Ionic strength effects on the stability and conformation of Penicillium chrysogenum mycophage double stranded RNA

The use of UV light as a cross-linking agent for cells and tissue sections in in situ hybridization

UV cross-linking is introduced as a novel method to stabilize tissue on microscopic slides and to immobilize target molecules in biological material for in situ hybridization. UV illumination dramatically improves the stability of tissue sections and isolated cells on slides coated with gelatin/poly-lysine. Even during prolonged high-stringency washes, specimens remain firmly attached to the support layer. At the same time, the signal intensity is increased significantly whereas background levels remain as low as without UV illumination. These results indicate that while target RNAs and other molecules in the biological material are covalently cross-linked with their nearest neighbor molecules, tissues nonetheless remain penetrable, and target molecules remain accessible. We expect that this simple and efficient technique will find widespread applications in in situ hybridization methodology.

Length, mass, and denaturation of double-stranded RNA molecules compared with DNA

The contour lengths of linear, double-stranded (ds) RNAs from mycovirus PcV and Pseudomonas bacteriophage phi 6 have been measured with samples prepared for the electron microscope from 0.05 to 0.5 M NH4Cl solutions. A linear dependence of contour length on the logarithm of ionic strength was found and compared with that of dsDNA (pBR322, linearized and open-circular forms). Conditions for molecular weight determinations of any natural dsRNA by electron microscopy have been established, and the method has been calibrated with phi 6 dsRNA of known nucleotide sequence. The results imply that dsRNA in 0.20 M NH4Cl solution has a rise per basepair of 0.271 nm, which is shorter than that in the A-conformation (4%) and in the A'-conformation (10%). The thermal behavior of dsRNA in terms of melting temperature and exhibition of fine structure of melting curves was found to be generally similar to that of dsDNA, as expected from the literature. Folding of dsRNA in ethanolic solution was similar to that of dsDNA. However, in contrast to dsDNA, coiled coils could not be induced by ethanol, which is consistent with dsRNA being stiffer than dsDNA. Concerning dsDNA, the results show that a contraction in rise per basepair by 0.1 nm is coupled with an increase in the winding angle between basepairs by 0.47 degrees, as qualitatively predicted by polyelectrolyte theory.

A circular dichroism study of the Turnip yellow mosaic virus-RNA

We examined the circular dichroism spectra of intact Turnip yellow mosaic virus, freezed/thawed virus, empty capsid particles, and phenol extracted RNA. The circular dichroism signal of the empty capsid was found to contribute for less than 1% to the circular dichroism of the virus. Differences in the circular dichroism spectra indicate that TYMV-RNA exhibits different conformations when it is in situ in the virus, when it has been ejected by freezing/thawing and when it has been phenol extracted. Increase of the ionic strength up to 0.1 M NaCl led to conformational change of the RNA either freezed/thawed ejected or phenol extracted but not in situ in the capsid. Addition of spermidine (3 mM) induced a conformational change only for the phenol extracted RNA. These results are discussed with respect to the origin of the various conformational states of viral RNA.

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.

A circular dichroism study of the structure of Penicillium chrysogenum mycovirus

We have examined the absorption and circular dichroism spectra of intact Penicillium chrysogenum virus, empty capsid particles, and isolated double-stranded RNA. The absorbance at 260 nm of intact virus was less than 4% hypochromic relative to the absorbances of the free double-stranded RNA and free viral protein, indicating very little change in the base stacking interactions of the RNA. Circular dichroism studies of intact virus indicate that the capsid protein consists of 45% alpha-helix. Empty capsids, containing a protein of the same molecular weight as intact virus protein, were found to have 30% alpha-helix, suggesting a conformational change in the capsid upon assembly with RNA. The conformation of double-stranded RNA in the virus was slightly altered from the solution structure of the RNA in 0.01 M Na+ and resembled the conformation of double-stranded RNA partially bound with spermidine. However, the virus does not appear to contain polyamines. Electrophoretic experiments indicate a pH- and salt-titratable RNA binding site on the capsid protein in virus disrupted by urea or non-ionic detergents. The results are consistent with significant ionic interactions between the RNA and the capsid protein in the virus.

Structural requirements of polynucleotides for the activation of (2' - 5')An polymerase and protein kinase

Two enzymatic pathways are involved in the inhibitory effects of double-stranded (ds)RNA on protein synthesis in cell extracts derived from interferon-treated human fibroblasts or HeLa cells, an oligonucleotide polymerase that synthesizes (2'-5')An from ATP and a protein kinase that phosphorylates the alpha subunit of initiation factor eIF-2 as well as a polypeptide of Mr = 72,000. We have now evaluated the activation of both the (2'-5')An polymerase and protein kinase by a large variety of polynucleotides, triple-stranded and synthetic dsRNAs, homopolymers, alternating copolymers, triple-stranded polymers, purine-purine duplexes and purine-pyrimidine duplexes with modifications at either the pyrimidine or ribose moieties. All these polynucleotides have been the subject of previous interferon induction studies. Some polynucleotides, i.e. (I)n.(C)n and mycophage dsRNA, which have been recognized as excellent interferon inducers, were also potent activators of both (2'-5')An polymerase and protein kinase, whereas non-inducers such as (A)n. (X)n and (A)n. (br5U)n did not activate either the kinase or the polymerase. However, some polymers like (I)n.(br5C)n, (difl)n(C)n and (dIcl)n (C)n, while potent interferon inducers and kinase activators, behaved poorly as activators of the (2'-5')An polymerase. Other polymers, i.e. (dAfl)n (U)n and (A)n.(U)nl (I)n, that do not induce interferon, activated the kinase but not the polymerase. Finally, (I)n (s2c)n, a relatively potent interferon inducer, did not activate either kinase or polymerase. These findings indicate that there is no simple relationship between the interferon-inducing ability of dsRNAs and their stimulating effects on (2'-5')An polymerase and protein kinase activity.

