Synthesis and properties of poly (6-methylpurinylic acid), poly (6-methoxypurinylic acid), and poly (6-methylthiopurinylic acid).
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Chromatography, DEAE-Cellulose↗
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The primary structure of yeast glutamic acid tRNA specific to the GAA codon.
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Adenine Nucleotides↗
Preparation and properties of poly(5-ethylcytidylic acid), a poly(5-methylcytidylic acid) analogue.
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Alkaline Phosphatase↗
Physical and coding properties of poly(5-aminouridylic acid) and of 5-aminouridine-containing trinucleotides.
This report concerns the synthesis of poly(5-aminouridylic acid) and of 5-aminouridine-containing trinucleotides. Starting from 5-aminouridine the nucleoside 5'-phosphate was prepared enzymatically with carrot phosphotransferase whereas the nucleoside 5'-diphosphate was prepared chemically and polymerised with polynucleotide phosphorylase. The aminouridine-containing trinucleotides were prepared by known enzymatic procedures. Besides an increase of stability in the secondary structure poly(nh25U) forms a triple-stranded complex with poly(A) and stimulates the poly(Phe) synthesis like poly(U). In contrast to U-nh25U-U, the triplet containing the 3'-terminal aminouridine does not stimulate the binding of Phe-tRNA to 70-S ribosomes. This behavior is discussed with respect to the influence of a modification on the stacking geometry of a codon and the base pairing scheme between the 5'-nucleotide of the anticodon and the 3'-nucleotide of the condon.
Escherichia coli↗
Polynucleotide duplexes based on poly(7-deazaadenylic acid).
In order to find a poly(A)-poly(U) analog which could not form a triple-stranded complex and which would have a sufficiently high thermal stability to survive under physiological conditions, the interaction of poly(7-deazaadenylic acid) (poly(c-7A)) with modified polyuridylic acids was examined. Mixing curves constructed by the method of continuous variation, isosbestic points and thermal melting profiles proved that poly(c-7A) formed only 1:1 complex with polyribothymidylic acid and poly(5-bromouridylic acid) (Tm values of 50 and 72 degrees C respectively, in 0.15 M NaCl, 0.01 M KH2 PO4, 0.001 M MgCl2, pH7). In addition poly(c-7A) formed a 1:1 complex with poly(I) (Tm equals 22 degrees C in 0.46 M salt, pH 7), and presumed duplexes were observed in the interaction of poly(c-7A) with poly(dT), poly(2'-azido-2'-deoxyuridylic acid) and poly(2'-O-methyluridylic acid) (Tm values of 35, 32 and 41 degrees C respectively, in 0.10 M NaCl, pH7).
Adenine Nucleotides↗
The effect of thioketo substitution on uracil-2-aminopurine and uracil-2, 6-diaminopurine interactions in polynucleotides.
The existence of the complexes poly[r(s4U)] . poly[r(n2h6A] and poly-[r(s4U)] . poly[r(n2A)] was demonstrated by means of spectrophotometric titration and sedimentation veolicty analysis. According to the absorption-temperature profiles thioketo substitution of poly[r(U)] . poly[r(n2h6A)] led to stabilisation of the helical structure, thus implying that the 4-thioketo group does not participate in s4U . n2h6A base pairing. In the case of poly[r(s4U)] . poly[r(n2A)] drastic destabilistaion of the helical structure by thioketo substitution was observed. This indicates that the thioketo substituents participate in s4U .n2A base pairing.
Binding Sites↗
Puromycin inhibition of eucaryotic ribosomes. Differences in sensitivity between polypeptide synthesis directed by endogenous mRNA and synthetic templates including poly(U).
