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PubMedDate not supplied

[Comparative study of slow 1H to 3H exchange in synthetic polynucleotides of A- and B-type conformations].

The rate of 1H leads to 3H exchange between water and C(8)H-groups of purinic residues in synthetic polynucleotides in wide temperature range measured. At temperatures below their Tm the rate of the exchange is shown to be lower as compared with that in corresponding mononucleotides. In the case of polynucleotides of A-conformation (poly(A).poly(U), poly(A).2poly(U) and poly(dA).2poly(dT), and poly(G).poly(C) the exchange is retarded by a factor of 5.7--7.5, whereas in the case of those of B-conformation (poly(dA).poly(dT), poly(dA--dT).poly(dA--dT) and poly(dG).poly(dC)) the exchange is retarded only by a factor of 2.3--2.5. Assuming the ylide mechanism of exchange the retardation is interpreted as a consequence of sterical hidrance in polynucleotides helical structure, which hampers contacts between purinic C(8)H-groups and OH-ions of solvent. Analysis of atomic arrangement around C(8)H-group and interatomic distances calculated on the basis of published atomic coordinates support our general conclusion that the sterical hindrance is more significant in the A-form as compared with that in the B-form. Elucidated correlation between the degree of the retardation in purine-containing polynucleotides and their conformation in solution allows to estimatf the type of conformation of polynucleotide with unknown structure on account of the slow 1H leads to 3H exchange data.

Hydrogen↗
PubMed2000

RNA-binding characteristics of the chloroplast S1-like ribosomal protein CS1.

The chloroplast ribosomal protein CS1, the homolog of the bacterial ribosomal protein S1, is believed to be involved in the process of ribosome binding to mRNA during translation. Since translation control is an important step in chloroplast gene expression, and in order to study initiation complex formation, we studied the RNA-binding properties of CS1 protein. We found that most of the CS1 protein in spinach chloroplast co-purified with the 30S ribosomal subunit. The relative binding affinity of RNA to CS1 was determined using the UV-crosslinking competition assay. CS1 protein binds the ribohomopolymer poly(U) with a relatively high binding affinity. Very low binding affinities were obtained for the other ribohomopolymers, poly(G), poly(A) and poly(C). In addition, no specific binding of CS1, either in the 30S complex or as a recombinant purified protein, was obtained to the 5'-untranslated region of the mRNA in comparison to the other parts. RNA-binding experiments, in which the N- and C-termini of the protein were analyzed, revealed that the RNA-binding site is located in the C-terminus half of the protein. These results suggest that CS1 does not direct the 30S complex to the initiation codon of the translation site by specific binding to the 5'-untranslated region. In bacteria, specific binding is derived by base pairing between 16S rRNA and the Shine-Dalagarno sequences. In the chloroplast, nuclear encoded and gene-specific translation factors may be involved in the determination of specific binding of the 30S subunit to the initiator codon.

5' Untranslated Regions↗
PubMed1996

Characterization of RNA binding activity and RNA helicase activity of the hepatitis C virus NS3 protein.

The Hepatitis C Virus (HCV) NS3 protein has RNA binding activity, RNA-stimulated NTPase activity, and RNA helicase activity. The RNA binding activity of the C-terminal domain of the HCV NS3 protein is less sensitive to pH, KCl, and MgCl2 than NTPase and the RNA helicase activity. The overall order of the binding of homoribopolymer for the NS3 protein was poly(U) > > poly(A) > poly(G), poly(C). The minimal RNA binding size of the HCV NS3 protein was determined using a gel retardation assay and is estimated between 7 nt and 20 nt. The HCV RNA helicase unwinds RNA/DNA heteroduplexes as well as RNA/RNA duplexes and it catalytically translocates in the 3' to 5' direction.

Base Sequence↗
PubMed1976

Main binding sites of the carcinogen, 4-nitroquinoline 1-oxide in nucleic acids.

4-Hydroxyaminoquinoline 1-oxide, the reduced metabolite of 4-nitroquinoline 1-oxide, was reacted with homopolyribonucleotides through the catalysis of an activating enzyme. It bound specifically to poly(G), poly(A) and poly(X) but negligibly to poly(C), poly (U) and poly(I). Chromatographic analysis of the acid hydrolysates of carcinogen-bound polynucleotides revealed that the reaction of the carcinogen with polynucleotides yielded two guanine, one adenine and two xanthine adducts. The same kinds of guanine and adenine adducts were found in DNA or RNA isolated from Escherichia coli and mammalian cells that had been exposed to the carcinogen. Analysis of nucleic acids isolated from 4-hydroxyaminoquinoline 1-oxide-treated cells revealed that 4-hydroxy-aminoquinoline reacts in vivo preferentially with guanines, to a less, but significant, extent with adenines and not significantly with pyrimidines.

