Properties of RNA in formamide

Towards safer stable isotope probing - effect of formamide on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation

RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that ¹³C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate ¹³C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.

Design and analysis of hammerhead ribozyme activity against an artificial gene target

In vitro cleavage assays are routinely conducted to properly assess the catalytic activity of hammerhead ribozymes (HHR) against target RNA molecules like dengue virus RNA. These experiments are performed for initial assessment of HHR catalysis in a cell-free system and have been simplified by the substitution of agarose gel electrophoresis for SDS-PAGE. Substituting mobility assays enables the analysis of ribozymes in a more rapid fashion without radioisotopes. Here we describe the in vitro transcription of an HHR and corresponding target from T7-promoted plasmids into RNA molecules leading to the analysis of HHR activity against the RNA target by in vitro cleavage assays.

Nonenzymatic RNA ligation in water

We describe the nonenzymatic ligation of RNA oligomers in water. Dimers and tetramers are formed in a time-, pH-, and temperature-dependent reaction. Ligation efficiency depends on oligonucleotide length and sequence and is strongly enhanced by adenine-based nucleotide cofactors. Ligation of short RNA fragments could have liberated the prebiotic polymerization systems from the thermodynamically demanding task of reaching a (pre)genetically meaningful size by stepwise addition of one precursor monomer at the time.

Molecular complexity favors the evolution of ribopolymers

We have explored the stability of selected ribo oligomers in water and have determined the physical-chemical conditions in which the key 3'-phosphoester bond is more stable when embedded in the polymer than when present in the monomer. In these conditions, the spontaneous formation and the survival of ribo polymers are potentially favored. A narrow pH range was identified in which complex sequences resist degradation markedly more than monotonous ones, thus potentially favoring the evolution of sequence-based genetic information. Given that the founding property of a polymer is to maintain its polymeric form and its sequence information, these findings support the view that the evolution of pregenetic molecular information occurred based on intrinsic properties of nucleic polymers.

Single-strand conformation polymorphism analysis of PCR-amplified ribosomal DNA internal transcribed spacers to differentiate species of Aspergillus section Flavi

A novel genetic approach for classifying the species of Aspergillus Section Flavi is described here. This approach consists of PCR amplification of the 5.8S ribosomal DNA-intervening internal transcribed spacer regions (ITS I-5.8S-ITS II) with universal primers and of analysis of the PCR product by the principle of single-strand conformation polymorphism (SSCP). The approximately 570- to 590-bp PCR products were denatured and subjected to electrophoresis on a polyacrylamide gel supplemented with 20% formamide. The SSCP patterns of these species became more distinct by the addition of formamide to the gel and by visualization with ethidium bromide staining. A little interspecific length polymorphism among amplified ribosomal DNAs was enhanced to be detected by PCR-SSCP analysis. This analysis was capable of classifying 67 of the 68 Aspergillus Section Flavi strains tested into the following four groups, regardless of origin: A. flavus/A. oryzae, A. parasiticus/A. sojae, A. tamarii, and A. nomius. The results of restriction fragment length polymorphism analysis with PCR products of the ITS regions were consistent with those of PCR-SSCP analysis, except for A. nomius, which was not clearly differentiated from A. parasiticus/A. sojae. Nonradiolabelled PCR-SSCP analysis is inexpensive and practical to perform without special apparatus or skill and should assist in fungal morphological identification.

A short autocomplementary sequence in the 5' leader region is responsible for dimerization of MoMuLV genomic RNA

Previous work has shown that a region of Moloney murine leukemia virus (MoMuLV) RNA located between nucleotides 280 and 330 in the PSI region (nt 215-565) is implicated in the dimerization process. We show with a deletion from nucleotides 290-299 in PSI RNA transcripts and through an antisense oligonucleotide complementary to nucleotides 275-291 that the 283-298 region is involved in RNA dimer formation in vitro. In an attempt to further characterize the mechanism of dimer formation, a series of short RNA transcripts was synthesized which overlapps the PSI region of MoMuLV RNA. The dimerization of these RNAs is temperature dependent. The predicted secondary structure of the 278-303 region, as a function of temperature, reveals that this sequence is able to adopt two conformations: (1) the U288 AGCUA293 sequence in a loop; (2) part of the same nucleotides implicated in a stem. These results, together with thermodynamic analysis, strongly suggest that (1) the loop conformation of the UAGCUA sequence modulates the relative amount of RNA dimer and (2) a 16 bp long Watson-Crick base pairing is involved in RNA dimer formation. We propose that loop-loop recognition via the U288 AGCUA293 sequence leads to a stable structure induced by a stem-loop opening. Furthermore, our results do not support purine quartet formation as necessary for the dimerization of the 5' leader MoMuLV RNA.