In a protein synthesis sytem derived from porcine uteri we have made the following observations: 1. Synthesis directed by the endogenous mRNA of the system is more sensitive to inhibition by puromycin than poly(U) directed synthesis. 2. Synthesis directed by the synthetic templates poly(G,U) and poly(C,U) is more sensitive to inhibition by puromycin than poly(U) directed synthesis and frequently shows a sensitivity to puromycin similar to that directed by endogenous mRNA. 3. Protein synthesis was inhibited by three aminoacyloligonucleotides (C-A-Phe, C-A-Asp, and C-A-Pro) which are analogs of the 3' terminus of aminoacyl tRNAs. Of the three, C-A-Phe was the most active and C-A-Asp the least active but, unlike puromycin, inhibition by these compounds was the same for endogenous and poly(U) directed synthesis. These results are interpreted as supporting the proposal that the acceptor site of ribosomes contains an hydrophobic binding region which interacts with the side chain of aliphatic amino acids, and particularly with the aromatic side chain of phenylalanine.
Amino Acids↗
Ionophorous polymers. Interaction with polynucleotides and effects on RNA-directed DNA polymerase activity.
Poly(vinylbenzo-18-crown-6), a water-soluble polymer endowed with ion-binding crown moieties as pendent groups, forms insoluble complexes with polyadenylate in the presence of K+; the corresponding monomeric benzo-18-crown-6, does not form a precipitate under the same conditions. In the presence of Na+ and Mn2+ which in aqueous solution complex weakly to crown compounds, no coprecipitation of the crown polymer and polyadenylate occurs; nevertheless, the crown polymer strongly binds to immobilized polyadenylate even under these conditions. The interactions of crown polymer with the poly-nucleotide result in a loss of templating ability of the latter. Using RNA-dependent DNA polymerase of murine leukemia virus it was found that (1) enzymatic action is efficiently inhibited even in the absence of ions which coprecipitate crown polymer and template, (2) inhibition is reversed by addition of excess polynucleotide and (3) monomeric crown does not inhibit the reaction.
Binding Sites↗
Studies on the formation and stability of aminoacyl-tRNA synthetase complexes from Ehrlich ascites cells.
Nine aminoacyl-tRNA synthetases from Ehrlich ascites cells were examined with respect to their ability to be isolated as high molecular weight complexes, soluble enzymes, and ribosome-bound enzymes. Several different methods were employed for cell homogenization and enzyme isolation, with particular attention paid to the effects of hypotonic, isotonic, and hypertonic buffers on enzyme isolation. The binding of all synthetases to ribosomes was eliminated if the low ionic strength of the isolation buffer was raised to isotonic levels. In contrast, neither the ionic strength or composition of the buffers, nor the procedures used for cell homogenization or enzyme isolation had any significant effect on the isolation of the high molecular weight synthetase complex. Certain enzymes (lysyl-, methionyl- and isoleucyl-tRNA synthetases) formed very stable complexes and high molecular weight species were the predominant forms of these enzymes under all conditions of cell homogenization and enzyme isolation. Other enzymes (glycyl-, tyrosinyl- and threonyl-tRNA synthetases) formed complexes very weakly, if at all, and always appeared predominately in the soluble enzyme fraction. Isolated soluble forms of the lysyl-, methionyl- and isoleucyl-tRNA synthetases did not associate to form significant amounts of complex upon re-isolATION, SUGGESTING THAT A COMPONENT NECESSARY FOR COMPLEX FORMATION WAS MISSING FROM THE SOLUBLE ENZYME FRACTION. However, the soluble forms of these enzymes, but not the glycyl-, tyrosinyl- and threonyl-tRNA synthetases, did for complexes when mixed with ribosomal RNA or polyuridylic acid. Preliminary experiments showed no significant differences between the complexed and soluble forms of the lysyl-, methionyl- and isoleucyl-tRNA synthetases with respect to Km values or ability to charge different isoaccepting tRNAs.
Amino Acyl-tRNA Synthetases↗
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↗
Interactions between 125-I-labelled RNA from RNA tumor viruses and RNA of other sources.
