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At least 505 records · Page 28Linked to original sources
PubMed1997

Effects of fasting on the expression of gastrin, cholecystokinin, and somatostatin genes and of various housekeeping genes in the pancreas and upper digestive tract of rats.

It is generally accepted that while the gene expression of many gut hormones in the pancreas and upper digestive tract is influenced by the prandial state, the expression of house-keeping genes (used as internal standards) is stable. We have analysed how food deprivation affects the messenger (m) RNA expression of gastrin, cholecystokinin (CCK), and somatostatin and of house-keeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta-actin and 18S ribosomal (r) RNA. RNA, isolated from oxyntic, antral and duodenal mucosa and pancreas, was subjected to Northern blot analysis using complementary RNA probes. Compared to fed rats, food-deprived rats exhibited reduced mRNA expression of gastrin (antrum), somatostatin (antrum), CCK (duodenum), GAPDH (all tissues studied) and beta-actin (all tissues studied) and unchanged 18S rRNA expression. We conclude that the assessment of gut hormone mRNA expression may be greatly influenced by the choice of internal standard and that 18S rRNA is superior.

Actins↗
PubMed1986

The primary structure of crossover regions of intertypic poliovirus recombinants: a model of recombination between RNA genomes.

The nucleotide sequence of crossover sites in the genome of four intertypic (type 3/type 1) poliovirus recombinants has been determined. The approximate boundaries of the crossover regions were first estimated by RNase T1 oligonucleotide mapping of the recombinant genomes; then appropriate regions were sequenced by the chain termination method using oligonucleotide-primed reverse transcription of the recombinant RNAs. The crossover sites (defined as the contiguous sequences shared by the recombinant and both parental genomes flanked, in the recombinant genome, by heterotypic RNA segments) are 5, 5, 7, and 11 nucleotides long, respectively. The recombination was precise and was not accompanied by any other genetic alterations. The recombination sites were found to be located within genome segments having a potential to form secondary structure elements. Based on this observation, a model of recombination between picornaviral RNA genomes has been proposed. The essence of this model consists in bringing together homologous regions of two recombining RNA genomes via formation of intermolecular duplexes, detachment of the nascent 3' end of the newly synthesized complementary RNA from a "parting" site on the first template and its subsequent "jumping" to the identical (or closely related) "anchoring" site on the other template. Features of this model are discussed in some detail.

Base Sequence↗
PubMed1962

Size distribution of "informational" RNA.

Previous investigations suggested that the size of "informational" or "messenger" RNA was confined to sedimentation rates lying between 8 and 14S. These involved procedures permitting extended contact of the RNA with enzymatically active extracts. The present study re-examined the size distribution of T2-complementary RNA isolated by a method which minimized enzymatic degradation. A much greater diversity in size distribution (4S to 25S) was observed. Experiments are described indicating that 8 to 12S informational RNA does not readily attach to the 16S and 23S ribosomal components under the conditions used for sedimentation analysis.

Escherichia coli↗
PubMed1982

RNA intermediates in potato spindle tuber viroid replication.

Two double-stranded RNA intermediates of viroid replication have been isolated from potato spindle tuber viroid (PSTV)-infected tomato tissue and characterized by polyacrylamide gel electrophoresis and DNA-RNA hybridization techniques. These replicative intermediates contain monomeric circular or linear PSTV strands complexed with a multimeric complementary RNA strand. Synchronous synthesis of single-stranded PSTV is accompained by a simultaneous marked increase in double-stranded PSTV RNA; thus, in vivo precursors of the characterized double-stranded PSTV RNAs seem to be involved in PSTV replication. A "rolling circle" model for viroid replication on a circular PSTV template can accommodate the double-stranded PSTV RNA species characterized.

Journal Article↗
PubMed2004

RNA structural rearrangement via unwinding and annealing by the cyanobacterial RNA helicase, CrhR.

