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PubMed1976

Deletion mapping of moloney type C virus: polypeptide and nucleic acid expression in different transforming virus isolates.

The viral polypeptides and viral RNA present in cells transformed by various replication-defective type C viruses derived from Maloney murine leukemia virus were examined. Different portions of the Maloney type C viral genome were retained in the different transforming viruses, thus providing an opportunity for deletion mapping of the Moloney type C genome. DNA transcripts were prepared that are complementary to three distinct nonoverlapping portions of the Moloney viral geonome. Based on an anlysis of the polypeptides produced in the different transformed cells, one complementary DNA apparently respresents sequences coding for Moloney gp70; one complementary DNA represents a region of the Moloney genome common to all of the transforming viruses examined, and one complementary DNA represents the sequences for p30, p15, p10,12. A partial map of the different replication-defective transforming viruses is suggested.

Antigens, Viral↗

PubMed1997

Dissociation of non-complementary second DNA from RecA filament without ATP hydrolysis: mechanism of search for homologous DNA.

RecA protein catalyzes the DNA annealing and mimics the DNA strand exchange reaction in vitro in the presence of ATP or its non-hydrolyzable analog, adenosine 5'-O-3-thiotriphosphate (ATPgammaS). For these activities RecA coordinates two DNA molecules [Takahashi, M. and Nordén, B. (1994) Adv. Biophys. 30, 1-35]. In order to get a better understanding of how RecA performs the search for sequence complementarity or homology between two DNA molecules, the association and dissociation kinetics of a second DNA molecule to and from RecA in the presence of ATPgammaS have been investigated. The kinetics were monitored by fluorescence measurements of partly etheno-modified poly(dA) assisted by linear dichroism measurements of the flow-oriented complex. The association of the second DNA is fast, regardless of whether the sequence is complementary or not. By contrast, the dissociation kinetics is strongly dependent on sequence complementarity. If the second DNA is complementary to the first, dissociation is extremely slow, whilst that of non-complementary second DNA is fast. In no case does the first DNA leave the RecA fiber. Our findings indicate that the dissociation step is important in the search for homology by RecA.

Adenosine Triphosphate↗

PubMed1989

Enzymatic synthesis of DNA probes complementary to a human variable number tandem repeat locus.

Both cloned and synthetic DNA probes complementary to human variable number tandem repeat (VNTR) loci have been used to detect restriction fragment length polymorphism. In this report, we describe an approach for the enzymatic synthesis of a DNA probe complementary to one VNTR locus. The probe is produced by annealing short synthetic oligonucleotides comprising single repeat units and enzymatically ligating them into a polymeric DNA probe. In HinfI digests of human genomic DNA separated by agarose gel electrophoresis, this ligated oligonucleotide probe (LOP) detects multiple polymorphic loci in the range of 3-23 kb producing highly informative DNA fingerprint patterns when different individuals are compared. The hybridization pattern is very stable even under high-stringency wash conditions. The LOP is more easily generated than cloned VNTR probes and is totally synthetic, avoiding problems associated with cloned probes including bacterial growth and maintenance as well as in vitro labeling.

Autoradiography↗

PubMed1985

Molecular cloning of DNA sequences complementary to rat liver glucose-6-phosphate dehydrogenase mRNA. Nutritional regulation of mRNA levels.

The nutritional regulation of rat liver glucose-6-phosphate dehydrogenase was studied using a cloned DNA complementary to glucose-6-phosphate dehydrogenase mRNA. The recombinant cDNA clones were isolated from a double-stranded cDNA library constructed from poly(A+) RNA immunoenriched for glucose-6-phosphate dehydrogenase mRNA. Immunoenrichment was accomplished by adsorption of polysomes with antibodies directed against glucose-6-phosphate dehydrogenase in conjunction with protein A-Sepharose and oligo(dT)-cellulose chromatography. Poly(A+) RNA encoding glucose-6-phosphate dehydrogenase was enriched approximately 20,000-fold using these procedures. Double-stranded cDNA was synthesized from the immunoenriched poly(A+) RNA and inserted into pBR322 using poly(dC)-poly(dG) tailing. Escherichia coli MC1061 was transformed, and colonies were screened for glucose-6-phosphate dehydrogenase cDNA sequences by differential colony hybridization. Plasmid DNA was purified from clones which gave positive signals, and the identity of the glucose-6-phosphate dehydrogenase clones was verified by hybrid-selected translation. A collection of glucose-6-phosphate dehydrogenase cDNA plasmids with overlapping restriction maps was obtained. Northern blot analysis of rat liver poly(A+) RNA using nick-translated, 32P-labeled cDNA inserts revealed that the glucose-6-phosphate dehydrogenase mRNA is 2.3 kilobases in length. RNA blot analysis showed that refeeding fasted rats a high carbohydrate diet results in a 13-fold increase in the amount of hybridizable hepatic glucose-6-phosphate dehydrogenase mRNA which parallels the increase in enzyme activity. These results suggest that the nutritional regulation of hepatic glucose-6-phosphate dehydrogenase occurs at a pretranslational level.