Structure of viroid replicative intermediates: physico-chemical studies on SP6 transcripts of cloned oligomeric potato spindle tuber viroid

The structure and structural transitions of transcripts of cloned oligomeric viroid were studied in physico-chemical experiments and stability calculations. Transcripts of (+) and (-) polarity, from unit up to sixfold length, were synthesized from DNA clones of the potato spindle tuber viroid (PSTV) with the SP6 transcription system. Their structural properties were investigated by optical denaturation curves, high performance liquid chromatography (HPLC), electron microscopy, sedimentation-diffusion equilibrium and velocity sedimentation. Secondary structures of the RNAs and theoretical denaturation curves were calculated using an energy optimization program. The secondary structure of lowest free energy for unit length and oligomeric transcripts is a rod-like structure similar to that of the mature circular viroids. When this structure is used as a model for calculations, there is a large degree of agreement between the theoretical and the experimental denaturation curves. At high temperatures, however, (+) strand transcripts exhibited a transition which was more stable than expected from the calculations or than was known from curves of mature viroids. This transition arises from a rearrangement of the central conserved region of viroids to a helical region of 28 stable base pairs either intermolecularly leading to bimolecular complexes, or intramolecularly giving rise to a branched secondary structure. The rearrangement could be detected by electron microscopy, HPLC, and analytical ultracentrifugation. The helical region serves to divide up the oligomeric (+) strand into structural units which may be recognized by cleavage and ligation enzymes which process the oligomeric intermediates to circular mature viroids.

Phytohormone control of translatable RNA populations in sexual organogenesis of the dioecious plant Mercurialis annua L. (2n = 16)

A cell-free translation system was programmed with total, poly(A), non poly(A) and polysomal RNAs from male and female flowers of this plant with separated sexes. The peptide patterns obtained reflected differences in corresponding translatable RNAs. In total RNA products, three peptides were specific for males, two for females. One of the two male-specific polypeptides of high molecular weight was obtained from poly(A) RNAs and a female-specific one from non poly(A) RNAs. Differences between peptides common to both sexes reflected different concentrations of corresponding messengers. Similar results were obtained with polysomal RNAs. The male-specific RNAs were depending on high endogenous auxin concentrations while the female on active cytokinins. Cytokinin feminization of males induced the female-specific RNAs showing cytokinin action at pretranslational stages. Phytohormone roles are discussed.

Use of S1 nuclease and formamide in combination for the reassociation studies on GC-rich DNA

The optimal parameters in the use of nuclease S1 in DNA reassociation kinetics in the presence of formamide have been determined. The conditions are especially suitable for the study of DNA rich in mole percent GC. A 10-fold dilution of the reassociation samples leading to a decrease in both NaCl and formamide concentrations, consequently resulting in a lowering of Tm by only 1.5 degree C, and the S1 digestion at temperatures identical to the reassociation assay in order to retain the stability of the duplex, are two important aspects of this system. Under these conditions, the kinetics of reassociation followed the theoretically predicted pattern, while the earlier reported methods have shown lower values.

Inhibitory action of high formamide concentrations on excitation-contraction coupling in skeletal muscle

Strips of guinea pig ileum lose over 70% of their contractility when bathed in Krebs-Ringer solution containing 0.4-0.9 M formamide (FMD). This effect is not accompanied by an appreciable loss of tissue water and is totally reversed by washing the preparation in normal solution. Frog sartorius muscles also paralyze when immersed in Ringer containing FMD, but higher concentrations (1.0-2.0 M) and longer exposure times are required. Contractility is not recovered upon transferring these muscles to normal Ringer. However, the contractile proteins still respond to activator calcium as shown by the fact that these muscles still contract in the presence of caffeine. The membrane of muscles uncoupled by FMD retain electrical excitability, and neuromuscular transmission appears to be unimpaired. However, alterations in the early after-potential of the spikes suggest the occurrence of a sarcotubular disruption. Therefore, FMD appears to exert two separate effects on muscle: a reversible inhibition of contractility, as observed in ileal strips and an irreversible blockade due to an osmotic shock observed when frog muscles are returned to normal Ringer. The reversible effect is probably related to interference with the availability of activator calcium, since no marked inhibitory effects on the activities of the actomyosin-like and the calcium-dependent and -independent ATPases could be observed on FMD-treated subcellular fractions.