4-Nitroquinoline-1-oxide↗
PubMed1993

Affinity gel electrophoresis of nucleic acids. Nucleobase-selective separation of DNA and RNA on agarose-poly(9-vinyladenine) conjugated gel.

Poly(9-vinyladenine) (PVAd) was immobilized within an agarose gel matrix to produce a novel affinity gel for the base-specific separation of nucleic acids by electrophoresis. The shape (single- or double-stranded) and base content of nucleic acids were specifically recognized by the affinity gel. Only single stranded DNA, of which the sequence is not regular enough to form a stable duplex hairpin structure, was selectively absorbed over double-stranded DNA. Among five polynucleotides having different bases such as poly(A), poly(G), poly(C), poly(U) and poly(I), poly(U) and poly(I) were base-specifically adsorbed by PVAd, probably by hydrogen bond formation. The effect of the molecular mass and size of poly(9-vinyladenine) was also examined.

Adenine↗
PubMed2004

LRP130, a single-stranded DNA/RNA-binding protein, localizes at the outer nuclear and endoplasmic reticulum membrane, and interacts with mRNA in vivo.

LRP130 (also known as a LRPPRC) is an RNA and single-stranded DNA-binding protein, and recently identified as a candidate gene responsible for the Leigh syndrome, a French-Canadian type cytochrome c oxidase deficiency. However, the biological function of LRP130 still remains largely unresolved. In the present study, we found that the C-terminal half of the mouse LRP130 located within a 120 amino acid sequence (a.a. 845-964) binds to synthetic RNA homopolymers, poly(G), poly(U), and poly(C), as well as r(CUGCC)(6). Assessment of the subcellular localization indicated both nuclear/endoplasmic reticulum (ER) and mitochondrial fractions to be positive. To further analyze the subcellular localization of LRP130, a nuclear/ER fraction was fractionated into the nucleoplasm (NP) and nuclear envelope (NE)/ER, and the latter was further separated into outer nuclear membrane (ONM)/ER and inner nuclear membrane (INM) by treatment with Triton X-100. LRP130 was detectable in all three fractions, and the distribution pattern was in good accordance with that known for ONM/ER proteins. Interestingly, immunostaining of HeLa cells demonstrated nuclear rim staining of LRP130, specifically at the outside of the NE and also at ER, and association of LRP130 with poly(A)(+) RNA was restricted only to the ONM/ER fraction. Overexpression of full-length mouse LRP130 fused with EGFP resulted in nuclear accumulation of poly(A)(+) RNA in HeLa cells. Taking all these results together, it is suggested that LRP130, a novel type of RNA-binding protein, associates with mRNA/mRNP complexes at the outside of NE and ER, and plays a role in control of mRNA metabolisms.

Animals↗
PubMed1985

Purification of a uridine-specific acid nuclease from chicken liver by fast protein liquid chromatography.

A rapid purification procedure for a novel uridine-specific nuclease from chicken liver based on the Pharmacia fast protein liquid chromatography (FPLC) system is presented. The purification was achieved by applying crude extract to a Mono S cation-exchange column equilibrated with 10 mM potassium phosphate buffer (pH 6.0). The enzyme was eluted in 20 min with a potassium chloride gradient at a flow-rate of 2 ml/min. The enzyme was then chromatographed on a Superose 12 size-exclusion column in less than 1 h at a flow-rate of 0.5 ml/min (Kav = 0.77). The enzyme was re-chromatographed on a second Mono S column to concentrate the protein. The uridine-specific nuclease hydrolyzed poly(U) and Escherichia coli 5S RNA. Poly(A) was hydrolyzed by the nuclease less efficiently (about 10% of the poly(U) activity). No hydrolysis was detected with poly(C), poly(G), poly(dT) or poly(dA) as substrate. The speed with which each purification step could be carried out facilitated the determination of optimal chromatographic conditions. We found that the resolution of the Mono S and Superose 12 columns was superior to that of conventional ion exchangers and size-exclusion columns respectively.

Animals↗
PubMed1998

Cloning and sequencing of the cDNA for an RNA-binding protein from the Mexican axolotl: binding affinity of the in vitro synthesized protein.