Rearrangement of RNA secondary structure is crucial for numerous biological processes. RNA helicases participate in these rearrangements through the unwinding of duplex RNA. We report here that the redox-regulated cyanobacterial RNA helicase, CrhR, is a bona fide RNA helicase possessing both RNA-stimulated ATPase and bidirectional ATP-stimulated RNA helicase activity. The processivity of the unwinding reaction appears to be low, because RNA substrates containing duplex regions of 41 bp are not unwound. CrhR also catalyzes the annealing of complementary RNA into intermolecular duplexes. Uniquely and in contrast to other proteins that perform annealing, the CrhR-catalyzed reactions require ATP hydrolysis. Through a combination of the unwinding and annealing activities, CrhR also catalyzes RNA strand exchange resulting in the formation of RNA secondary structures that are too stable to be resolved by helicase activity. RNA strand exchange most probably occurs through the CrhR-dependent formation and resolution of an RNA branch migration structure. Demonstration that another cyanobacterial RNA helicase, CrhC, does not catalyze annealing indicates that this activity is not a general biochemical characteristic of RNA helicases. Biochemically, CrhR resembles RecA and related proteins that catalyze strand exchange and branch migration on DNA substrates, a characteristic that is reflected in the recently reported structural similarities between these proteins. The data indicate the potential for CrhR to catalyze dynamic RNA secondary structure rearrangements through a combination of RNA helicase and annealing activities.

Base Sequence↗
PubMed1975

[Presence of autocomplementary RNA with viral specificity in cells infected with herpes virus].

RNA from cells infected with Herpes simplex virus contain a higher percentage of double-stranded RNA than non-infected cells. This percentage increases three-fold upon self-annealing. The complementary RNA sequences were shown to be virus-specific by the following criteria: (1) high melting temperature than double-stranded RNA from non infected cells; (2) higher density in caesium sulphate; (3) specific hybridization with viral DNA.

Animals↗
PubMed1989

Number and distribution of methylphosphonate linkages in oligodeoxynucleotides affect exo- and endonuclease sensitivity and ability to form RNase H substrates.

Oligodeoxynucleotides with different arrangements of methylphosphonate linkages were examined for nuclease sensitivity in vitro, stability in tissue culture, and ability to form RNase H-sensitive substrates with complementary RNA. After nuclease treatment, resistance was demonstrated by the ability to alter the electrophoretic mobility of a labeled complementary phosphodiester oligodeoxynucleotide. Both 5'- and 3'-exonuclease activities were retarded by methylphosphonate linkages. Methylphosphonate-containing oligodeoxynucleotides with 1-5 adjacent phosphodiester linkages were tested as substrates for the endonucleases DNase I and DNase II. The results indicated that a span of three or fewer contiguous internal phosphodiester linkages led to the greatest resistance to endonuclease. However, in serum-supplemented culture medium half-lives of these oligodeoxynucleotides were independent of the number of contiguous phosphodiester linkages. Methylphosphonate-containing oligodeoxynucleotides were hybridized to RNA runoff transcripts and tested as substrates for RNase H. The results indicated that a span of three internal phosphodiester linkages in the oligodeoxynucleotide was necessary and sufficient to direct cleavage of the RNA in the duplex.

Base Sequence↗
PubMed1990

RNA levels of neuronal nicotinic acetylcholine receptor subunits are differentially regulated in axotomized facial motoneurons: an in situ hybridization study.

In situ hybridization histochemistry using complementary RNA probes revealed that alpha 3 and beta 2 neuronal nicotinic acetylcholine receptor subunit mRNAs were expressed in 12% and 40% of facial motoneurons of the rat, respectively. The alpha 3 subunit mRNA signals disappeared in response to axotomy, whereas the beta 2 subunit mRNA signal was remarkably enhanced, suggesting that mRNA levels of receptor subunits are differentially regulated in axotomized motoneurons.

Animals↗
PubMed1997

Localization of platelet-activating factor receptor messenger RNA in the rat eye.

