Structure Of Ribonucleic Acid Research Articles

Structure and function of nucleic acids affected by high pressure

Recently we have shown that oligodeoxynucleotides and oligoribonucleotides change their conformation at high pressure from B to Z and from A to Z respectively [Krzyzaniak et al. 1991, 1994a]. Now we are interested what is the effect of pressure on the native RNA. The structure of transfer ribonucleic acids (tRNA) and ribosomal 5S RNA undergo small conformational changes at high pressure. The changes were studied by circular dichroism (CD) but difficult to identify precisely. At high pressure conditions (6 kbar) Escherichia coli phenylalanine specific tRNA Ph~ can be aminoacylated (charged) specifically with amino acid, in absence of the specific aminoacyl tRNA synthetases and ATP [Krzyzaniak et al. 1994b]. We found that the esterification reaction at high pressure, similarly to the enzymatic one, occured at the 3'-end of the tRNA molecules. It seems plausible that a conformation oftRNA induced by the aminoacyl tRNA synthetase during enzymatic aminoacylation and that one induced at high pressure are very similar or identical. We think that the "unique" tertiary structure of tRNA creates an active centre where ester bond is formed. If so, it is obvious that a structure of the amino acid stem of tRNA determines specificity of specific tRNA with amino acid. The product of the aminoacylation reaction at high pressure, PhetRNA Phe was as good substrate as that one obtained enzymatically for in vitro polyphenylalanine synthesis in the presence of poly U. We have also shown that high pressure can catalyse elongation of short peptides. These observations have some relevance to the origin of protein synthesis. On the early stages of evolution (RNA world), RNA molecule played dual role. It could function as an enzyme and information carrier. For this reaction aminoacyl-tRNA is used as an amino acid donor. This paper and our current work strongly supports that RNA dependent amino

Rearrangement of snRNA Structure during Assembly and Function of the Spliceosome

This chapter discusses the idea that spliceosomal ribonucleic acid (RNA) works in fundamentally the same way in all systems is used to develop a cohesive representation of the rearrangement of the most conserved RNA–RNA interactions during splicing. The core of the spliceosome contains a highly conserved RNA structure, suggesting that the chemical events of splicing are based heavily on RNA–RNA interactions. Yet, spliceosomes from different organisms are not exactly the same. Most studies on splicing have used human (HeLa) cells or the yeast, Saccharomyces cerevisiae. Differences in splicing, and the intrinsic strengths and weaknesses of the experimental materials, have restricted some findings to one or other system, but the conservation of small nuclear RNA (snRNA), splicing factor structure, and hnction means that the yeast and human spliceosomes are very similar. Some RNA–RNA interactions are essential in both systems. Some make more important contributions to the function in one system than in the other, at least as assayed in the laboratory. Other interactions have not yet been shown to contribute to the function, but are inferred to be critical for success in the ultimate bioassay evolution.

A new model for the tertiary structure of 5S ribonucleic acid in plants

Chemical, enzymatic and physicochemical methods of a structural analysis of 5S rRNAs in lupine, wheat germ, and other plants led us to propose a new three-dimensional model of these molecules The main features of the model are tertiary interactions between the β- and γ-domains of the molecule, specifically nucleotides (34)CCCA(37) in loop C and nucleotides (85)GGGU(88) in loop D. In addition we propose tertiary base-pairing in A100-U53 between loops B and E. We have confirmed this model by NMR spectroscopy and by chemical modification with diethylpyrocarbonate. Our results are consistent with the proposed model and are also applicable to all eukaryotic 5S rRNAs. Our model is clearly differentiated from others by intramolecular tertiary hydrogen bonds between the two domains.

Modelling the three-dimensional structure of ribonucleic acids

An approach developed for modelling the three-dimensional (3D) architecture of large RNA molecules and its theoretical basis is described. In parallel, approaches for modelling the 3D structures of proteins are discussed. Although knowledge-based modelling is nowadays the most powerful method for proteins, it is still inadequate for nucleic acids. In order to obtain the 3D information necessary for modelling nucleic acids, especially RNA molecules, one must rely either on chemical and enzymatic probing at the nucleotide level or on comparative sequence analysis if enough sequences with appropriate randomness are available. With either method, one can hopefully obtain sufficient information not only for determining the two-dimensional structure but also for constructing the 3D architecture of complex RNA molecules. Molecular mechanics and molecular dynamics methods are still inappropriate for modelling large RNA molecules and would require new developments for dealing with the electrostatic problem and the inclusion of solvent.

Automatic display of RNA secondary structures.

