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At least 865 records · Page 48Linked to original sources
PubMed1985

A-form to A'-form conformational switch of double helices in rat liver 5S and 5.8S rRNA. Solution X-ray scattering evidence and circular dichroic measurements.

The wide-angle X-ray scattering of rat liver 5S rRNA and 5.8S rRNA molecules showed significant differences in the positions of the scattering maxima when dissolved in Mg2+-containing Tris/HCl buffer or in Mg2+-depleted buffer. A comparison of the experimental curves with theoretical curves calculated from atomic coordinates of double-helical models proved a switch from A form to A' form of the double-helical regions within the molecules by changing the buffer conditions. This result was supported by circular dichroic measurements. The A to A' transition may have important consequences for RNA-protein interactions.

Animals↗
PubMed2006

Brief communication: stability and catalytic activity of novel circular DNAzymes.

UNLABELLED: DNAzymes represent a new generation of catalytic nucleic acids for specific RNA targeting in order to inhibit protein translation from the specifically cleaved mRNA. The 10-23 DNAzyme was found to hydrolyze RNA in a sequence-specific manner both in vitro and in vivo. Although single-stranded DNAzymes may represent the most effective nucleic acid drug to date, they are nevertheless sensitive to nuclease degradation and require modifications for in vivo application. However, previously used stabilization of DNAzymes by site-specific phosphorothioate (PT) modifications reduces the catalytic activity, and the PTO displays toxic side effects when applied in vivo. Thus, improving the stability of DNAzymes without reducing their catalytic activity is essential if the potential of these compounds should be realized in vivo. RESULTS: The Circozyme was tested targeting the mRNA of the most common genetic rearrangement in pediatric acute lymphoblastic leukemia TEL/AML1 (ETV6/RUNX1). The Circozyme exhibits a stability comparable to PTO-modified DNAzymes without reduction of catalytic activity and specificity and may represent a promising tool for DNAzyme in vivo applications. CONCLUSION: The inclusion of the catalytic site and the specific mRNA binding sequence of the DNAzyme into a circular loop-stem-loop structure (Circozyme) of approximately 70 bases presented here represents a new effective possibility of DNAzyme stabilization.

Base Sequence↗
PubMed1985

RNA-like conformational properties of a synthetic DNA poly(dA-dU).poly(dA-dU).

Differences in the circular dichroism of poly(dA-dT).poly(dA-dT) and poly(dA-dU).poly(dA-dU) and in its temperature induced changes are reported. A comparison to the data obtained with DNA and RNA indicates that an absence of thymine methyl groups in the polynucleotide results in promoting its RNA-like conformational properties. However, poly(dA-dU).poly(dA-dU) is not an A-DNA type of double helix.

Animals↗
PubMed1999

Functional importance of regions in Escherichia coli elongation factor NusA that interact with RNA polymerase, the bacteriophage lambda N protein and RNA.

The association of the essential Escherichia coli protein NusA with RNA polymerase increases pausing and the efficiency of termination at intrinsic terminators. NusA is also part of the phage lambda N protein-modified antitermination complex that functions to prevent transcriptional termination. We have investigated the structure of NusA using various deletion fragments of NusA in a variety of in vitro assays. Sequence and structural alignments have suggested that NusA has both S1 and KH homology regions that are thought to bind RNA. We show here that the portion of NusA containing the S1 and KH homology regions is important for NusA to enhance both termination and antitermination. There are two RNA polymerase-binding regions in NusA, one in the amino-terminal 137 amino acids and the other in the carboxy-terminal 264 amino acids; only the amino-terminal RNA polymerase-binding region provides a functional contact that enhances termination at an intrinsic terminator or antitermination by N. The carboxy-terminal region of NusA is also required for interaction with N and is important for the formation of an N-NusA-nut site or N-NusA-RNA polymerase-nut site complex; the instability of complexes lacking this carboxy-terminal region of NusA that binds N and RNA polymerase can be compensated for by the presence of the additional E. coli elongation factors, NusB, NusG and ribosomal protein S10.

Bacterial Proteins↗
PubMed1975

Ribonucleoproteins of Uukuniemi virus are circular.