Animals↗

PubMed1995

Immunocytochemical localization of the striatal enriched protein tyrosine phosphatase in the rat striatum: a light and electron microscopic study with a complementary DNA-generated polyclonal antibody.

The present study concerns the immunocytochemical localization of the striatal enriched protein tyrosine phosphatase in the rat striatum. A novel molecular biology technique allowed us to produce a complementary DNA-generated polyclonal antibody raised against the non-catalytic domain of the striatal enriched protein tyrosine phosphatase, which selectively recognized the striatal enriched protein tyrosine phosphatase protein with 46,000 mol. wt on western blots. Immunocytochemical analysis with the specific antibody revealed strong striatal enriched protein tyrosine phosphatase immunoreactivity in the striatum. Light microscopy showed striatal striatal enriched protein tyrosine phosphatase-immunopositive neurons to be of medium size (mean diameter of 14.4 microns), and to comprise approximately 80% of the total neuronal population in the striatum. These cells had round, triangular or polygonal cell bodies with relatively little cytoplasm. Nerve fibers stained positively for striatal enriched protein tyrosine phosphatase were also present in the globus pallidus and the substantia nigra, and the nigral labeling on the ipsilateral side almost disappeared subsequent to cerebral hemitransection, suggesting these immunolabeled structures to be striatal projections. Double-immunofluorescence analysis demonstrated separate populations of striatal enriched protein tyrosine phosphatase-positive cells and neurons stained for parvalbumin. Also, ultrastructural study showed that the striatal enriched protein tyrosine phosphatase-positive neurons (n = 50) possessed no nuclear indentations or intranuclear inclusions. Thus, most striatal striatal enriched protein tyrosine phosphatase-positive neurons were thought to be of the medium-sized spinous type. At the light microscopic level, stained striatal neurons exhibited striatal enriched protein tyrosine phosphatase immunolabeling in their somata, dendrites and axonal processes, but not in their nuclei. Electron microscopic observation showed strong striatal enriched protein tyrosine phosphatase-immunoreactivity on the inner surface of the plasmalemma, on the outer surfaces of mitochondria and on microtubules, particularly of dendrites. A heavy deposit of immunoreaction product was also present on postsynaptic densities in labeled dendrites, while a light deposit was seen on the synaptic vesicles of nerve terminals. The characteristic distribution profile of striatal enriched protein tyrosine phosphatase suggested that the enzyme may play a role in a variety of functional properties of striatal neurons, especially in postsynaptic signaling processes and in regulation of microtubular functions. On the basis of the present findings, we propose the following conclusions: (i) a protein tyrosine phosphorylation system regulated by striatal enriched protein tyrosine phosphatase is involved in certain specialized cellular processes (e.g. signal transduction cascades) of medium-sized spinous neurons distinct from those of other neuronal subsets in the striatum; (ii) a striatal medium spiny neuron is characterized by its expression of striatal enriched protein tyrosine phosphatase and, therefore, the enzyme is useful for detection of the distinct subset of striatal cells or for tracing their axonal projection fibers in the basal ganglia.

Animals↗

PubMed2005

Supramolecular nanostamping: using DNA as movable type.

Here we present a novel printing technique (that we call supramolecular nanostamping), based on the replication of single-stranded DNA features through a hybridization-contact-dehybridization cycle. On a surface containing features each made of single-stranded DNA molecules of known sequence, the complementary DNA molecules are hybridized, spontaneously assembling onto the original pattern due to sequence-specific interactions. These complementary DNA strands, on the end that is assembled far from the original surface, are 5' modified with chemical groups ("sticky ends") that can form bonds with a target surface that is brought into contact. Heating induces dehybridization between DNA strands, leaving the original pattern on the original surface and the copied pattern on the secondary substrate, and thus stamping (see Figure 1). Molecular recognition provides the unique and disruptive ability of transferring large amounts of information in a single printing cycle, that is the simultaneous stamping of spatial information (i.e., the patterns) and of chemical information (i.e., the features' DNA sequence--their chemical composition). This method combines high resolution (<40 nm) with the advantage of an exponential increase in the number of masters; in fact, any printed substrate can be reused as a master. Patterns fabricated via very different lithographic techniques can be replicated.

