Effect of CDP-choline on the biosynthesis of nucleic acids and proteins in brain regions during hypoxia

The effect of CDP-choline on the in vivo incorporation of labeled precursors into DNA, RNA, and proteins in cerebral hemispheres, cerebellum, and brainstem of guinea pigs after hypoxic treatment was studied. The labeling of macromolecules extracted from the various subcellular fractions of these brain regions was also determined. Hypoxic treatment affected macromolecular labeling to a different extent in the three brain regions examined. CDP-choline treatment was not able to reverse the effect of hypoxia on DNA labeling, but it was able to remove the effect of hypoxia on RNA and protein labeling. The action of CDP-choline was particularly evident on the labeling of RNA in nuclei and mitochondria of the cerebellum and on the labeling of proteins in microsomes of the three brain regions examined.     

Differential accumulation of virus-specific RNA during the cell cycle of adenovirus-transformed rat embyro cells.

In adenovirus type 2-transformed rat embryo cells there is a threefold greater incorporation of [3-H]uridine into virus-specific RNA early in S phase than in late S or G2. This heightened accumulation of labeled RNA is true for both nuclear and cytoplasmic virus-specific labeling. Inhibition of DNA synthesis decreases the virus-specific RNA labeling, whereas reversal of inhibition again allows the elevated level of virus-specific RNA labeling.     

LABELING DURING CLEAVAGE (LDC), A NEW LABELING APPROACH FOR RNA

A new and efficient strategy for labeling of RNA sequences prior to their hybridization on high density DNA chip has been developed. Our approach which combines the fragmentation and the labeling is based on the reactivity of the 3′-phosphate of cleaved RNA fragments with a fluorescent molecule bearing aromatic bromomethyl function.     

Effects of -amanitin on in vitro labeling of RNA from defined nuclear components in salivary gland cells from Chironomus tentans

The effect of α-amanitin on nucleoside labeling of RNA in nucleoli, chromosomes, nuclear sap, and cytoplasm from Chironomus tentans salivary gland cells was investigated by radioautography and gel electrophoresis. Preribosomal RNA formation and processing in the nucleolus was not measurably influenced by the drug, and both 28 S and 18 S ribosomal RNA were transferred to the cytoplasm. In the chromosomes the heterogeneous RNA labeling was completely inhibited for the large size range (above 45–50 S) and partially for the low range. The labeling of 4–5 S chromosomal RNA was only moderately reduced. Most of the chromosomes showed radioautographically a disappearance of the normal band pattern, but some retained a pattern of weakly labeled bands. The electrophoretic results for the nuclear sap paralleled those for the chromosomes. The effect of α-amanitin on RNA labeling in these cells is similar but not identical to that of the substituted benzimidazole 5,6-dichloro-1(β-D-ribofuranosyl) benzimidazole (DRB).     

Site-specific chemical labeling of long RNA molecules

Site-specific labeling of RNA molecules is a valuable tool for studying their structure and function. Here, we describe a new site-specific RNA labeling method, which utilizes a DNA-templated chemical reaction to attach a label at a specific internal nucleotide in an RNA molecule. The method is nonenzymatic and based on the formation of a four-way junction, where a donor strand is chemically coupled to an acceptor strand at a specific position via an activated chemical group. A disulfide bond in the linker is subsequently cleaved under mild conditions leaving a thiol group attached to the acceptor-RNA strand. The site-specific thiol-modified target RNA can then be chemically labeled with an optional group, here demonstrated by coupling of a maleimide-functionalized fluorophore. The method is rapid and allows site specific labeling of both in vitro and in vivo synthesized RNA with a broad range of functional groups.     

Small molecular weight RNA components in sea urchin embryos

Polyacrylamide gel electrophoresis of RNA from Paracentrotus lividus embryos has shown this material to contain five RNA components of small molecular weight. The components are synthesized early in sea urchin development, simultaneously with tRNA and heterodisperse RNA. After the blastula stage, when synthesis of ribosomal RNA is activated, the labeling incorporated into small molecular weight RNA components constitutes a relatively decreasing proportion of the total labeling in RNA. When labeling is performed prior to the blastula stage, three of the small molecular weight RNA components are labeled to a similar or greater extent than “5” S RNA and the 26-ass RNA. The gel electrophoretic mobilities of the small molecular weight RNA components have been compared with those in Ehrlich ascites cells and found to be different.     