The internal ribonucleoprotein (RNP) of Uukuniemi virus was released with Triton X-100 and analyzed on sucrose gradients. Three species of RNP sedimenting at 140 to 150, 105 to 120, and 85 to 90S could be separated. All of them contained the same ratio of core polypeptide (mol wt, 25,000) to RNA. Eelctron microscopy using rotatory shadowing showed that all three species were circular. Free ends were rarely seen. Measurements of the strands revealed three distinct length classes of about 2.8, 1.4 and 0.7 mu m. Polyacrylamide-agarose gels showed that the largest RNP contained the L RNA, the medium-sized RNP the M RNA, and the smallest RNP the S RNA.

Animals↗
PubMedDate not supplied

'Z-RNA'--a left-handed RNA double helix.

In contrast to double-stranded DNA, there has so far been little evidence that double-stranded RNA can undergo major conformational transitions. We have investigated the conformation in different conditions of the double-stranded RNA molecule poly(G-C).poly(G-C), by NMR, circular dichroism and absorbance spectroscopy. We report here evidence obtained by these different spectroscopic techniques that poly(G-C).poly(G-C) undergoes a transition from the A-form to a left-handed Z-form in conditions of high ionic strength and at temperatures above 35 degrees C. This conformational transition may be of relevance to the biological situations in which double-stranded RNA occurs, such as in ribosomes and in some viruses.

Circular Dichroism↗
PubMed1995

RNA footprint mapping of RNA polymerase II molecules stalled in the intergenic region of polyomavirus DNA.

RNA polymerase II molecules that transcribe the late strand of the 5.3-kb circular polyomavirus genome stall just upstream of the DNA replication origin, in a region containing multiple binding sites for polyomavirus large T antigen. Stalling of RNA polymerases depends on the presence of functional large T antigen and on the integrity of large T antigen binding site A. To gain insight into the interaction between DNA-bound large T antigen and RNA polymerase II, we mapped the position of stalled RNA polymerases by analyzing nascent RNA chains associated with these polymerases. Elongation of RNA in vitro, followed by hybridization with a nested set of DNA fragments extending progressively farther into the stalling region, allowed localization of the 3' end of the nascent RNA to a position 5 to 10 nucleotides upstream of binding site A. Ribonuclease treatment of nascent RNAs on viral transcription complexes, followed by in vitro elongation and hybridization, allowed localization of the distal end of stalled RNA polymerases to a position 40 nucleotides upstream of binding site A. This RNA footprint shows that elongating RNA polymerases stall at a site very close to the position of DNA-bound large T antigen and that they protect approximately 30 nucleotides of nascent RNA against ribonuclease digestion.

Animals↗
PubMed1992

Catalytic RNA reactions of yeast tRNA(Phe) fragments.

We describe 12 new catalytic RNA reactions which are intermolecular variants of the well-known intramolecular Pb(2+)-promoted hydrolysis of yeast tRNA(Phe). Fragments derived from the native yeast tRNA(Phe) which possess the T stem-loop can function as catalysts for the site-specific hydrolysis at p18 of D stem-loop-containing fragments. An initial report described the catalytic cleavage of an unmodified T7 transcript corresponding to the 5' half of tRNA(Phe) by a 3' half-molecule derived from the native tRNA. [Sampson, J. R., Sullivan, F. X., Behlen, L. S., DiRenzo, A. B., & Uhlenbeck, O. C. (1987) Cold Spring Harbor Symp. Quant. Biol. 52, 267-275]. We have investigated the trans reaction further by creating a family of substrate and catalyst RNA molecules by dissection of the native tRNA(Phe) using a combination of chemical and enzymatic methods. A search for cleavage activity in trans was conducted using a combinatorial approach with the available T and D stem-loop-containing fragments. Twelve combinations were found to be catalytic, and initial rates, kcat's, and Km's are reported for each. The kcat's for the reactions differ by approximately 20-fold, whereas Km's vary by only approximately 2-fold. Differences in some of the cleavage rates argue that tertiary interactions present in the intact molecule can be reconstituted in the fragment combinations. Secondary structural features remote from the cleavage site can also affect the apparent cleavage rates. A minimum catalytic complex consisting of a substrate fragment corresponding to nucleotides 1-24 of the native molecule and a catalytic RNA corresponding to 46-76 is identified. This complex is of interest since the transition state for cleavage involves only three helices, with no elements of the anticodon required for cleavage. This is reminiscent of the proposed secondary structure of the hammerhead catalytic RNA cleavage motif.