DNA↗

PubMed1990

Kinetic analysis of Escherichia coli RNase H using DNA-RNA-DNA/DNA substrates.

The kinetic properties of Escherichia coli ribonuclease H (RNase H) were investigated using oligonucleotide substrates that consist of a short stretch of RNA, flanked on either side by DNA (DNA-RNA-DNA). In the presence of a complementary DNA strand, RNase H cleavage is restricted to the short ribonucleotide stretch of the DNA/RNA heteroduplex. The DNA-RNA-DNA substrate utilized for kinetic studies: (formula; see text) is cleaved at a single site (decreases) in the presence of a complementary DNA strand, to generate (dT)7-(rA)2-OH and p-(rA)2-(dT)9. Anion exchange high performance liquid chromatography was used to separate and quantitate the cleavage products. Under these conditions, RNase H-specific and nonspecific degradation products could be resolved. Kinetic parameters were measured under conditions of 100% hybrid formation (1.2-1.5 molar excess of complementary DNA, T much less than Tm). A linear double reciprocal plot was obtained, yielding a Km of 4.2 microM and a turnover number of 7.1 cleavages per s per RNase H monomer. The kinetic properties of substrate analogs containing varying lengths of RNA (n = 3-5) and 2'-O-methyl modifications were also investigated. Maximal turnover was observed with DNA-RNA-DNA substrates containing a minimum of four RNA residues. Kcat for the rA3 derivative was decreased by more than 100-fold. The Km appeared to decrease with the size of the internal RNA stretch (n = 3-5). No significant difference in turnover number of Km was observed when the flanking DNA was replaced with 2'-O-methyl RNA, suggesting that RNase H does not interact with this region of the heteroduplex.

Base Sequence↗

PubMed1992

RNA-primed complementary-sense DNA synthesis of the geminivirus African cassava mosaic virus.

The plant DNA virus African cassava mosaic virus (ACMV) is believed to replicate by a rolling circle mechanism. To investigate complementary-sense DNA (lagging strand) synthesis, we have analysed the heterogenous form of complementary-sense DNA (H3 DNA) from infected Nicotiana benthamiana by two-dimensional agarose gel electrophoresis and blot hybridisation. The presence of an RNA moeity is demonstrated by comparison of results for nucleic acids resolved on neutral/alkaline and neutral/formamide gels, suggesting that complementary-sense DNA synthesis on the virus-sense single-stranded DNA template is preceded by the synthesis of an RNA primer. Hybridisation with probes to specific parts of ACMV DNA A genome indicates that synthesis of the putative RNA primer initiates between nucleotides 2581-221, a region that includes intergenic sequences that have been implicated in geminivirus DNA replication and the control of gene expression.

DNA, Viral↗

PubMed1992

Complementary DNA-DNA hybridization in Drosophila.

We have performed DNA-DNA hybridization experiments among several species of Drosophila using the evolutionarily conserved portion of the genome representing sequences coding for amino acids of proteins. This was done by using as tracer, radioactively labeled complementary DNA that was reverse transcribed from adult mRNA. We show that this procedure extends phylogenetically the distance over which the technique can be applied to fast-evolving groups such as Drosophila. The major phylogenetic conclusions are (1) the subgenus Sophophora is a monophyletic lineage; (2) within Sophophora the melanogaster subgroup is closer to the obscura group than either group is to the willistoni group; (3) the subgenus Drosophila is complex with most major lineages originating deep in the phylogeny; the subgenus may not be monophyletic; (4) as with most groups classically placed in Drosophila, the Hawaiian Drosophila originate early, supporting the notion that this lineage is older than the extant islands; and (5) the virilis/repleta lineage is monophyletic within Drosophila.

Animals↗

PubMed1984

Haploid expression of a mouse testis alpha-tubulin gene.

A complementary DNA clone for an alpha-tubulin has been isolated from a mouse testis complementary DNA library. The untranslated 3' end of this complementary DNA is homologous to two RNA transcripts present in postmeiotic cells of the testis but absent from meiotic cells and from several tissues including brain. The temporal expression of this alpha-tubulin complementary DNA provides evidence for the haploid expression of a mammalian structural gene.

Animals↗

PubMed1974

Studies of nondefective adenovirus 2-simian virus 40 hybrid viruses. IX. Template topography in the early region of simian virus 40.