Size heterogeneity of ribosomal RNA in eukaryote evolution--1. rRNA molecular weights in species containing intact large ribosomal subunit RNA

1. The molecular weights of the two major rRNA species (L-rRNA, large ribosomal subunit RNA, and S-rRNA, small ribosomal subunit RNA) of a variety of deuterostomia, green plants and fungi have been investigated by gel electrophoresis in 99% formamide, pH 9; the overall pattern obtained under these conditions differs to some extent from that deduced by electrophoresis in neutral-salt solutions. 2. The molecular weights of the deuterostomian S-rRNA species have been conserved at a value of 0.65 X 10(6), whereas those of the L-rRNA have been kept at 1.40 X 10(6) in the lower species but have increased to 1.55 X 10(6) in birds and to 1.65 X 10(6) in mammals. 3. The molecular weights of the L-rRNA and S-rRNA components of the green plants (Dycotyledons, Monocotyledons and Gymnosperms) have been generally conserved at 1.30 X 10(6) and 0.65 X 10(6). 4. The molecular weight of the L-rRNA of the fungi has been conserved at 1.36-1.38 X 10(6), being 0.1 X 10(6) daltons heavier than that of the plants; the S-rRNA exhibits a limited degree of variability, ranging between 0.65 X 10(6) and 0.72 X 10(6).

Post-maturation of the plastid ribosomal RNA in the plant kingdom

The in vivo fragmentation of the plastid rRNA from plants situated at different places in the evolutionary sclae, with the exception of Algae, was analysed by electrophoresis using fully denaturing conditions. This fragmentation corresponds to an in vivo post-maturation. It exists only in some bacteria and is not random. Five main groups of fragments with the following real molecular weights (Mr) are found in 23 S: ca 0.9 x 10(6); 0.7 x 10(6); 0.45 x 10(6); 0.35 x 10(6) and 0.15 x 10(6). The existence of a large fragment (Mr = 0.9 x 10(6)) corresponds to a primitive type of fragmentation found in some archaic plants. Dicotyledons and several other groups have the same pattern of 23 S fragmentation, often comprising all the fragments mentioned above, whilst Graminaceae (Monocotyledons) constitute a special group with a very predominant 0.35 x 10(6) dalton fragment and the absence of the 0.45 x 10(6) dalton fragment. The plastid 16 S rRNA in all plants studied here has a Mr of 0.54 x 10(6) which is smaller than the 16 S of Escherichia coli taken as reference (0.56 x 10(6) dalton).

Genetic organization of the ribosomal transcription units of the yeast Saccharomyces carlsbergensis

The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S. 73, 2294-2298). Plasmid pBR 322, the molecular weight of which is known, was used as a standard for converting contour length of double-stranded DNA into molecular weight. The 140 yeast RTUs were found to be arrayed in tandem repeats, each repeat containing at most 0.4 X 10(6) D (about 6% of the length of the RTU) of non-transcribed spacer DNA. The repeats, in turn, are arranged in a number of clusters separated by much longer stretches of non-ribosomal DNA.

Synthesis of heterogeneous nuclear RNA in full-grown oocytes of Xenopus laevis (Daudin)

At various times following injection of either 3H-GTP or 32PO4 into full-grown (stage 6) Xenopus laevis oocytes, RNA has been extracted and fractionated on polyacrylamide gels. Based on size, base composition and incorporation data, we have defined the kinetics of synthesis and accumulation of ribosomal RNA (40S, 28S, 18S), heterogeneous RNA of high molecular weight (greater than 40S) and heterogeneous RNA migrating with molecular weights of from 4S to 40S. Nuclear isolations have been performed to determine the cellular distribution of these classes of RNA as a function of time. Evidence is presented which shows that stage 6 oocytes synthesize RNA which by virtue of its size, base composition, rapid turnover and nuclear location is equivalent to the heterogeneous nuclear RNA observed in somatic cells. In addition, the data suggest synthesis of a class of nuclear RNA with a half-life of several hours. A small fraction (5%) of the nuclear RNA is stable, enters the cytoplasm and may represent RNA added to the stockpile of maternal transcripts known to be present in stage 6 oocytes.