Base Sequence↗
PubMed1997

Production of hepatitis B virus covalently closed circular DNA in transfected cells is independent of surface antigen synthesis.

Covalently closed circular DNA (cccDNA) is the first hepatitis B virus (HBV) DNA replicative intermediate formed from the genomic DNA and serves as the template for synthesis of viral mRNA and pregenomic RNA. It also appears to be produced by intracellular recycling of relaxed circular DNA intermediates. Here, we report that none of the forms of HBV surface antigen affect this intracellular recycling of HBV DNA. Elimination of the initiation codons for the large and middle surface proteins did not affect the detection of surface antigen in culture supernatants. In contrast, detection of surface antigen was eliminated by the removal of, or the introduction of two stop codons downstream of, the initiation codon of the small (major) surface antigen. None of the mutations affected the production, in transfected HepG2 cells, of HBV DNA replicative intermediates, including cccDNA.

Cell Line↗
PubMed2004

Arabidopsis thaliana has the enzymatic machinery for replicating representative viroid species of the family Pospiviroidae.

Viroids, subviral noncoding RNAs, replicate, move, and incite diseases in plants. Viroids replicate through a rolling-circle mechanism in which oligomeric RNAs of one or both polarities are cleaved and ligated into the circular monomers. Attempts to transmit viroids to Arabidopsis have failed for unknown reasons. To tackle this question, Arabidopsis was transformed with cDNAs expressing dimeric (+) transcripts of representative species of the families Pospiviroidae and Avsunviroidae, which replicate in the nucleus and the chloroplast, respectively. Correct processing to the circular (+) monomers was always observed, demonstrating that Arabidopsis has the appropriate RNase and RNA ligase. Northern blot hybridization also revealed the multimeric (-) RNAs of Citrus exocortis viroid and Hop stunt viroid (HSVd) of the family Pospiviroidae, but not of Avocado sunblotch viroid of the family Avsunviroidae, showing that the first RNA-RNA transcription of the rolling-circle mechanism occurs in Arabidopsis for the two nuclear viroids and that their multimeric (-) RNAs remain unprocessed as in typical hosts. Moreover, transgenic Arabidopsis expressing HSVd dimeric (-) transcripts accumulated the circular (+) monomers, although at low levels, together with the unprocessed primary transcript that served as the template for the second RNA-RNA transcription. Agroinoculation of Arabidopsis with the dimeric (+) Citrus exocortis viroid, HSVd, and Coleus blumei viroid 1 cDNAs showed that these viroids could not move to distal plant parts, in contrast with the situation observed in their experimental hosts. Therefore, deficiencies in movement or low replication appear to be the factors limiting infectivity of some viroids in Arabidopsis.

Arabidopsis↗
PubMed1969

Some observations on the near ultraviolet circular dichroism of tRNA from E. coli.

The circular dichroism arising from 4-thiouridine residues in E. coli transfer RNA has been studied under conditions in which the secondary and tertiary structure of the macromolecule is either intact or totally disrupted. Studies on both unfractionated tRNA and on highly purified species of methionine-, valine-, and lysine-specific tRNA suggest that the circular dichroism of the 4-thiouridine residue is highly sensitive to its local environment in the macro-molecule and reveal interesting differences between these purified species. A new chromophore, resembling 4-thiouridine in some respects but showing distinctive chemical and optical properties, has been detected. The implications of these results on model-building studies of tRNA are discussed.

Escherichia coli↗
PubMed1976

Isolation and characterization of Sendai virus DI-RNAs.

When passaged at high multiplicity, four strains of Sendai virus all showed evidence that they contained defective interfering (DI) particles. RNA isolated from nucleocapsids of cells infected with the high multiplicity passage stocks was found to consist of only minor amounts of nondefective genome length RNA and major amounts of smaller RNAs, the DI-RNAs. These DI-RNAs were found to have unusual and variable sedimentation properties in sucrose gradients, but were found to represent unique segments of the viral genome by length measurements in the electron microscope and by hybridization. A striking feature of the DI-RNAs is their ability to form circular structures, indicating that the ends of the DI-RNA are complementary. The implications of this finding in terms of the mechanism of genome replication is discussed.