A full length cDNA for an RNA-binding protein (axolotl RBP) with consensus sequence (RNP-CS) from the Mexican axolotl, Ambystoma mexicanum, has been cloned from a subtraction library. In vitro translation with synthetic mRNA and subsequent hybrid-arrested translation with a specific antisense oligonucleotide confirms that the axolotl RBP cDNA encodes an approx. 16 kDa polypeptide. Computer-assisted analyses revealed amino acid similarities of 58-60% to various RNA-binding proteins and a 90 amino acid region at the amino-terminal end constituting the putative RNA-binding domain (RNP-CS) with two highly conserved motifs, RNP2 and RNP1. Phylogenetic analysis suggests that the putative RNA-binding protein from axolotl is unique. A binding assay with radiolabeled axolotl RBP showed that this RNA-binding protein bound strongly with poly(A) and to a lesser degree with poly(U), but not at all with poly(G), poly(C), or DNA.

Ambystoma mexicanum↗
PubMed2000

Direct measurement of electrical transport through DNA molecules.

Attempts to infer DNA electron transfer from fluorescence quenching measurements on DNA strands doped with donor and acceptor molecules have spurred intense debate over the question of whether or not this important biomolecule is able to conduct electrical charges. More recently, first electrical transport measurements on micrometre-long DNA 'ropes', and also on large numbers of DNA molecules in films, have indicated that DNA behaves as a good linear conductor. Here we present measurements of electrical transport through individual 10.4-nm-long, double-stranded poly(G)-poly(C) DNA molecules connected to two metal nanoelectrodes, that indicate, by contrast, large-bandgap semiconducting behaviour. We obtain nonlinear current-voltage curves that exhibit a voltage gap at low applied bias. This is observed in air as well as in vacuum down to cryogenic temperatures. The voltage dependence of the differential conductance exhibits a peak structure, which is suggestive of the charge carrier transport being mediated by the molecular energy bands of DNA.

DNA↗
PubMed1969

Interactions of hormonal steroids with nucelic acids. I. A specific requirement for guanine.

Under equilibrium conditions testosterone, progesterone, estradiol, and corticosterone bind to denatured but not to native DNA. Among synthetic polynucleotides, steroids bind only to guanine containing polymers:poly dG, poly G, poly UG, poly AG, and "denatured" poly dG:dC; however, they do not bind to rRNA, sRNA, TMV-RNA, poly CG, or native poly dG:dC. These data indicate a preferential affinity for guanine residues and for single-stranded regions of polynucleotides. That different functional groups of the purine are involved in the associations with different steroids is indicated by the observation that only estradiol binds to poly I. Restrictions are also imposed by structural attributes of the steroids: an alpha-substitution at C-17 reduces binding, polyhydroxylated steroids bind poorly or not at all.

Binding Sites↗
PubMed1971

Inhibition of the DNA polymerase of Rauscher leukemia virus by single-stranded polyribonucleotides.

The DNA polymerase of Rauscher murine leukemia virus is strongly and specifically inhibited by nontemplate, single-stranded polyribonucleotides with either the resident viral RNA, native calf-thymus DNA, or poly[d(A-T)] as templates. These inhibitory homopolymers are apparently bound to the template site of the polymerase, since they interact competitively with the template. The strength of the inhibition depends on the particular homopolymer used: poly(U) > poly(G) >> poly(A) > poly(C). The K(i) for poly(U) was 0.08 mug/ml, which represents an apparent affinity six times greater than that observed for viral RNA. No such inhibition was observed with a highly purified DNA polymerase from mouse embryos or the Escherichia coli enzyme.

Adenine Nucleotides↗
PubMed1980

Repeating structure of cytoplasmic poly(A)-ribonucleoprotein.

A repeating structure of cytoplasmic poly(A)-ribonucleoprotein is revealed by digestion with T2 RNase. A pattern of fragments that are multiples of about 27 residues is obtained. The repeating structure is readily reconstituted from purified poly(A) and cytoplasmic factors. Reconstitution is specific for poly(A), as shown by the lack of competition by poly(G), poly(C), poly(dA), and tRNA. The repeating structure is absent from the nucleus, and so appears to be formed upon transport to the cytoplasm.

Animals↗
PubMed1986

Poly(riboadenylic acid) preferentially inhibits in vitro translation of cellular mRNAs compared with vaccinia virus mRNAs: possible role in vaccinia virus cytopathology.