The DNAs of the five nondefective adenovirus 2 (Ad2)-simian virus 40 (SV40) hybrid viruses contain overlapping segments of the early region of wild-type SV40 DNA. The complementary DNA strands of these five viruses have been separated with synthetic polyribonucleotides in isopycnic cesium chloride gradients. The relative amounts of early and late SV40 template in the DNA of each virus were determined by RNA-DNA hybridization with late lytic SV40 RNA, which contains sequences complementary to both templates. From the distribution of early and late templates in the five overlapping SV40 segments, we conclude that either the entire early region of SV40 is symmetrically transcribed in vivo, or, more probably, that the early SV40 templates are not contiguous.

Adenoviridae↗

PubMed1975

The mitotic chromosomes of Notophthalmus (=Triturus) viridescens: localization of C banding regions and DNA sequences complementary to 18S, 28S and 5S ribosomal RNA.

The metaphase chromosomes of Notophthalmus (Triturus) viridescens have been studied by C-banding and in situ hybridization. The chromosomes show the pericentric C-banding seen in many organisms and in addition have interstitial C-bands located a short distance from the pericentric C-bands on each chromosome arm. A few C-bands are seen in telomeric regions. Regions which hybridize in situ with 18S and 28S ribosomal RNA were found on three chromosome pairs. The animals studied fell into three groups with respect to which of the six possible sites showed detectable hybridization with 18S and 28S RNA. Individual animals differed not only in the pattern of in situ hybridization of ribosomal RNA but also in the number of ribosomal RNA cistrons in the genome as measured by saturation hybridization on purified DNA. In situ hybridization showed five pairs of chromosomes which contained DNA complementary to 5S RNA. The four pairs of subtelocentric chromosomes in the N. viridescens karyotype all have 5S DNA in the pericentric regions. The fifth cluster of 5S DNA is in the middle of one arm of the chromosomes in one of the two smallest submetacentric pairs in the genome. The five sites of 5S DNA differ markedly in the level of in situ hybridization with 5S cRNA.

Animals↗

PubMed1998

Isolated lung liposome-mediated gene transfer produces organ-specific transgenic expression.

BACKGROUND: Gene therapy is a promising strategy for the treatment of inoperable pulmonary tumors and rejection after lung transplantation. However, unlike ex vivo administration, intravenous in vivo transfection lacks organ specificity and has a limited duration of expression. The objectives of this study were to limit transfection to a single lung and to increase the duration of gene expression in vivo. METHODS: Sixteen male Fisher rats were anesthetized and divided into two groups. Animals in group I (n = 7) received an intrajugular administration of 1,320 microg of chloramphenicol acetyl transferase (CAT) complementary DNA complexed with cationic liposomes. Animals in group II (n = 9) received 660 microg of CAT complementary DNA complexed with cationic liposomes into the pulmonary artery of an isolated left lung over 10 minutes. After 40 minutes of incubation, the lung was flushed with 10 mL of normal saline solution, and the perfusate was suctioned through a left pulmonary venotomy. The circulation to the left lung was then restored. After 48 hours, the animals were divided into subgroups (a and b) and CAT activity was assessed in the lungs, hearts, livers, and kidneys of groups Ia (n = 3) and IIa (n = 5). After 21 days, CAT activity was assessed in the left lungs of groups Ib (n = 4) and IIb (n = 4). RESULTS: After 48 hours, animals that had received intravenous administration of CAT cDNA showed strong expression in the lungs and hearts and negligible expression in the livers and kidneys. In contrast, animals in group IIa, which had received isolated left lung perfusion of CAT cDNA showed expression only in the left lung. After 21 days, the left lungs of animals in group Ib, which had received intravenous administration of CAT complementary DNA, showed no CAT expression, but the left lungs of animals in group IIb, which had received isolated left lung perfusion of CAT complementary DNA, exhibited strong CAT expression. CONCLUSIONS: Compared with intravenous administration, isolated lung liposome-mediated gene transfer provides prolonged organ-specific gene expression. This provides a useful model to study the effects of gene therapy on pulmonary tumors, which may have further application when gene therapy is used in clinical practice.

Animals↗

PubMed1979

Inserts within the mRNA sequence on the 15 S globin mRNA precursor from chicken.