Fragmented 125I-labelled RNA from RNA tumor viruses was hybridized to unlabelled RNA from cells, viruses, and homoribopolymers. The viral RNA interacted with all RNA tested, except for certain homoribopolymers. Complex formation with unlabelled RNA was verified by nuclease resistance, buoyant density measurements, and thermal stability in solutions of different ionic strength. The RNAase-resistant complex involved 20-30% of the sequences in the 125I-labelled viral RNA and formed preferentially with nuclear RNA of cells. 125I-labelled hemoglobin mRNA, 125I-labelled immunoglobulin light chain (lambda2) mRNA, or 125I-labelled viral RNA from encephalomyocarditis virus (EMC) dit not from RNAase-resistant complexes with unlabelled cellular RNA.
Animals↗
Calf lens messenger ribonucleoprotein complexes. Characterization and comparison of template activity with corresponding mRNAs.
Lens messenger ribonucleoprotein complexes have been isolated from calf lens polysomes by sucrose gradient centrifugation after puromycin-induced dissociation. A 10 S mRNA was released from a 13 S messenger ribonucleoprotein complex and a 14 S mRNA from a 19 S messenger ribonucleoprotein complex. Two major protein components with molecular weights of approx. 64 000 and 40 000 were isolated from each of the messenger ribonucleoprotein complexes after RNAase digestion. Buoyant density determinations suggest that the messenger ribonucleoprotein complexes contain approximately one mol of each major protein species per mol mRNA. In contrast to lens mRNA, lens messenger ribonucleoproteins are poor templates for transcription with avian myeloblastosis virus reverse transcriptase. Similar results were also obtained with globin messenger ribonucleoprotein containing either two major protein species (or deficient in the lower molecular weight protein species). Polynucleotide phosphorylase eliminates the reverse transcription template activity of the lens mRNA. This effect is blocked in the messenger ribonucleoprotein. Such observations suggest that at least one of the protein components associated with lens messenger ribonucleoprotein may be located in the 3'-terminal region. Only a small variation in translation activity was observed between the messenger ribonucleoproteins and their respective mRNAs.
Animals↗
Influence of temperature and magnesium ions on the secondary and tertiary structures of tRNAPhe and 23 S RNA - infrared investigations.
Band splitting and/or bands shifting in opposite directions due to coupling of vibrations of neighboring groups observed in the infrared spectra of tRNAPhe and 23 S RNA give information on the secondary structure. The base pairing, dependent on temperature, is investigated, discussing coupling effects with the base residues' vibrations in the region 1700-1500 cm-1. The secondary structure of the backbone is studied, discussing coupling effects with vibrations in the region 1300-1000 cm-1. The 2'OH groups are cross-linked with the O atoms of the neighboring ribose residues via hydrogen bonds. Probably the greater than PO-2 groups are turned inward at the backbone, i.e. towards the base residues. The base pairs as well as the secondary structure of the backbone melt with increasing temperature and with dialysis against distilled water. The comparison of the Mg2+ and the K+ salts of the tRNAPhe shows that the changes of base pairing due to Mg2+ are small. At the backbone, however, Mg2+ favor somewhat more the discussed secondary structure than K+ does. All Mg2+ effects on secondary structure are, however, too small to explain the considerable increase in melting temperature due to Mg2+. Thus it is supposed that the rise in the melting temperature due to Mg2+ is not caused by a change in secondary but in the tertiary structure of tRNAPhe. Furthermore, the influence of Mg2+ on the secondary structure of 23 S RNA is studied. The following results are obtained: (1) The double helical regions become more compact and probably increase due to the influence of Mg2+. (2) At the backbone, Mg2+ induces strong hydrogen bonding between the 2'OH groups and the ether O atoms of neighboring ribose residues. Probably they turn the greater than PO-2 groups toward the base residues, i.e., inward at the backbone. Schulte, Morrison and Garrett found that a critical level of Mg2+ is required for binding certain proteins to rRNA (Biochemistry (1974) 13, 1032). Thus the observed conformation is probably necessary for binding these proteins.