PURPOSE: To determine the distribution of platelet-activating factor (PAF) receptor in the rat eye. METHODS: Platelet-activating factor receptor messenger RNA (mRNA) expression was evaluated with reverse transcription-polymerase chain reaction (RT-PCR) in RNAs from several rat ocular tissues. Distribution of the expression was determined with in situ hybridization in adult rat eye sections and a 35S-labeled complementary RNA probe synthesized from the rat PAF receptor complementary DNA. In situ hybridization was also done with sections immunostained with OX-42, a microglia marker. RESULTS: RT-PCR revealed that levels of PAF receptor expression were similar among the ocular tissues studied. The in situ hybridization signals were found in the corneal epithelium, iris and ciliary body, and ganglion and microglial cells in the retina. CONCLUSIONS: Platelet-activating factor receptor mRNA was ubiquitously expressed in the rat eye with relative concentration in the corneal epithelium, iris and ciliary body, and retinal ganglion and microglial cells.

Animals↗
PubMed2003

Antisense inhibition of Escherichia coli RNase P RNA: mechanistic aspects.

The ribonucleoprotein enzyme RNase P catalyzes endonucleolytic 5'-maturation of tRNA primary transcripts in all domains of life. The indispensability of RNase P for bacterial cell growth and the large differences in structure and function between bacterial and eukaryotic RNase P enzymes comply with the basic requirements for a bacterial enzyme to be suitable as a potential novel drug target. We have identified RNA oligonucleotides that start to show an inhibitory effect on bacterial RNase P RNAs of the structural type A (for example, the Escherichia coli or Klebsiella pneumoniae enzymes) at subnanomolar concentrations in our in vitro precursor tRNA (ptRNA) processing assay. These oligonucleotides are directed against the so-called P15 loop region of RNase P RNA known to interact with the 3'-CCA portion of ptRNA substrates. Lead probing experiments demonstrate that a complementary RNA or DNA 14-mer fully invades the P15 loop region and thereby disrupts local structure in the catalytic core of RNase P RNA. Binding of the RNA 14-mer is essentially irreversible because of a very low dissociation rate. The association rate of this oligonucleotide is on the order of 10(4) M(-1) s(-1) and is thus comparable to those of many other artificial antisense oligonucleotides. The remarkable inhibition efficacy is attributable to the dual effect of direct interference with substrate binding to the RNase P RNA active site and induction of misfolding of the catalytic core of RNase P RNA. Based on our findings, the P15 loop region of bacterial RNase P RNAs of the structural type A can be considered the "Achilles' heel" of the ribozyme and therefore represents a promising target for combatting multiresistant bacterial pathogens.

Bacillus subtilis↗
PubMed2003

Crystal structure of a decamer RNA r(ggcggucgcu)2 with terminal and tandem G x U wobble base-pairs.

The data set of the crystal structure of a self-complementary RNA duplex r(ggcggucgcu)2 with terminal and tandem G x U wobble base-pairs has been collected to 2.3 A resolution. Crystals belong to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2; a = b = 50.0 A, c = 102.7 A, and alpha = beta = gamma = 90 degrees, with two duplexes in the asymmetric unit. The structural analysis using the MAD method is currently in progress.

Base Pairing↗
PubMed1983

Proton NMR studies on the covalently linked RNA-DNA hybrid r(GCG)d(TATACGC). Assignment of proton resonances by application of the nuclear Overhauser effect.

Proton NMR spectra of a covalently linked self-complementary RNA X DNA hybrid, r(GCG)-d(TATACGC), are recorded in H2O and D2O. Imino proton resonances as well as the non-exchangeable base and H-1' resonances are unambiguously assigned by means of nuclear. Overhauser effect measurements. Additional information was obtained by 31P NMR and circular dichroism spectra. The RNA parts in the duplex attain full conformational purity and adopt the usual A-RNA conformation. The DNA residues opposite the RNA tract do not adopt an A-type structure completely. Their respective sugar rings still appear to possess a certain conformational freedom. The same holds true for the central d(-TATA-) sequence which forms a DNA X DNA duplex. There appears to be a structural break in this part: the first two residues, T(4) and A(5), are clearly influenced by the adjacent RNA structure, whereas residues T(6) and A(7) behave quite similar to what usually is found in DNA duplexes in aqueous solution.

Base Sequence↗
PubMed1995

Bent helix formation between RNA hairpins with complementary loops.

