Quenching of polyadenylic acid emission by divalent metal ions at room temperature

A quenching of poly A emission at 293K in neutral pH by transition metal ions and alkaline earth ions has been studied. The results indicate that the longer wavelength emission of poly A is quenched by not only Co(II) and Ni(II) but also Mg(II). The measured large values of quenching efficiency suggest that the excitation energy migrate more than 10 adenine bases even at 293K.     

Immunological studies on the interaction of polyadenylic acid and human liver ribonuclease

The effect of polyadenylic acid, a potent inhibitor of mammalian and bacterial RNAses, on the binding of human liver RNAse to its antibody was studied. To do this, a human liver RNAse antibody was immobilized on Sepharose 4B. Examination of the ability of the enzyme to bind to the immobilized anti-RNAse in the presence or absence of polyadenylic acid indicated that enzyme-antibody binding was more sensitive to the presence of polyadenylic acid than was enzyme activity. Furthermore, the effect of polyadenylic acid on enzyme-antibody binding was specific since neither polycytidylic acid nor polyuridylic acid had much effect on the antigenicity of the enzyme. The metal cation, Mg2+, and the polyamine, spermidine, but not putrescine, readily reversed the effects of polyadenylic acid on enzyme-antibody binding.     

Interaction of polyadenylic acid with methylated xanthines

Polyadenylic acid forms both 1 : 1 and 2 : 1 complexes with 3-methylxanthine under appropriate conditions. While the binding isotherms for formation of these complexes are typical of strongly cooperative processes, their melting profiles are anomalous and indicate that intermediate species are present during the thermal dissociation process. Theobromine and theophylline do not form complexes with polyadenylic acid under similar conditions, and they do not hydrogen-bond very strongly with 9-ethyludenine in chloroform solution.     

The measurement of plant polyadenylic acid by hybridisation with radioactive polyuridylic acid

Summary Saturation hybridisation of polyadenylic acid with [³H]polyuridylic acid is described. Under conditions of [³H]poly(U) excess, poly(A) is detected in the RNA of a number of higher plants. The ribonuclease resistant hybrids melt sharply when subjected to thermal denaturation. Plant RNA which contains poly(A) sequences detected by [³H]poly(U) hybridisation is polydisperse in molecular weight. Data presented shows that the amount of poly(A) in plant RNA is variable. This technique is useful for the qualitative and quantitative detection of poly(A) sequences in higher plant RNA.Abbreviations A.R. Analar Reagent - Poly(A) Polyadenylic acid - Poly(U) Polyuridylic acid - Oligo(dT)-cellulose oligo(deoxythymidylate)-cellulose - Tm melting temperature - SSC standard saline citrate     

Specific interaction between GroEL and denatured protein measured by compression-free force spectroscopy

We investigated the interaction between GroEL and a denatured protein from a mechanical point of view using an atomic force microscope. Pepsin was bound to an atomic force microscope probe and used at a neutral pH as an example of denatured proteins. To measure a specific and delicate interaction force, we obtained force curves without pressing the probe onto GroEL molecules spread on a mica surface. Approximately 40 pN of tensile force was observed for approximately 10 nm while pepsin was pulled away from the chaperonin after a brief contact. This length of force duration corresponding to the circumference of GroEL's interior cavity was shortened by the addition of ATP. The relation between the observed mechanical parameters and the chaperonin's refolding function is discussed.     

Interaction of nitroaromatic radiosensitizers with irradiated polyadenylic acid as measured by an indirect immunochemical assay with specificity for the 8,5'-cycloadenosine moiety

The relative reactivity of a series of nitroaromatic radiosensitizers toward the C(5') radical intermediate leading to 8,5'-cycloadenosine formation in deoxygenated solutions of irradiated polyadenylic acid (poly A) was assessed using standard competition kinetic analysis. Formation of 8,5'-cycloadenosine was assayed by an indirect, competitive, enzyme-linked immunosorbent assay (ELISA) described in an earlier report. In the absence of oxygen, the nitroaromatics inhibit 8,5'-cyclonucleoside formation in a way which generally increases with radiosensitizer electron affinity. Although hydroxyl radical scavenging by the nitroaromatics may account for a relatively small decrease in 8,5'-cyclonucleoside formation, the data suggest that oxidation of the C(5') radical intermediate is the more plausible explanation for the decreased yield of the 8,5'-cyclonucleoside with increasing nitroaromatic electron affinity.     

Complex formation between polyadenylic acid and formycin B

Polyadenylic acid forms a 2:1 complex with the C-nucleoside formyein B at both pH 7.0, 0.15 m-Na⁺ and pH 6.0, 0.15 M-Na⁺. The formation of this complex has been followed by equilibrium dialysis, and by optical rotatory dispersion measurements in the range 333 to 450 nm. At pH 7, melting curves for thermal dissociation of the complex (followed by the optical rotation at 345 nm) show a strongly co-operative helix-coil transition. From the variation of T_m with the free formyein B concentration at this temperature, the partial molar enthalpy of formation of the complex, at the mid-point of the transition, has been calculated as -12.8 kcal./mol of formyein B. Viscometry and optical rotatory dispersion measurements indicate that the structure of the complex at pH 6 is the same as at pH 7, and that it may be formed in preference to the double-helical acid form of poly (A). The structure and properties of the complex are discussed.     

