Denaturation of RNA with dimethyl sulfoxide

The denaturation of single-stranded and double-stranded RNA's in solutions with varying proportions of dimethyl sulfoxide has been followed by changes in absorbancy, optical rotation, and—with a double-stranded form of bacteriophage of MS2 RNA— infectivity for bacterial spheroplasts. By these criteria the RNA's studied, including the synthetic polynucleotide rG:rC, are completely denatured at room temperature in high concentrations of this solvent. In lower concentrations, the T_m of the RNA preparation is decreased only slightly as the dimethyl sulfoxide concentration is raised until a critical concentration is reached. The T_m falls sharply with small further increases in dimethyl sulfoxide concentration. Sedimentation studies can be conducted directly in these media. The determination of sedimentation velocity in 99% dimethyl sulfoxide containing 0.001M EDTA provides a reliable estimate of RNA molecular weights.     

Regulation of gene expression by cytokines and virus in human cells lacking the type-I interferon locus.

A number of genes that are induced by type-I interferons are also activated by one or more other inducers, including double-stranded RNA, viruses, interferon-gamma, interleukin-1 and tumor necrosis factor. However, these inducers can also activate the expression of type-I interferons. Thus, the activation of type-I interferon-inducible genes by these other inducers could be direct, or a secondary consequence of the induction of interferon. To distinguish between these possibilities, we have used cell lines lacking all type-I interferon genes to study the direct effect of potential inducers on the expression of 14 interferon-inducible human genes. We show that double-stranded RNA, virus, interferon-gamma or tumor necrosis factor-alpha can act directly to induce specific subsets of type-I interferon-inducible genes in the absence of any possible type-I interferon involvement. The cis-acting element which confers inducibility by type-I interferon has been shown in some cases to confer inducibility by interferon-gamma, double-stranded RNA or virus as well. However, not all promoters containing such an element respond to both interferon and other inducers. Thus, the ability of a given gene to respond to different inducers most likely depends on the exact nature and specific combination of cis-acting elements present in its promoter.     

Complex of fd gene 5 protein and double-stranded RNA

We report the formation of complexes of the single-stranded DNA binding protein encoded by gene 5 of fd virus, with natural double-stranded RNAs. In the first direct visualization of a complex of the fd gene 5 protein with a double-stranded nucleic acid, we show by electron microscopy that the double-stranded RNA complex has a structure which is distinct from that of complexes with single-stranded DNA and is consistent with uniform coating of the exterior of the double-stranded RNA helix by the protein. Circular dichroism spectral data demonstrate that the RNA double helix in the complex is undisrupted, and that perturbation of the 228-nm circular dichroism assigned to protein tyrosines can occur in the absence of intercalation of nucleotide bases with protein aromatic residues. Our findings emphasize the potential importance of interaction with the sugar-phosphate polynucleotide backbone in binding of the fd gene 5 protein to nucleic acids.     

Interferon induction and utilization

The interferon mechanism offers the hope for moderate to high level prophylactic immunity of broad antiviral spectrum but of relatively short duration. Economic and biological considerations offer little hope for utilization of exogenous interferon as a prophylactic or therapeutic substance, unless but a small part of the total molecule be found to carry the activity. The real promise for interferon application is in the administration of suitable inducers so as to cause the body to produce and distribute its own interferon. Certain ribonucleic acids (RNA's) offer hope for high level potency as inducers without adverse effect. The condition for interferon induction by ribonucleic acids appears to be double- or multistrandedness and freedom from inhibitors. These can be of biologic or synthetic origin. The mechanism of action of interferon is not fully understood but appears to fit into the Jacob-Monod model involving two phases: first, a derepression by the inducer to cause the cell to form interferon and second, a derepression by interferon to cause recipient cells to form the active substance which acts by preventing translation from viral messenger RNA. Double or multistranded RNA of viral or other origin appears to be unique to the cell and serves as the alert to it to produce interferon in phase 1. Greatest need for interferon is clearly for those diseases in which there is a multiplicity of immunologic types in excess of the numbers which could be put into a vaccine as, e.g., the common cold and enteric viruses. There might be some overall therapeutic benefit also if inducer were given early enough in infection. Special value for interferon induction might derive by administration in early life before the development of immunologic maturity, as a means for preventing infection with oncogenic or other viruses. Additionally, suitable inducers might be capable of interrupting the reinfection cycle in virus-dependent malignancies. The favorable outlook for interferon utilization must always be tempered with the realization that under certain as yet undiscovered situations, adverse rather than beneficial effects might result from indution of interferon. It is not impossible that in certain special circumstances, as in ordinary immunologic responses, it might be more beneficial to negate rather than to promote the effect.     

