within genes. Thus, in the mammalian hepadnavirus genome, the presurface, surface, and X transcript promoters reside within the polymerase gene while the pregenome transcript promoter is located within the X gene. In this study we have identified two additional promoters within the woodchuck hepatitis virus (WHV) X gene that stimulate production of transcripts in vitro. First, we cloned regions of the WHV X gene into a promoterless expression vector (pGL2) to examine their ability to promote expression of firefly luciferase and mapped a previously unidentified promoter to positions 1475-1625 of the WHV8 genome. Deletion analysis revealed that the essential domain of this promoter, termed the ORF5/deltaX transcript promoter, mapped to nucleotides 1525-1625. Analysis revealed that this transcript initiated at nucleotide 1572 in both human (HuH-7) and woodchuck (WLC-3) hepatoma cell lines. Consistent with this finding, DNA footprinting analysis revealed protection of nucleotides 1567-1578 on the positive strand of the WHV8 genome. The function of this transcript in vivo is unclear, however, it may be used to produce a truncated form of the X protein that initiates at an AUG codon at position 1743-1745 on the WHV8 genome. Next, a second promoter was identified at positions 1625-1975 that was responsible for production of an antisense transcript. The activity of this promoter was comparable to that of the previously characterized surface transcript promoter of WHV in the absence of an enhancer. The antisense transcript promoter resides immediately upstream of open reading frame (ORF) 6, a previously identified ORF on the strand opposite of the known WHV protein-encoding sequences, that is thought to represent a vestigial gene. Analysis indicates that the antisense transcript had multiple start sites: nucleotides 1683 and 1762 on the WHV8 genome when assayed in HuH-7 cells, and nucleotide 1786 when assayed in WLC-3 cells. These data are consistent with footprinting analysis of supercoiled WHV DNA that revealed that the regions encompassing nucleotides 1696-1685, 1781-1766, and 1801-1787 on the negative sense DNA strand were protected from nuclease degradation. It is possible that such a transcript was once used in protein expression in an ancestral virus and may now be used for genetic control of WHV replication and/or gene expression. Overall, these data are consistent with the presence of a bidirectional promoter complex within the WHV X gene.

Animals↗

DNA biosensor for detection of Helicobacter pylori using phen-dione as the electrochemically active ligand in osmium complexes.

A surface-based method for the study of the interactions of DNA with redox-active 1,10-phenantroline-5,6-dione (phen-dione) osmium complexes is described. The study was carried out using gold electrodes modified with DNA via adsorption and [Os(bpy)(2)(phe-dione)](3+/2+) (bpy = 2,2'-bipyridyl) or [Os(phen)(2)(phen-dione)](3+/2+) (phen = 1,10-phenantroline) as electrochemical reported molecules. The method, which is simple and reagent-saving, allows the accumulation of osmium complexes within the DNA layer. The amount of osmium complex bound by the adsorbed layer of DNA was determined from the voltammetric charge associated with the osmium redox process of the immobilized metal complex. The quinone moiety of the phen-dione ligand was useful as an indicator for electrochemical DNA sensing because of its redox response at low potentials. A thiol-linked single-stranded Helicobacter pylori DNA probe was immobilized, through S-Au bonds on to a gold electrode (density of modification 86 pmol/cm(2)). Following hybridization with the complementary DNA sequence, the osmium complex was electrochemically accumulated within the double-stranded DNA layer. Electrochemical detection was performed by differential pulse voltammetry over the potential range where the quinone moiety was redox active (i.e., at very low potentials, -0.020 V vs SSCE); with this approach, a sequence of the H. pylori could be quantified over the range from 5 to 20 pmol with a linear correlation of r = 0.9888 and a detection limit of approximately 6 pmol.

Biosensing Techniques↗

Cloning and characterization of a transcription termination signal in bacteriophage lambda unresponsive to the N gene product.

The pHA10 plasmid was designed for the cloning and selection of transcriptional termination signals. This study demonstrates the use of pHA10 as a cloning vehicle in the selection and characterization of an N-unresponsive terminator. Following the random cloning of lambda DNA, and N-unresponsive transcription terminator was isolated. Hybridization of in vivo 32P-labeled RNA to various DNA fragments, using the Southern (1975) blotting technique, revealed that the transcriptional barrier that cannot be overridden in the presence of N is located close to the end of gene J of lambda DNA. The terminator determines the 3'-end of the pL operon and prevents the transcription of the anti-sense DNA strand of lambda late genes. The primary structure and other characteristics of this terminator are now under investigation.

Bacteriophage lambda↗