Vaccinia virus-induced inhibition of host protein synthesis seems to be mediated by viral transcripts based on their differential inhibition of cellular mRNA translation in a rabbit reticulocyte lysate system. In this study, we demonstrated that the removal of poly(riboadenylic acid) [poly(A)] from the in vitro viral transcripts abolished this inhibition in the same cell-free system. This observation led us to the finding that less than 1 microM poly(A) completely inhibited HeLa cell mRNA translation in the reticulocyte lysate, whereas only 50% inhibition of vaccinia virus mRNA translation was observed at the same concentration. Similar results were also obtained in a wheat germ protein-synthesizing system. This inhibitory effect of poly(A) was totally abrogated by the addition of polydeoxythymidylate. This selective inhibition was highly specific for poly(A) since other homopolymers, including poly(G), poly(C), and poly(dA), were not capable of causing such an inhibition. Poly(U), however, had a moderate selective inhibitory effect. Among the several mRNAs tested, the translation of L-cell, encephalomyocarditis virus, and reovirus RNAs was also sensitive to poly(A). However, vesicular stomatitis virus mRNA translation was strikingly more resistant. These results suggest that poly(A), which is also synthesized by the virion-associated poly(A) polymerase may be involved in vaccinia virus-mediated host cell shutoff.

Animals↗
PubMed1999

RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex.

The vaccinia virus-encoded heterodimer responsible for poly(A) tail elongation comprises a polyadenylylation catalytic subunit (VP55) and associated processivity factor (VP39). We show that monomeric VP39's affinity for RNA homopolymers follows the hierarchy poly(I) >poly(U) >>poly(G) >poly(A) >poly(C), that the heterodimer interacts stably with 40-45 nucleotide nucleic acid segments, and that its homopolymer preference for polyadenylylation priming is comparable to the VP39 affinity hierarchy (above). For oligonucleotide ligands possessing the previously-identified (rU)2-(N)25-rU heterodimer-binding motif, the heterodimer's affinity and base-type preference are mediated via both the (rU)2and rU portions, with the greater contribution coming from (rU)2. VP39's R107 sidechain contributes to specificity at the downstream rU. Substitution of each ribouridylate of the motif with either ribothymidine or 4-thiodeoxythymidine indicated that the downstream rU interacts with both heterodimer subunits, whereas the upstream (rU)2interacts only with VP55. A 'crosslinking SELEX' approach indicated VP39-base proximity around position -10 of a 4-thioribouridine/deoxycytidine ligand pool. Upon incubating the heterodimer with a panel of identical-sequence oligonucleotides derivatized with azidophenacyl bromide at various phosphate positions, those derivatized at positions -11 to -21 photocrosslinked to both subunits in a coordinated manner. This region may therefore pass through a 'cleft' or enclosed 'channel' at the subunit interface.

Binding Sites↗
PubMed1986

Metabolic activation of 1-nitropyrene and 1,6-dinitropyrene by nitroreductases from Bacteroides fragilis and distribution of nitroreductase activity in rats.

Nitrated polycyclic aromatic compounds, 1-nitropyrene (1-NP) and 1,6-dinitropyrene (1,6-diNP), are environmental mutagens and carcinogens. Nitroreductases purified from an anaerobic bacterium, Bacteroides fragilis, catalyzed the metabolic activation of these compounds to produce DNA- and tRNA-bound adducts in vitro. Formation of the adducts was inhibited by p-chloromercuribenzoic acid, which is an inhibitor of nitroreductases from B. fragilis. The enzyme and coenzyme (NADPH) were essential for the adduct formation. These results suggest that nitroreduction is a necessary step in the metabolic activation of nitropyrenes. 1-NP bound specifically to poly(G) and poly(dG), and 1,6-diNP bound to poly(G), poly(dG), and poly(X). The other purine polynucleotides were weak acceptors. However, the reactive products of nitropyrenes formed by nitroreductases could not bind to pyrimidine polynucleotides. Enzymatic hydrolysis of 1-NP-bound DNA and subsequent analysis by high-performance liquid chromatography showed one major and two minor adducts in the hydrolysate. The peak of the major adduct corresponded to that of N-(deoxyguanosin-8-y1)-1-aminopyrene, which is the same as an adduct formed by xanthine oxidase, a mammalian nitroreductase. Nitroreductase activity in the various organs and intestinal contents of Sprague-Dawley rats was assayed in the presence of NADPH or NADH under nitrogen gas. Nitroreductase activity was widely distributed in the organs of the rats; in particular, that of the liver and of the small intestine was relatively high, but that of the respiratory organs such as lung and alveolar macrophages was very low. Intestinal contents had high nitroreductase activity, which was proportional to the number of bacteria, especially anaerobic bacteria, in the intestine. These results suggest that the nitroreductase activity of the normal bacterial flora is very high in rats and that the intestinal bacteria play a major role in the metabolism of nitropyrenes in vivo.