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

Structured RNAs must fold into their native structures and discriminate against a large number of alternative ones, an especially difficult task given the limited information content of RNA''s nucleotide alphabet. The simplest motifs within structured RNAs are two helices joined by nonhelical junctions. To uncover the fundamental behavior of these motifs and to elucidate the underlying physical forces and challenges faced by structured RNAs, we computationally and experimentally studied a tethered duplex model system composed of two helices joined by flexible single- or double-stranded polyethylene glycol tethers, whose lengths correspond to those typically observed in junctions from structured RNAs. To dissect the thermodynamic properties of these simple motifs, we computationally probed how junction topology, electrostatics, and tertiary contact location influenced folding stability. Small-angle X-ray scattering was used to assess our predictions. Single- or double-stranded junctions, independent of sequence, greatly reduce the space of allowed helical conformations and influencing the preferred location and orientation of their adjoining helices. A double-stranded junction guides the helices along a hinge-like pathway. In contrast, a single-stranded junction samples a broader set of conformations and has different preferences than the double-stranded junction. In turn, these preferences determine the stability and distinct specificities of tertiary structure formation. These sequence-independent effects suggest that properties as simple as a junction''s topology can generally define the accessible conformational space, thereby stabilizing desired structures and assisting in discriminating against misfolded structures. Thus, junction topology provides a fundamental strategy for transcending the limitations imposed by the low information content of RNA primary sequence.     

Design of nucleoside, oligonucleotide and polynucleotide analogues as antiviral agents

Several approaches can be envisaged in the design of nucleoside and oligo- or polynucleotide analogues with selective antiviral activity: (i) deoxythymidine (dThd) or deoxycytidine (dCyd) analogues which are specifically recognized as substrate by the virus-induced dThd-dCyd kinase; (ii) adenosine analogues which impair transmethylation reactions (or polyamine biosynthesis), by virtue of an inhibition of S-adenosylhomocysteine hydrolase; (iii) (2'-5')-oligonucleotide analogues derived from pppA(2'p5'A)2, an important intermediate in the antiviral action of interferon; (iv) oligo(deoxy)nucleotides that are complementary to a well-defined nucleotide sequence of the viral genome; (v) single-stranded homopolynucleotides that act as antitemplates for virus-associated RNA or DNA polymerases; and (vi) double-stranded homopolynucleotides that may be pursued for their interferon-inducing potentials.     

Interaction of poly-L-lysine with nucleic acids. II. Poly(A+U), poly(A+2U), and rice dwarf virus RNA

The optical density–temperature profile of double-stranded poly(A + U), triple stranded poly(A + 2U), and double-stranded RNA from rice dwarf virus in solutions with and without poly-L -lysine has been examined. When poly-L -lysine is added, more than one melting temperature T_m is observed for poly(A + U) and poly(A + 2U). One of them is considered to correspond to the melting of the polynucleotide molecule free from poly-L -lysine, and another to the melting of a polynucleotide–poly-L -lysine complex. For rice dwarf virus RNA, the T_m assignable to the complex is not found to be lower than 99°C. In every case, however, the hyperchromicity observed at the T_m of the free poly-nucleotide molecule is lowered linearly as the amount of poly-L -lysine added to the solution increases. This fact is taken as indicating that there is a stoichiometric complex formed. The stoichiometric ratio lysine/nucleotide in each complex is determined by examining the relation between the amount of poly-L -lysine added to the solution and the percentage of hyperchromicity remaining at T_m of the free polynucleotide molecule. The ratio is found to be 2/3 for all of the three complexes. A discussion is given on the molecular conformations of four types of polynucleotide–polylysine complex hitherto found: (A) double-stranded DNA plus poly-L -lysine in which the lyslne/nucleotide ratio is 1, (B) three-stranded RNA [poly(A + 2U)] plus poly-L -lysine in which the ratio is 2/3, (C) double-stranded RNA [poly (A + U) or rice dwarf virus RNA] plus poly-L -lysine in which the ratio is 2/3, and (D) double-stranded RNA [poly(I + C)] plus poly-L -lysine in which the ratio is 1/2.     

Effect of the virus-inhibiting factor or interferon on the division and differentiation of murine leukemic cells]

Myeloblasts of a clone originating from a spontaneous myeloid leukemia in mice were induced to form macrophages by the virus-inhibiting factor or interferon or its inducers such as Newcastle disease virus and double-stranded RNA.     