Effects of cordycepin on the synthesis of nuclear and cytoplasmic RNAs in embryonic cells of Xenopus laevis

Effects of cordycepin on the incorporation of [3H] guanosine into embryonic Xenopus cells were examined. Cordycepin inhibited the labeling not only of poly(A) + RNA, but of all the other major classes of RNAs. Cellular fractionation showed that this inhibition was much stronger in the labeling of cytoplasmic RNAs than of nuclear RNAs. [3H]Cordycepin was incorporated into both poly(A) + RNA and other RNA species.     

LIGHT AND ELECTRON MICROSCOPIC RADIOAUTOGRAPHY OF HEPATIC CELL NUCLEOLI IN MICE TREATED WITH ACTINOMYCIN D

Nucleolar partition induced by actinomycin D was used to demonstrate some aspects of nucleolar RNA synthesis and release in mouse hepatic cells, with light and electron microscopic radioautography. The effect of the drug on RNA synthesis and nucleolar morphology was studied when actinomycin D treatment preceded labeling with tritiated orotic acid. Nucleolar partition, consisting of a segegration into granular and fibrillar parts was visible if a dosage of 25 µg of actinomycin D was used, but nucleolar RNA was still synthesized. After a dosage of 400 µg of actinomycin D, nucleolar RNA synthesis was completely stopped If labeling with tritiated orotic acid preceded treatment with 400 µg of actinomycin D, labeled nucleolar RNA was present 15 min after actinomycin D treatment while high resolution radioautography showed an association of silver grains with the granular component. At 30 min after actinomicyn D treatment all labeling was lost. Since labeling was associated with the granular component the progressive loss of label as a result of actinomycin D treatment indicated a release of nucleolar granules. The correlation between this release and the loss of 28S RNA from actinomycin D treated nucleoli as described in the literature is discussed.     

Biochemical studies of mammalian oogenesis: synthesis and stability of various classes of RNA during growth of the mouse oocyte in vitro

The synthesis of various classes of RNA in mouse oocytes at different stages of growth has been examined after incubating follicles in medium containing radiolabeled uridine. After fractionation on poly(U)-Sepharose of radiolabeled oocyte RNA, of which about 83% is associated with the nucleus after a 5-hr labeling period, revealed that about 40–50% of the radiolabeled RNA behaved as poly(A)-containing RNA. This value remained fairly constant during the period of oocyte growth in which oocyte diameter increased from about 35 to about 55 μm. After a 5-hr labeling, the percentage of radiolabeled poly(A)-containing RNA in either the fully grown dictyate oocyte, metaphase II oocyte, or one-cell embryo was about 20%. After a 5-hr labeling, agarose gel electrophoretic analysis of the radiolabeled species of oocyte RNA obtained after fractionation on poly(U)-Sepharose revealed the presence of a putative ribosomal RNA precursor, ribosomal (28 and 18 S) RNA, transfer plus 5 S RNA and heterodisperse poly(A)-containing RNA. A significant fraction of the radiolabeled RNA species was quite large (>40 S). The ratios of the relative proportions of the radiolabeled ribosomal RNAs and transfer plus 5 S RNA remained essentially constant during oocyte growth. The stability of various classes of RNA was examined by incubating follicles with radiolabeled uridine, washing the follicles free of radioactivity and culturing the follicles under conditions which support oocyte growth in vitro (Eppig, 1977). Under these conditions, total oocyte radiolabeled RNA was quite stable as determined by retention of acid-insoluble radioactive material ($\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 28}\text{days}$). However, under conditions in which oocytes are viable but do not grow, the half-life of total RNA was about 4.5 days. Poly(A)-containing RNA was also very stable; after 8 days in culture, about 50% of the radiolabeled poly(A)-containing RNA present after 5 hr of labeling was still present. Agarose gel electrophoretic analysis of radiolabeled RNA in oocytes after 4 days of culture and after fractionation on poly(U)-Sepharose revealed the presence of ribosomal (28 and 18 S) RNA, transfer plus 5 S RNA, and heterodisperse poly(A)-containing RNA. At this time, these RNAs are located in the oocyte cytoplasm. In addition, the molecular weight distribution of poly(A)-containing RNA was significantly lower than that after 5 hr of labeling. The ratios of the relative proportions of radiolabeled ribosomal RNAs and transfer plus 5 S RNA were quite similar to those after 5 hr of labeling.     