A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overlapping displays of secondary structures of ribonucleic acids. The first program, rnasearch, implements a new search procedure that dynamically rearranges overlapping portions of the two-dimensional drawing while preserving clear and readable displays of the two-dimensional structure. The algorithm is fast (the execution time for the command rnasearch is 38.6 s for the 16S rRNA of Escherichia coli with 1542 bases), accepts outputs from two-dimensional prediction programs and therefore allows for rapid comparison between the various two-dimensional folds generated. A second program, rnadisplay, allows the graphical display of the computed two-dimensional structures on a graphics workstation. Otherwise, it is possible to obtain a paper output of the two-dimensional structure by using the program print2D which builds a Postscript file. Moreover the two-dimensional drawing can be labelled for representing data coming from chemical modifications and/or enzymatic cleavages. Application to a few secondary structures such as RNaseP, 5S rRNA and 16S rRNA are given.

A comparative study of the relationship between thermostability and function of phenylalanyl-tRNA synthetases from Escherichia coli and Thermus thermophilus

The relationship between thermostability and functional activities of phenylalanyl-tRNA synthetases (EC 6.1.1.20) from E. coli and Thermus thermophilus has been studied. In the case of the E. coli enzyme, the activity decreased after the 43°C treatment, both in the [ 32P]PP i-ATP exchange reaction and the overall aminoacylation reaction, due to thermo-inactivation of the phenylalanyl-tRNA synthetase, whereas tRNA Phe preserved its native structure. In the Th. thermophilus system, the enzyme showed extreme thermostability (up to 90°C), and the reduction in the tRNA aminoacylation rate after the 78°C treatment was ascribed to denaturation of the tRNA Phe. Since the enzyme did not lose the [ 32P]PP i-ATP exchange activity up to 80°C, the observed lower thermo-resistance of the tRNA is evidence that the native structure of ribonucleic acids should be one of the most difficult to stabilize at high temperatures.

A parallel algorithm for estimating the secondary structure in ribonucleic acids

A parallel algorithm for estimating the secondary structure of an RNA molecule is presented in this paper. The mathematical problem to compute an optimal folding based on free-energy minimization is mapped onto a graph planarization problem. In the planarization problem we want to maximize the number of edges in a plane with no two edges crossing each other. To solve a sequence of n bases, n(n -- 1)/2 processing elements are used in our algorithm.

Differential distribution of factors involved in pre-mRNA processing in the yeast cell nucleus.

The yeast cell nucleus has previously been shown to be divided into two regions by a variety of microscopic approaches. We used antibodies specific for the 2,2,7-trimethylguanosine cap structure of small nuclear ribonucleic acids (snRNAs) and for a protein component of small nuclear ribonucleoprotein particles to identify the distribution of small nuclear ribonucleoprotein particles within the yeast cell nucleus. These studies were performed with the fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae. By using immunofluorescence microscopy and immunoelectron microscopy, most of the abundant snRNAs were localized to the portion of the nucleus which has heretofore been referred to as the nucleolus. This distribution of snRNAs is different from that found in mammalian cells and suggests that the nucleolar portion of the yeast nucleus contains functional domains in addition to those associated with RNA polymerase I activity.

Differential Distribution of Factors Involved in Pre-mRNA Processing in the Yeast Cell Nucleus

The yeast cell nucleus has previously been shown to be divided into two regions by a variety of microscopic approaches. We used antibodies specific for the 2,2,7-trimethylguanosine cap structure of small nuclear ribonucleic acids (snRNAs) and for a protein component of small nuclear ribonucleoprotein particles to identify the distribution of small nuclear ribonucleoprotein particles within the yeast cell nucleus. These studies were performed with the fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae. By using immunofluorescence microscopy and immunoelectron microscopy, most of the abundant snRNAs were localized to the portion of the nucleus which has heretofore been referred to as the nucleolus. This distribution of snRNAs is different from that found in mammalian cells and suggests that the nucleolar portion of the yeast nucleus contains functional domains in addition to those associated with RNA polymerase I activity.

Parallel algorithms for finding a near-maximum independent set of a circle graph

A parallel algorithm for finding a near-maximum independent set in a circle graph is presented. An independent set in a graph is a set of vertices, no two of which are adjacent. A maximum independent set is an independent set whose cardinality is the largest among all independent sets of a graph. The algorithm is modified for predicting the secondary structure in ribonucleic acids (RNA). The proposed system, composed of an n neural network array (where n is the number of edges in the circle graph of the number of possible base pairs), not only generates a near-maximum independent set but also predicts the secondary structure of ribonucleic acids within several hundred iteration steps. The simulator discovered several solutions which are more stable structures, in a sequence of 359 bases from the potato spindle tuber viroid, than previously proposed structures.