Binding Sites↗
Iodination-deiodination. A radiochemical method for detection of structure and changes in structure in RNA.
Bound iodine is released from radioiodinated nucleotides in polymers exposed to sodium bisulfite. The rate of bisulfite-catalyzed deiodination of pyrimidines can be controlled both by change of temperature of pH and is also dependent on the molecular association of the nucleotide. The rate of release of iodine from iodocytidine in polycytidylate is greater than the rate of elimination from RNA. Experiments testing the influence of base-pairing of the iodopyrimidines in synthetic polynucleotides showed that pairing of the substituted nucleotide protected the iodine bond. The rates of bisulfite-catalyzed deiodination of several radioiodinated RNAs were measured. The action of bisulfite on all single stranded RNAs tested was multiphasic consisting of a rapid early deiodination reaction supplanted by a slower phase which was followed by reacceleration of release. The release of iodine from double stranded RNA and DNA-RNA duplexes was retarded in comparison with the release from ribosomal and messenger RNA fractions. The deiodination profiles of single and double stranded RNA suggested that the intermediate stage iodine release is governed by melting of paired zones of low stability. Late release may result from destablization of the molecule through the addition of bisulfite to the pyrimidine ring or deamination. The effect of several substances expected to complex with polynucleotides was tested. Acridine orange and ethidium bromide increased loss of iodine from ribosomal RNA but slightly decreased elimination from double stranded viral RNA. A basic protein fraction isolated from ribosomal particles accelerated the deiodination of ribosomal RNA. While the destabilization caused by this protein fraction was greater than that caused by an equal amount of albumin, as tested the effect was non-specific. The results show that a change in sensitivity to chemical deiodination may folow the interaction of small amounts of protein with polynucleotides.
Animals↗
Factors causing release of ribosomal subunits from isolated nuclei of regenerating rat liver in vitro.
Incubation medium II causes release of ribosomal subunits from isolated prelabeled nuclei of regenerating rat liver in vitro (Sato, T., Ishikawa, K. and Ogato, K. (1976) Biochim. Biophys. Acta 000, 000-000). The effects of individual components of this medium on release of subunits were studied and the following results were obtained. 1. Dialyzed cytosol was effective in causing release of total labeled RNA, but its effect on release of labeled ribosomal subunits was rather lower than that of low molecular yeast RNA. Spermidine inhibited the release of total labeled RNA as well as that of labeled ribosomal subunits. 2. Low molecular yeast RNA was the most effective component for inducing release of labeled ribosomal subunits. Homologous ribosomal RNA was as effective as yeast RNA. Cytoplasmic ribosomes, prepared by washing with solution of high salt concentration, and their subunits were also effective. 3. Transfer RNA was not so effective as yeast RNA and ribosomal RNA and even after heat treatment it had little effect. 4. Among the homopolyribonucleotides tested, polyuridylic acid had a strong effect but polyadenylic acid, polycytidylic acid and polyinosinic acid had no effect. 5. The effects of yeast RNA and polyuridylic acid in causing release of labeled ribosomal subunits were dependent upon their concentrations in the reaction mixture. The characteristics of the factors which cause release of labeled ribosomal subunits in vitro are discussed on the basis of the results.
Animals↗
Two functional states of poly(adenylic acid) polymerase in isolated nuclei.
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Animals↗
Mechanism of the inhibition by RNA of the RNA polymerases of Histoplasma capsulatum.
4 S RNA isolated from the dimorphic fungus Histoplasma capsulatum inhibited the DNA-dependent RNA polymerase activity of the yeast phase of this fungus. Inhibition was specific for initiation, and resulted from binding of the RNA to the enzyme. Among a variety of synthetic polynucleotides tested, only poly(G) and oligo(dG) were effective inhibitors, suggesting a role for guanines or guanine-rich sequences of RNA in the inhibition reaction.
DNA-Directed RNA Polymerases↗