Denaturation and renaturation of Penicillium chrysogenum mycophage double-stranded ribonucleic acid in tetraalkylammonium salt solutions

The base composition dependence of double-stranded ribonucleic acid (RNA) melting was studied by observing the structure and widths of melting transitions for Penicillium chrysogenum mycophage RNA as well as differences in melting temperatures of two RNAs of different base composition. Double-stranded RNA melting is independent of base compositions in 3.5 M Et4NCl and 4.6 M Me4NCl, where the melting temperatures are 25 and 92 degrees C, respectively. Double-stranded RNA renaturation rate constants are reported in Et4NCl solutions. The nucleation rate constant is about 10 times lower than that for double-stranded deoxyribonucleic acid. Analyses of renaturation kinetics results lead to the conclusion that each of the three similar but separable RNA segments of Penicillium chrysogenum mycophage is unique.

The effects of tetraalkylammonium salts on helix-coil transition parameters in natural and synthetic ribo- and deoxyribo-polynucleotides

Thermal transition profiles were recorded for a variety of natural and synthetic DNA and double-stranded RNA preparations in the presence of tetramethylammonium (TMA+) and tetraethylammonium (TEA+) cations. Double-stranded RNAs of natural origin, with GC contents of 50% exhibited the same profiles and Tm values as native DNA containing normal bases. Hence the tetraalkylammonium cations liquidate not only the effects of base composition, and the difference in stability between A-T and A-U base pairs (further confirmed by measurements with uracil-containing DNA from phage PBS-2), but also that of the 2'OH. In the presence of TMA+ cations, there is very marked enhancement of the stability of U-U base pairs in poly(rU) and poly(Um). In 2.4 M TEA, the 1:1 complex of poly(G) with poly (C) formed readily and melted reversibly with a Tm as low as 87 degrees C. At concentrations of TMA and TEA for which dTm/dXGC = 0, the Tm values for various phage DNA preparations containing atypical bases (phages T2, T4, phi e, phi W-14, PBS-2) differ appreciably from those with 'normal bases'. Analysis of these findings indicates that the selective interaction of TMA and TEA cations with A-T base pairs occurs in the minor groove of the DNA helix. The overall results show that the action of these quaternary ammonium cations is not due exclusively to preferential binding to A-T base pairs, but must involve other factors, including modifications of solvent structure. They also underline the utility of TMA and TEA solvent systems for placing in evidence transition profiles not accessible in other solvent systems.

The interaction of adriamycin and adriamycin analogues with nucleic acids in the B and A conformations

The reinforced intercalative binding to DNA typical of adriamycin and daunomycin can still occur if there is epimerisation at C4' or if the O-methyl group is lost or if the 9-substituents are deleted or if the 4'-hydroxyl group is lost. In the latter two cases however, there is a reduction in affinity for the DNA, supporting the suggested role of the 9-hydroxyl and 4'-hydroxyl groups in secondary stabilization of the complex. Epimerisation at C-1' or at C-3' alters but does not abolish the intercalative mode of binding to DNA whereas epimerisation at C-7 precludes intercalation of the chromophore into the helix of DNA. In contrast to the interaction with the B-form found in DNA, the parent drugs do not intercalate into nucleic acids possessing the A-conformation and none of the above-mentioned structural changes will allow intercalation into A-form nucleic acids.

Saltatory thermal denaturation of double-stranded viral RNAs

The double-stranded RNAs from bacteriophage phi6 and the replicative form of mengovirus denature upon heating in a series of abrupt steps which resemble the subtransitions (thermalites) observed within the high resolution profiles of small, naturally occurring DNA molecules. Such RNA thermalites are approximately an order of magnitude narrower than typical thermal subtransitions of nominally single-stranded RNA. We conclude that the same features of nucleotide sequence that give rise to cooperative denaturation in DNA genomes are to be found also in RNA genomes. Thus, high resolution thermal denaturation profiles are useful for characterizing double-stranded RNA molecules as well as native DNA in the size range of common viruses. A medium containing dimethylsulfoxide was required to lower the Tm of the RNA samples to a satisfactory temperature range. For double-stranded RNA in 50% dimethylsulfoxide, the dependence of Tm on G . C composition was greater than that of DNA in the same medium and also greater than that of double-stranded RNA in an aqueous medium. The fact that RNA thermalites are broader than DNA thermalites and that the melting temperature of double-stranded RNA has a greater dependence on base composition than that of DNA, indicates that at least one of the thermodynamic parameters for double helix formation in RNA is different from that in DNA.