Optimal alphabets for an RNA world

Experiments have shown that the canonical AUCG genetic alphabet is not the only possible nucleotide alphabet. In this work we address the question ''is the canonical alphabet optimal?'' We make the assumption that the genetic alphabet was determined in the RNA world. Computational tools are used to infer the RNA secondary structure (shape) from a given RNA sequence, and statistics from RNA shapes are gathered with respect to alphabet size. Then, simulations based upon the replication and selection of fixed-sized RNA populations are used to investigate the effect of alternative alphabets upon RNA''s ability to step through a fitness landscape. These results show that for a low copy fidelity the canonical alphabet is fitter than two-, six- and eight-letter alphabets. In higher copy-fidelity experiments, six-letter alphabets outperform the four-letter alphabets, suggesting that the canonical alphabet is indeed a relic of the RNA world.     

Depression of hepatic cytochrome P-450-dependent monooxygenase systems with administered interferon inducing agents.

Cytochrome P-450-dependent monooxygenase activities and cytochrome P-450 levels were depressed in hepatic microsomes from rats treated with 12 interferon inducing agents of various types: small molecules (e.g. tilorone), an RNA virus (Mengo), a fungal mycophage (statolon), liver RNA, a synthetic double-stranded polynucleotide (poly rI · poly rC), a bacterial lipopolysaccharide ($\text{E.}\text{coli}$ endotoxin) and an attenuated bacteria ($\text{B.}\text{pertussis}$ vaccine). The results suggest that the depression of hepatic cytochrome P-450-dependent monooxygenase systems may be a general property of interferon inducing agents.     

Mechanisms of chain folding in nucleic acids. The (omega, omega) plot and its correlation to the nucleotide geometry in yeast tRNAPhe1.

The (omega', omega) polot depicting the internucleotide P-O bond rotation angles in yeast phenylalanyl transfer RNA has established the interdependence of the phosphodiesters and the nucleotide geometries in the folding of the polynucleotide backbone. The plot distinguishes the regions characteristic of secondary helical structures and tertiary structural loops and bends. The folding of the polynucleotide chain is accomplished either solely by rotations around the P-O bonds or in concert with rotations around the nucleotide C4'-C5' bond with or without changes in the sugar ring pucker. In spite of differences in nucleotide sequence and intraloop tertiary interactions in the anticodon and pseudouridine loops, a characteristic repeating structural unit is found for the sugar-phosphate backbone of the tetranucleotide segment around the sharp turns.     

Ebolavirus VP35 Coats the Backbone of Double-Stranded RNA for Interferon Antagonism

Recognition of viral double-stranded RNA (dsRNA) activates interferon production and immune signaling in host cells. Crystal structures of ebolavirus VP35 show that it caps dsRNA ends to prevent sensing by pattern recognition receptors such as RIG-I. In contrast, structures of marburgvirus VP35 show that it primarily coats the dsRNA backbone. Here, we demonstrate that ebolavirus VP35 also coats the dsRNA backbone in solution, although binding to the dsRNA ends probably constitutes the initial binding event.     

Raman spectral studies of nucleic acids. XI. Conformations of yeast tRNAPhe and E. coli ribosomal RNA in aqueous solution and in the solid state

Laser-excited Raman spectra of tRNA^Phe from yeast and of fractionated 16S and 23S rRNA from E. coli are reported for samples in aqueous solution and in the solid state. The Raman scattering spectrum of each RNA is not significantly altered by the change from an aqueous to a solid environment and displays the same characteristic frequencies and intensities associated with ordered polyribonucleotide structures. Unlike DNA, the backbone conformation of RNA thus appears to be largely insensitive to gross changes in the degree of hydration. Raman scattering from the phosphate group vibrations of aqueous tRNA_yeast^Phe is qualitatively and quantitatively the same as obtained from previously studied tRNA's and is indicative of a highly ordered conformational structure in which some 85% of the nucleotide residues are in ordered configurations. The major differences observed between spectra of tRNA and rRNA are attributed to differences in base composition of these RNA's.     