The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3' side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5'-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication.

Bacterial Proteins↗
PubMed1990

The gene for the RNA component of the mitochondrial RNA-processing endoribonuclease is located on human chromosome 9p and on mouse chromosome 4.

Mitochondrial RNA-processing endoribonuclease (RNAase MRP) has the capacity to cleave mitochondrial RNA complementary to the light strand of the displacement loop at a unique site. The enzyme is a ribonucleoprotein whose RNA component is a nuclear gene product. The 5' flanking region of the primary transcript has control elements characteristic of RNA polymerase II transcription, and the coding region has features of RNA polymerase III transcription signals. The RNA associated with RNAase MRP is the first known RNA encoded by a single-copy gene in the nucleus and believed to be imported into mitochondria. The gene (RMRP) for this RNA component of RNAase MRP was assigned to human chromosome 9 and mouse chromosome 4 by Southern blot analyses of 11 human X rodent hybrids and 11 mouse X rodent hybrids with probe pHM1.0 and probe pSP270, respectively. In situ hybridization of probe pHSTU300 to normal human chromosomes revealed 29 of 100 cells with label on 9p and 9.6% of 302 silver grains located at 9p21--p12.

Animals↗
PubMed1975

Variations in hybridization of RNA from different mouse tissues and embryos to endogenous C-type virus DNA transcripts.

Several adult tissues, newborns, and embryos of uninfected BALB/c mice were analysed for RNA complementary to [3H]-DNA transcripts synthesized from an endogenous type-C virus of BALB/c 3T3. The technique of RNA:DNA hybridization was used and the extent of hybridization was measured by the use of a single-strand-specific nuclease (S-I), purified from Aspergillus oryzae. Virus-specific RNA was detected in all adult and embryonic tissues tested. However, the RNA extracted from tissues having higher proliferative activity, such as spleen, small intestine, uterus and embryos, hybridize the [3H]-DNA probe to a greater extent than the RNA from tissues with low proliferative activity, such as kidney and liver. These observations add further support to the view that the repression of the virus genome in normal cells is not complete, and suggest the existence of a correlation between a qualitative or quantitative change in the endogenous C-type virus genome transcription pattern and cell proliferation.

Animals↗
PubMed1994

NMR solution structure of a peptide nucleic acid complexed with RNA.

Peptide nucleic acids (PNA) incorporating nucleic acid bases into an achiral polyamide backbone bind to DNA in a sequence-dependent manner. The structure of a PNA-ribonucleic acid (RNA) complex was determined with nuclear magnetic resonance methods. A hexameric PNA formed a 1:1 complex with a complementary RNA that is an antiparallel, right-handed double helix with Watson-Crick base pairing similar to the "A" form structure of RNA duplexes. The achiral PNA backbone assumed a distinct conformation upon binding that differed from previously proposed models and provides a basis for further structure-based design of antisense agents.

Magnetic Resonance Spectroscopy↗
PubMed1977

RNA synthesized in vitro by calf thymus RNA polymerase III (C), as well as by E. coli RNA polymerase, is restricted to a subset of calf thymus DNA.

RNA synthesized in vitro from chromatin and DNA by calf thymus RNA polymerase III was evaluated by hybridization in vast DNA excess. The RNA contains RNA complementary to both moderately repeated and unique DNA sequences. Very highly repeated DNA is not transcribed. A greater portion of RNA transcribed from DNA by RNA polymerase III hybridizes to moderately repeated DNA than RNA transcribed by Escherichia coli RNA polymerase. In studies utilizing DNA absorbed to filters, RNA transcribed from chromatin in short incubations hybridized to a greater extent than RNA transcribed for longer times. Similar results were obtained with RNA transcribed from DNA by E. coli RNA polymerase. These results suggest: 1) RNA polymerase III may be responsible for the synthesis of RNA species in addition to tRNA and 5 S ribosomal RNA and a portion of this RNA is transcribed from unique DNA; and 2) in vitro there may be selectivity in the initiation of transcription by both E. coli RNA polymerase and calf thymus RNA polymerase III.

Animals↗