Animals↗
PubMed1993

Purification and characterization of the major 50-kDa repressor protein from cytoplasmic mRNP of rabbit reticulocytes.

A 50-kDa protein has been purified to homogeneity from free mRNP of rabbit reticulocytes. This protein, designated as p50, is present within both free mRNP (approximately 4 mol protein/mol globin mRNA) and polyribosomal mRNP (approximately 2 mol protein/mol globin mRNA). p50 is a basic protein (pI approximately 9.5) and is characterized by a high glycine content of approximately 20%. Nitrocellulose-filter analysis has shown that p50 interacts with globin mRNA with an association constant of approximately 2.5 x 10(8) M-1 (100 mM KAc, 4 degrees C). Various RNA and polyribonucleotides have the following relative affinity for p50; poly(G) > poly(U) > globin mRNA approximately 16S rRNA > poly(A) > poly(C). p50 can be phosphorylated both in vitro and in vivo.

Amino Acids↗
PubMed1995

Identification of an RNA binding region within the N-terminal third of the influenza A virus nucleoprotein.

The influenza A virus nucleoprotein (NP) has been examined with regard to its RNA-binding characteristics. NP, purified from virions and devoid of RNA, bound synthetic RNAs in vitro and interacted with the ribonucleotide homopolymers poly(A), poly(G), poly(U), and poly(C) in a salt-dependent manner, showing higher binding affinity for polypyrimidine homopolymers. To map the NP regions involved in RNA binding, a series of deleted forms of the NP were prepared, and these truncated polypeptides were tested for their ability to bind poly(U) and poly(C) homopolymers linked to agarose beads. Proteins containing deletions at the N terminus of the NP molecule showed reduced RNA-binding activity, indicating that this part of the protein was required to bind RNA. To identify the NP region or regions which directly interact with RNA, proteins having the maltose-binding protein fused with various NP fragments were obtained and tested for binding to radioactively labeled RNAs in three different assays: (i) nitrocellulose filter binding assays, (ii) gel shift assays, and (iii) UV light-induced cross-linking experiments. A maltose-binding protein fusion containing the N-terminal 180 amino acids of NP behaved as an RNA-binding protein in the three assays, demonstrating that the N terminus of NP can directly interact with RNA. This NP region could be further subdivided into two smaller regions (amino acids 1 to 77 and 79 to 180) that also retained RNA-binding activity.

Amino Acid Sequence↗
PubMed1993

NAB2: a yeast nuclear polyadenylated RNA-binding protein essential for cell viability.

A variety of nuclear ribonucleoproteins are believed to associate directly with nascent RNA polymerase II transcripts and remain associated during subsequent nuclear RNA processing reactions, including pre-mRNA polyadenylation and splicing as well as nucleocytoplasmic mRNA transport. To investigate the functions of these proteins by using a combined biochemical and genetic approach, we have isolated nuclear polyadenylated RNA-binding (NAB) proteins from Saccharomyces cerevisiae. Living yeast cells were irradiated with UV light to covalently cross-link proteins intimately associated with RNA in vivo. Polyadenylated RNAs were then selectively purified, and the covalent RNA-protein complexes were used to elicit antibodies in mice. Both monoclonal and polyclonal antibodies which detect a variety of NAB proteins were prepared. Here we characterize one of these proteins, NAB2. NAB2 is one of the major proteins associated with nuclear polyadenylated RNA in vivo, as detected by UV light-induced cross-linking. Cellular immunofluorescence, using both monoclonal and polyclonal antibodies, demonstrates that the NAB2 protein is localized within the nucleus. The deduced primary structure of NAB2 indicates that it is composed of at least two distinct types of RNA-binding motifs: (i) an RGG box recently described in a variety of heterogeneous nuclear RNA-, pre-rRNA-, mRNA-, and small nucleolar RNA-binding proteins and (ii) CCCH motif repeats related to the zinc-binding motifs of the largest subunit of RNA polymerases I, II, and III. In vitro RNA homopolymer/single-stranded DNA binding studies indicate that although both the RGG box and CCCH motifs bind poly(G), poly(U), and single-stranded DNA, the CCCH motifs also bind to poly(A). NAB2 is located on chromosome VII within a cluster of ribonucleoprotein genes, and its expression is essential for cell growth.

Amino Acid Sequence↗