In retrospect: a commentaryon ‘Studies on the structure of ribonucleic acids’ by B. Magasanik and E. Chargaff Biochim. Biophys. Acta 7 (1951) 396–416

In retrospect: a commentaryon ‘Studies on the structure of ribonucleic acids’ by B. Magasanik and E. Chargaff Biochim. Biophys. Acta 7 (1951) 396–416

Structure of phenylalanine-accepting transfer ribonucleic acid and of its environment in aqueous solvents with different salts.

Yeast tRNA(Phe) was studied in different salt-containing solvents by UV absorbance and small-angle neutron scattering (SANS). This extends results obtained previously in NaCl and KCl solutions [Li, Z.-Q., Giegé, R., Jacrot, B., Oberthür, R., Thierry, J. C., & Zaccai, G. (1983) Biochemistry 22, 4380-4388]. As expected, at low concentrations of all salts studied, the tRNA molecule is unfolded. The importance of specific counterion interactions and the flexibility of the macromolecule are emphasized by the observation that it cannot take up its folded structure in N(CH3)4Cl solvents, even when that salt concentration is increased to 1 M, in the absence of Mg ions. In CsCl solvents, on the other hand, the folded conformation is obtained in salt concentrations above about 0.2 M, similar to NaCl or KCl. By a comparison of SANS results in CsCl H2O and CsCl 2H2O solvents with the data from NaCl and KCl solvents, thermodynamic and structural parameters were derived for the solvated macromolecule. All the data are accounted for, quantitatively, by a model for the particle in NaCl, KCl, or CsCl solution made up of tRNA76-, closely associated with 76 positive hydrated counterions, surrounded by an aqueous solvent layer that excludes salt (and, therefore, of density different from that of bulk solvent). The mass of water in that layer depends on salt concentration, and the values found are consistent with those predicted by the Donnan effect.

Pyrimidinones as biodynamic agents.

In view of the diverse types of biological activities associated with pyrimidinones and molecules having pyrimidinone as a component substructure, the pyrimidinone moiety may be considered as an important pharmacophore for incorporation in the design of molecules of biological interest. Pyrimidinones are also important because they are building blocks in the structures of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) which provide genetic material to the cell, direction for protein synthesis and also act as carriers of genetic information from one generation to another. Because of these reasons pyrimidinone nucleosides have shown great potential in the chemotherapy of cancer and viral infections. Although pyrimidinediones, e.g. ureidines, have also shown anticancer and antiviral activities and many condensed heterocyclic systems having pyrimidinone as a substructure, e. g. quinazolone, thienopyrimidone and thiazolopyrimidinone, etc., are associated with a variety of biological activities, these have not been considered in the present article.KeywordsAntiviral ActivityPyrimidine NucleosideMuscle Relaxant ActivityNormal Human LymphocyteAnorexigenic ActivityThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Effect of magnesium ion on the structure of the 5S RNA from Escherichia coli. An imino proton magnetic resonance study of the helix I, IV, and V regions of the molecule.

The imino proton nuclear magnetic resonance spectrum of Escherichia coli 5S ribonucleic acid (RNA) changes when the Mg2+ ion concentration drops below physiological levels. The transition between the physiological and low magnesium spectral forms of 5S RNA has a midpoint at approximately 0.3 mM Mg2+. Many of the most conspicuous changes observed in the downfield spectrum of 5S RNA as the magnesium concentration is reduced are due to adjustments in the structures of helices I and IV and the disappearance of resonances originating in helix V. The binding of ribosomal protein L25 to 5S RNA in the absence of magnesium stabilizes helix V structures.

Influence of charge on the stability of 5′-cytidine monophosphate in solution

The nucleotides constitute the back bone structure of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The importance of metal ions in biological processes like transcription, replication and translation reactions are very well established. Therefore, the attention the metal-nucleotide interactions have received, especially during the last decade is not surprising (Marzilli et al 1980; Hodgson 1977; Gillert and Ban 1977; Martin and Mariam 1979; Wilson et al 1982; Orenburg et al 1980; Scheller et al 1981). Among the nucleotides, mostly the nucleotide triphosphates have been studied (Taqui Khan and Rabindra Reddy 1973a, b, 1975, 1976; Taqui Khan and Martell 1967; Wallas 1958). However, very little is known on metal-mononucleotide interactions and that too with bivalent metal ions. The data with metals of higher oxidation states are not available in the literature. Therefore, it was considered important to investigate the interaction of 5'-cytidine monophosphate with various metal ions. Earlier we have studied the interaction of 5'-cytidine monophosphate with transition and alkaline earth metal ions along with other related systems (Rabindra Reddy et al 1985). In the present manuscript, we have extended our investigations to the trivalent lanthanides to study the influence of charge on the stability of the mononucleotides.