Comparison of polyadenylic acid and oligouridylic acid messenger RNA associated proteins

Various subclasses of messenger ribonucleoprotein particles were prepared from free cytoplasmic and polysome fractions of rat liver on the basis of the homopolymeric content of the constituent RNA's. Two major proteins were evident in the free cytoplasmic preparations: the poly(A)-binding protein was the major constituent of polyadenylated components and a 60 kilodalton protein was the major protein in oligouridylated components. In addition to the poly(A)-binding protein, the polysome fractions contained a 74 kilodalton protein that was present in all subclasses of particles. With both free cytoplasmic and polysome preparations, chromatography on columns of poly(U)-sepharose separated poly-adenylated mRNP's largely on the basis of the length of the poly(A) tract; mRNP's containing short poly(A) tracts (fragment distribution centered on 34 residues) were not retained by the columns, presumably because of the interaction of the poly(A) with poly(A)-binding protein.     

Membrane-bound polyribosomes in HeLa cells: association of polyadenylic acid with membranes

Polyadenylic acid of membrane-bound polyribosomes is shown to be associated with rapidly sedimenting membrane structures. Most of this poly(A) remains attached to membranes after extensive degradation of polyribosomal messenger RNA with pancreatic ribonuclease. Previously, it was shown that exposure to EDTA removes up to 40% of the membrane-associated mRNA. In our experiments, 57% of the membrane-associated poly(A) still sediments with membrane structures after treatment with pancreatic ribonuclease followed by the addition of EDTA. This indicates that the association of about 60% of the membrane-bound poly(A) is EDTA-resistant, while the remainder is labile after removal of magnesium ions. Reconstruction experiments suggest that poly(A) from detergent-treated, membrane-derived polyribosomes is not trapped by other membrane structures. The poly(A)-containing RNA fragment that remains associated with the membranes after pancreatic ribonuclease treatment is shown to be a single peak at about 7 S, or about the size of cellular poly(A). Thus, the attachment site is almost pure poly(A). The poly(A)-containing, membrane-bound mRNA appears to be of a larger average size than total cellular poly(A)-containing RNA, as judged by its greater sedimentation value.     

Studies on the stability of tritium-labeled polyuridylic acid and polyadenylic acid

Results are presented on the stability of high specific activity [uridylate-5,6-³H]polyuridylic acid and [adenylate-2,8-³H]polyadenylic acid stored under various conditions. Polyacrylamide disc gel electrophoresis in the presence of SDS was used to assess qualitatively the change in molecular weight distribution of the polynucleotides stored under different conditions. Products stored for a period of months in ethanol; water solution [1:1, $\text{v}\text{v}$] were found to have a significantly slower rate of decomposition than polynucleotides stored in frozen aqueous solution or as lyophilized solid.     

Destabilization of secondary structure in polyadenylic acid by formaldehyde

Results of circular dichroism and ultraviolet absorption measurements of poly A in neutral aqueous formaldehyde solution are presented, which show that the hydroxymethylated residues retain the ability to stack, but the stacking tendency is diminished. The midpoint of the thermal denaturation profile falls from about 38°C to about 18°C on complete hydroxymethylation. Hydroxymethylation, however, appears to have only a small effect on the apparent standard enthalpy and entropy of stacking, both of which become slightly more negative. When present at concentrations greater than about 2 g/100 ml, formaldehyde has a further and somewhat more dramatic denaturing effect on poly A. This ability is probably related to the chemical similarity of aqueous formaldehyde (methylene glycol) and ethylene glycol, which is known to be an effective denaturant for nucleic acids. In the presence of 20 g/100 ml formaldehyde, a very broad thermally induced transition of poly A is observed through the loss of ultraviolet hypochromism. Only the low-temperature part of the transition is observed; it appears to be completed only at temperatures well over 100°C where the hypochromism with respect to adenosine has largely disappeared. The transition cannot be identified with the unstacking reaction usually observed through thermal denaturation experiments in the absence of formaldehyde, although the associated structure may be related in some way. The molecular nature of the structure associated with the transition is not known.     

Association of polyadenylic acid with messenger RNA of vesicular stomatitis virus

Polyadenylate (poly(A)) sequences are associated with the 28 S and 13–15 S messenger RNA species of vesicular stomatitis virus. These sequences contain approximately 125 to 150 nucleotides. Virion RNA contains little or no poly(A) sequences. The association of poly(A) with viral messenger RNA species and the gross distribution of poly(A) among these species remain unaltered even when the RNA is synthesized in the presence of cordycepin or cycloheximide and whether viral messenger RNA is polyribosome-bound or free. Also, when viral translation is completely inhibited by superinfection with poliovirus, there is no effect on poly(A) association with the messenger RNA of vesicular stomatitis virus.