Interferon: ten stories in one. A short review of some of the highlights in the history of an almost quinquagenarian

This short review article on some pertinent observations in the unfolding story of interferon is dedicated to Professor Ilona Béládi on the occasion of her 80th birthday. This by no means covers the whole story on interferon. It just highlights some of the more striking findings made with interferon (or its inducers) over a time span of almost 50 years since its original discovery (in 1957) by Isaacs and Lindenmann. These observations concern (i) the induction of interferon by synthetic polyanions such as polyacrylic acid and polymethacrylic acid; (ii) the prolonged antiviral activity shown by polyacrylic acid in vivo; (iii) the interferon-inducing ability of double-stranded RNAs such as poly(I) x poly(C) and (iv) mismatched derivatives thereof (i.e. ampligen); (v) the cloning and expression of interferon-beta, and (vi) its usefulness in the treatment of multiple sclerosis; (vii) the potential of (pegylated) interferon-alpha in the treatment of hepatitis C and (viii) the therapy/prophylaxis of SARS; (ix) the efficacy of interferon (inducers) in the experimental treatment of flavivirus encephalitis and enterovirus myocarditis; and, finally, (x) the role of interferon in the activity shown by S-adenosylhomocysteine inhibitors such as 3-deazaneplanocin A against experimental Ebola virus infections in mice.     

Delayed cytosolic exposure of Japanese encephalitis virus double-stranded RNA impedes interferon activation and enhances viral dissemination in porcine cells

Interferon is a principal component of the host antiviral defense system. In this study, abortive focus formation by Japanese encephalitis virus (JEV) in primate cells was accompanied by early interferon induction, while productive focus formation in porcine cells was associated with a late interferon response. Neutralization antibodies against interferon relieved the restricted infection in primate cells, and increasingly larger foci were generated as treatment with exogenous interferon was delayed, thereby establishing a solid correlation between interferon response and viral dissemination. However, delayed interferon induction in JEV-infected porcine cells occurred in the absence of active inhibition by the virus. We further demonstrated that JEV mediates interferon activation through double-stranded RNA and cytosolic pattern recognition receptors. Immunofluorescence and subcellular fractionation studies revealed that double-stranded RNA is concealed in intracellular membranes at an early phase of infection but eventually appears in the cytosol at later periods, which could then allow detection by cytosolic pattern recognition receptors. Interestingly, cytosolic exposure of double-stranded RNA was delayed in porcine cells compared to primate cells, independent of total double-stranded RNA levels and in correlation with the timing of the interferon response. Furthermore, when double-stranded RNA was artificially introduced into the cytosol of porcine cells, more rapid and robust interferon activation was triggered than in viral infection. Thus, cytosolic exposure of JEV double-stranded RNA is imperative for interferon induction, but in cell lines (e.g., porcine cells) with delayed emergence of cytosolic double-stranded RNA, the interferon response is late and viral dissemination is consequently enhanced.     

Induced circular dichroism of acridine orange bound to double-stranded RNA and transfer RNA

The induced circular dichroism (CD) in the visible region of acridine orange bound to the double-stranded RNA from cytoplasmic polyhedrosis virus and to yeast tRNA has been measured as a function of RNA phosphate-to-dye ratio (P/D), under the conditions of 0.01 M Na⁺ at pH 7.0. The shape of the CD spectrum of acridine orange bound to the double-stranded RNA was quite different from the spectrum of the dye bound to DNA. The CD spectral features of acridine orange bound to the double-stranded regions in tRNA closely resembled those of the double-stranded RNA-dye complex, suggesting that the dyes bind similarly to the two RNA's. It was further found that the CD spectrum of the tRNA-dye complex at sufficiently high P/D ratios, which is assignable to monomeric, intercalated dye to the base-paired parts in tRNA, is also distinct from the corresponding spectrum of the DNA-dye complex.     

Synthesis of the small molecular weight monodisperse nuclear RNA's in contact-inhibited cell cultures

The small molecular weight monodisperse nuclear RNA's are synthesized in contact-inhibited cultures of 3T3 cells. The level of synthesis of these RNA's, and of ribosomal and transfer RNA's, appears to be only 8–20% of that observed in growing cultures. The synthesis of all of these relatively stable RNA species may thus be coordinately controlled.     

Antisense RNA regulation of the fatB iron transport protein gene in Vibrio anguillarum

We have recently identified an antisense RNA (RNAα) that regulates the expression of the fatA iron transport gene encoding the outer membrane receptor for the iron-anguibactin complex. In this work, we demonstrate that RNAα also inhibits the expression of fatB , which encodes a 35 kDa iron transport protein and has domains homologous to other periplasmic transport proteins. The expression of fatA and fatB is repressed under iron-rich conditions, in which RNAα is induced. RNAα is homologous to two-thirds of the coding region of fatB . By cloning RNAα coding sequences immediately downstream of a tet promoter, we were able to obtain constitutive expression of the antisense RNA. The cloned region contains approximately 83% of the 650 nucleotide RNAα and is complementary to only 51% of the fatB mRNA but is still capable of causing a repression of the expression of the fatB gene. Our results in this work demonstrate that RNAα probably affects the stability of the fatB -specific mRNA.