Specific labeling approaches to guanine and adenine imino and amino proton assignments in the AMP–RNA aptamer complex

The secondary structure of a recently identified ATP-binding RNA aptamer consists of apurine-rich 11-residue internal loop positioned opposite a single guanine bulge flanked oneither side by helical stem segments. The ATP ligand targets the internal loop and bulgedomains, inducing a structural transition in this RNA segment on complex formation.Specifically, 10 new slowly exchanging proton resonances in the imino, amino and sugarhydroxyl chemical shift range are observed on AMP–RNA aptamer complex formation.This paper outlines site-specific labeling approaches to identify slowly exchanging imino(guanine) and amino (guanine and adenine) protons in internal loop and bulge segments ofcompact RNA folds such as found in the AMP–RNA aptamer complex. One approachincorporates 15N-labeled guanine (N1 imino and N2 amino positions) and 15N-labeledadenine (N6 amino position), one residue at a time, in the AMP-binding RNA aptamer, withlabeling incorporation through chemical synthesis facilitated by generating the aptamer fromtwo separate strands. The unambiguous assignments deduced from the 15N labeling studieshave been verified from an independent labeling strategy where individual guanines in theinternal loop have been replaced, one at a time, by inosines and assignments were made onthe basis of the large 2 ppm downfield shift of the guanine imino protons on inosinesubstitution. The strengths and limitations of the inosine-for-guanine substitution approachemerge from our studies on the AMP–RNA aptamer complex. The assignment of theinternal loop and bulge imino and amino protons was critical in our efforts to define thesolution structure of the AMP–RNA aptamer complex since these slowly exchangingprotons exhibit a large number of long-range intramolecular NOEs within the RNA, as wellas intermolecular NOEs to the AMP in the complex. The current application of specific 15Nand inosine labeling approaches for exchangeable imino and amino proton assignments in thenonhelical segments of an RNA aptamer complex in our laboratory complements selective 2Hand 13C approaches to assign nonexchangeable base and sugar protons in RNA andligand–RNA complexes reported in the literature.     

Age-dependent changes of nucleic acid labeling in different rat brain regions

The effects of aging on in vivo DNA and RNA labeling and on RNA content in various brain regions of 4-, 12-, and 24-month-old rats were investigated. No difference in [methyl-¹⁴C]thymidine incorporation into DNA of cerebral cortex and cerebelllum during aging was observed.The ratio of RNA/DNA content significantly decreased from 4 to 24 months of age in cerebral cortex, cerebellum and striatum. RNA labeling decreased by 15% in cerebral cortex of 24-month-old animals while in the other brain areas examined (cerebellum, hippocampus, hypothalamus, brainstem, striatum) did not change during aging.In the cerebral cortex, the ratio of the specific radioactivity of microsomal RNA to that of nuclear RNA, determined by in vivo experiments, was not affected by the aging process. A significant decrease of total, poly(A)+ RNA and poly(A)- RNA content was observed in the same brain area of 24-month-old rats compared to 4-month-old ones. Moreover, densitometric and radioactivity patterns obtained by gel electrophoresis of labeled RNA after in vitro experiments (tissue slices of cerebral cortex) showed a different ribosomal RNA processing during aging. In vivo chronic treatment with CDP-choline was able to increase RNA labeling in corpus striatum of 24-month-old animals.