An effective method for the synthesis of the cap structure of eukaryotic messenger ribonucleic acids

A new promising “capping agent” (9) was synthesized by use of a lipophilic amino protecting group and an activatable pyrophosphate protecting group. This agent reacted homogeneously with 5′ 5′-nucleotides in the presence of AgNO 3 to afford the cap structures (m7G pppNu).

RNA secondary structures and their prediction

This is a review of past and present attempts to predict the secondary structure of ribonucleic acids (RNAs) through mathematical and computer methods. Related areas covering classification, enumeration and graphical representations of structures are also covered. Various general prediction techniques are discussed, especially the use of thermodynamic criteria to construct an optimal structure. The emphasis in this approach is on the use of dynamic programming algorithms to minimize free energy. One such algorithm is introduced which comprises existing ones as special cases.

X-ray structure of cytidine-5'-O-dimethylphosphate. Novel stacking between the ribosyl O(2') hydroxyl oxygen atom and the base.

The anionic oxygen atoms of the phosphodiester backbone of RNA and DNA are particularly susceptible to esterification by many mutagenic and carcinogenic alkylating agents. To better understand the geometric, electronic and conformational properties of the alkylated sugar phosphate moiety, the X-ray structure of the phosphotriesterified nucleotide, cytidine-5'-O-dimethylphosphate (C11H18N3O8P), was undertaken. The compound crystallizes in the monoclinic space group P2, with unit cell parameters of a = 5.741(2), b = 11.625(1), c = 11.425(1)A, beta = 94.43(2) degrees. The structure was solved by direct methods and refined by block-diagonal least-squares technique to an R index of 0.034 (Rw = 0.046). The D-ribofuranosyl ring is in the 3T2 twist conformation (P = 13.1(2) degrees, tau m = 36.7(2) degrees) and the conformation about the C(1')-N(1) glycosyl bond is anti (XCN = 8.3(2) degrees). The four P-O bond lengths are significantly shorter than those of the nonalkylated nucleotides. The three sets of phosphodiester linkages, (omega 'A, omega A), (omega 'B, omega B) and (omega 'C, omega C), take the (g-,t), (t,g) and (g-,t) conformations, respectively. There is no base-base or alkyl-base stacking, however, a novel intermolecular stacking is found between the ribosyl O(2') hydroxyl oxygen atom and a neighboring pyrimidine ring. This hydroxyl-base stacking interaction may have implications in the stabilization of the tertiary and quarternary structure of ribonucleic acids and nucleic acid-protein complexes.

Structure of phenylalanine-accepting transfer ribonucleic acid and of its environment in aqueous solvents with different salts.

Thermodynamic and structural parameters were measured for brewers' yeast tRNAPhe in solution in the range of 0.1-0.9 M monovalent salt (with and without 1 mM MgCl2), pH 7.0, by small-angle neutron scattering. Partial specific volumes and preferential interaction parameters were found to be similar to corresponding values measured by more conventional means in DNA [Eisenberg, H. (1981) Q. Rev. Biophys. 14, 141-172]. There is no evidence of a large conformational change in tRNAPhe in this range, and the molecule has a radius of gyration that is the same as that calculated from the crystal-structure coordinates (23 A). Transfer RNA in solution is made up of polyion tRNA76- and 76 positive monovalent ions (in absence of Mg2+). The data show the polyion to be surrounded by a shell of solvent that is significantly denser than bulk, whose structure depends on salt conditions. In 0.1 M NaCl, it has an excess mass of approximately 85 molecules of water. This would be accounted for, for example, by approximately 850 molecules of water if their density were 10% higher than that for bulk. The radius of gyration of the dense shell is approximately 30 A for NatRNA and approximately 35 A for KtRNA. The present study shows that the solvent around tRNA is a component of its structure that must be taken into account in understanding its function.

Structure of eukaryotic 5S ribonucleic acid: a study of Saccharomyces cerevisiae 5S ribonucleic acid with ribonucleases.

Structure of eukaryotic 5S ribonucleic acid: a study of Saccharomyces cerevisiae 5S ribonucleic acid with ribonucleases.