[3H]Uridine pulse-labelled nuclear RNA of chicken immature red blood cells contains two RNA species with globin coding sequences sedimenting at 9 S and 15 S, the latter representing most probably the precursor to 9 S globin mRNA. Whether the globin mRNA sequence on the 15 S precursor is interrupted by interspersed sequences was investigated by hybridization of labelled nuclear 15 S RNA with an excess of unlabelled globin complementary DNA. After degradation of nonhybridized RNA by RNAase A the enzyme was removed by proteinase K and a subsequent phenol extraction. The complementary DNA hybrids were melted and the complementary DNA degraded by DNAase I. For the separation of complementary DNA protected RNA polyacrylamide gel electrophoresis in formamide was used. Three RNA fragments with approximately 320, 200 and 120 nucleotides were found in the case of the 15 S RNA, whereas only one 650-700 nucleotide fragment was detected when the same procedure was carried out with nuclear 9 S RNA. This means, that the chicken 15 S globin mRNA precursor contains at least two inserts within the mRNA sequence, which originate presumably by transcription of a gene with intervening sequences.

Animals↗

PubMed1989

A mouse analogue of the human carcinoembryonic antigen.

Functional human carcinoembryonic antigen (CEA)-like genes have been shown to be present in the mouse. Southern analyses of murine DNA using both human and murine CEA complementary DNA probes have revealed the presence of multiple CEA-like genes, while analyses of RNA from different mouse tissues showed CEA-like transcripts in adult colon and liver. Furthermore, a CEA-like protein, immunoprecipitable with a rabbit polyclonal serum raised against human CEA, has been detected in adult murine colon tissue. Several murine CEA complementary DNA clones have been isolated from a murine colon complementary DNA library, and characterization of one such clone demonstrates that both the N-terminal and the internal domains have been conserved between the two species. The existence of a murine counterpart of CEA strengthens the case for an essential function for this human tumor marker and provides an experimentally amenable system for elucidation of its biological properties.

Animals↗

PubMed2003

Characterization of reverse transcriptase activity of the L1Tc retroelement from Trypanosoma cruzi.

The recombinant protein RTL1Tc, encoded by the non-LTR (long terminal repeat) retrotransposon L1Tc from Trypanosoma cruzi, has been shown to have reverse transcriptase (RT) activity using poly(rA)/oligo(dT) and poly(rC)/oligo(dG) homopolymers as template/primers. The optimal RT activity was detected at a concentration of 5 mM Mg2+, pH 8 and between 28 and 37% degrees C. Site-directed mutagenesis in the RT catalytic site proved that substitution of aspartic acid 313 for isoleucine (RT D313IL1Tc) practically abolishes the RT activity of the RTL1Tc protein. RT-polymerase chain reaction assays revealed that the RTL1Tc protein has the ability to use both homologous and heterologous RNA templates. Also, it is shown that the RTL1Tc protein is capable of synthesizing complementary DNA molecules by consecutive switching of the oligo molecule, which the protein uses as a template. This template switching may be involved in the retroelement integration process.

Animals↗

PubMed1987

Secondary structure at the bacteriophage G4 origin of complementary-strand DNA synthesis: in vivo requirements.

The bacteriophage G4 origin of complementary strand DNA synthesis, G4 ori, contains several regions of potential secondary structure. In this study, we ask whether DNA secondary structure is important for G4 ori function in vivo. Point mutations were generated within a region of potential secondary structure so as to disrupt intrastrand base pairing. These mutations led to a strong temperature-dependent reduction in ori function in vivo. A double point mutation which introduces the same base substitutions without destabilizing intrastrand base pairing did not cause a temperature-dependent disruption in ori function. The double mutant did display a slight temperature-independent reduction in ori function compared to the wild-type G4 ori. Based on these findings, we conclude that DNA secondary structure, as well as recognition of specific sequences, is required for G4 ori activity in vivo.

Coliphages↗

PubMed1999

[Differentially expressed cDNA sequences homologous with known genes in human nasopharyngeal carcinoma].

In order to search the tumor suppressor genes correlated with pathogenesis of human nasopharyngeal carcinoma(NPC), we applied the PCR-based subtractive hybridization technique of representational difference analysis (RDA) to the primary culture cells of normal human nasopharyngeal epithelial and HNE1, a poorly differentiated NPC cell line. Following four successive subtractions of HNE1 complementary DNA from normal human nasopharyngeal epithelial cells complementary DNA, difference products were cloned into pGEM-T easy vector and nucleotide sequences determined. Comparison of cDNA sequences against the databases identified 9 known genes. Known genes included TRIP1(TGF beta receptor interacting protein), TAF, ezrin, MHC II, actinin, Histone H1 zero, Cytokeratin 13, Squalene Synthetase and RNA Synthetase-like. Some of them have an effective suppressive ability on the tumor. In this study, we have demonstrated that cDNA RDA is an effective strategy for systematically isolating differences in gene expression between two related but functionally distinct cells. Our results also indicated that the NPC includes interaction of multigenes and this experiment offers a new route for NPC research.

Carcinoma, Squamous Cell↗