Size distribution of rat liver nuclear RNA containing mRNA sequences

Total rat liver poly(A)-containing polysomal mRNA was size-fractionated on polyacrylamide gels in 98% formamide. Complementary DNA (cDNA) was prepared from the 8--14-S mRNA fraction and separated into sequences representing abundant and non-abundant mRNAs. The cDNA complementary to the abundant small mRNA of the rat liver cell (approximately 20 species) was hybridized to nuclear RNA of different lengths to determine the size distribution of nuclear RNA molecules which contain these messenger sequences. It was found that: 1. All abundant 8--14-S poly(A)-containing mRNAs have larger nuclear precursor molecules; 20% of the different messenger sequences are found in nuclear RNA of several times their cytoplasmic length. 2. 70% of the mass of the examined nuclear messenger sequences is in RNA molecules of a size similar to their polysomal mRNA; 30% are in larger than 18-S RNA and 2% are between 37 S and 44 S. 3. The majority of small messenger-containing RNA molecules in the RNA prepared from isolated nuclei are of true nuclear origin, since their frequency distribution differs significantly from that of the polysomal 8--14-S mRNA.

Poly(A)-containing RNA in Tetrahymena pyriformis

Poly(A)-containing RNAs with sedimentation coefficients in the range 10-45 S and 10-35 S (Mr 0.2-3.3 x 10(6) and 0.2-2.2 x 10(6) approximately) are present in the nucleus and cytoplasm of T. pyriformis respectively. The poly(A) segments present in both nuclear and cytoplasmic poly(A)-containing RNAs have a chain length of 80 - 150 nucleotides. Significant amounts of high-molecular-weight poly(A)-containing RNAs (35 S, Mr 2.2 x 10(6) are found in the post-polysomal fraction of the cytoplasm (messenger ribonucleoprotein particles?) and also in large polysomes. In order to exclude the possibility that these high-molecular-weight species are products of non-specific aggregation, RNA preparations were submitted to severe denaturing conditions before analysis and all electrophoreses were carried out in the presence of 95% (v/v) formamide.

Size and structure of the genome of infectious pancreatic necrosis virus

The genome of infectious pancreatic necrosis virus consists of two segments of dsRNA, in equimolar amounts, with molecular weights of 2.5 X 10(6) and 2.3 X 10(6) daltons, as determined by polyacrylamide gel electrophoresis and autoradiography. The viral RNA was resistant to ribonuclease, and in sucrose gradient it co-sedimented at 14S with RNase resistant RNA from virus infected cells. Upon denaturation in 98% formamide, the viral genome sedi-mented at 24S in formamide sucrose gradient and became sensitive to RNase. Denatured 24S viral RNA did revert to its undenatured 14S form upon recentrifugation in aquaeous sucrose gradient (0.1 M NaCL), but co-sedimented with the denatured large size class of reovirus 25S RNA. The same results were obtained if the native viral RNA was pre-treated with ribonuclease before denaturation, indicating the absence of exposed single strainded regions in the viral genome. Since infectious pancreatic necrosis virus contains only two dsRNA segments it does not belong to the family Reoviridae and may represent a new group of viruses.

The molecular weights of yeast ribosomal precursor RNAs

The molecular weights of the predominant rRNA precursors as well as those of 26-S and 17-S mature rRNA from Saccharomyces carlsbergensis were determined by polyacrylamide gel electrophoresis in the presence of formamide. Mature 26-S + 5.8-S rRNA was found to have a molecular weight of 1.24 X 10(6) while their immediate precursor, 29-S RNA, had a molecular weight of 1.52 X 10(6). Values of 0.70 X 10(6) and 0.82 X 10(6) were obtained for the molecular weights of mature 17-S rRNA and its 18-S precursor. Finally the 37-S precursor, common to both 29-S and 18-S RNA, was found to have a molecular weight of 2.80 X 10(6). Each precursor rRNA, therefore, contains extra sequences not found at the next stage of maturation.