Cell Line↗
PubMed1988

Nucleotide sequence of the Varkud mitochondrial plasmid of Neurospora and synthesis of a hybrid transcript with a 5' leader derived from mitochondrial RNA.

The Mauriceville and Varkud mitochondrial plasmids of Neurospora are closely related, closed circular DNAs (3.6 and 3.7 kb, respectively; 1 kb = 10(3) bases or base-pairs), whose characteristics suggest relationships to mitochondrial DNA introns and retrotransposons. Here, we characterized the structure of the Varkud plasmid, determined its complete nucleotide sequence and mapped its major transcripts. The Mauriceville and Varkud plasmids have more than 97% positional identity. Both plasmids contain a 710 amino acid open reading frame that encodes a reverse transcriptase-like protein. The amino acid sequence of this open reading frame is strongly conserved between the two plasmids (701/710 amino acids) as expected for a functionally important protein. Both plasmids have a 0.4 kb region that contains five PstI palindromes and a direct repeat of approximately 160 base-pairs. Comparison of sequences in this region suggests that the Varkud plasmid has diverged less from a common ancestor than has the Mauriceville plasmid. Two major transcripts of the Varkud plasmid were detected by Northern hybridization experiments: a full-length linear RNA of 3.7 kb and an additional prominent transcript of 4.9 kb, 1.2 kb longer than monomer plasmid. Remarkably, we find that the 4.9 kb transcript is a hybrid RNA consisting of the full-length 3.7 kb Varkud plasmid transcript plus a 5' leader of 1.2 kb that is derived from the 5' end of the mitochondrial small rRNA. This and other findings suggest that the Varkud plasmid, like certain RNA viruses, has a mechanism for joining heterologous RNAs to the 5' end of its major transcript, and that, under some circumstances, nucleotide sequences in mitochondria may be recombined at the RNA level.

Amino Acid Sequence↗
PubMed1974

The amplified ribosomal DNA of dytiscid beetles.

During oogenesis in many animals there is a massive extrachromosomal synthesis of the genes for ribosomal RNA. In Dytiscid beetles, as in the toad Xenopus, the amplified ribosomal DNA occurs as circular molecules of different sizes. The circles fall into size classes that are integral multiples of a unit circle. It is probable that the unit circle contains the coding sequence for one precursor ribosomal RNA molecule plus accompanying spacer sequences.

Animals↗
PubMed1983

Topological linkage of circular DNA molecules promoted by Ustilago rec 1 protein and topoisomerase.

We studied the formation of linked circular DNA molecules promoted by the combined action of rec 1 protein and type I topoisomerase of Ustilago maydis. When ATP was added as cofactor to reactions containing rec 1 protein, pairs of homologous circular DNA molecules became linked after addition of topoisomerase. Closed circular duplex molecules could be joined at homologous sites with circular single-stranded molecules or with other circular duplex molecules, provided that homologous single-stranded DNA fragments or RNA polymerase and nucleoside triphosphates were also added. Complexes formed were topologically linked through regions of heteroduplex DNA. When the analog adenylyl-imidodiphosphate was substituted for ATP, nonhomologous pairs of circular DNA molecules became linked.

Adenosine Triphosphate↗
PubMed1982

Alterations of the conformation of the RNAs of alfalfa mosaic virus upon binding of a few coat protein molecules.

Structural changes in the single-stranded genome RNAs (RNAs 1, 2 and 3) and the subgenomic coat protein messenger (RNA 4) of alfalfa mosaic virus upon addition of a few coat protein molecules of the virus were investigated by measuring the fluorescent intensity of bound ethidium bromide and by circular dichroism. No effect could be observed in the case of the genome RNAs. However, in RNA 4, which is of much less complexity than the genome RNAs, a reduction of the ethidium bromide binding by 30% was found, whereas the positive molar ellipticity at 265 nm was reduced by 9% upon binding of the coat protein. Both changes point to a reduction of the ordered structure of the RNA. Since the protein is known to bind first at the 3'-terminus of RNA 4 and probably also of the genome RNAs, the conformational changes observed could be those thought to be necessary for replicase recognition in this positive-stranded RNa virus which needs the coat protein for starting an infection cycle.

Circular Dichroism↗