Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA modifications”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,621 records · Page 90Linked to original sources
PubMed1979

A unique method utilizing antinucleotide antibodies for evaluating changes in the levels of modified nucleosides of tRNAs from crude extracts of whole cells.

The utilization of antibodies directed toward modified nucleosides in evaluating changes in the levels of certain modified nucleosides in transfer RNA is reported. Antibodies directed toward the N6-(delta 2-isopentenyl)adenosine modification were used in this model system with a mutant strain of Escherichia coli designated ipaA. The procedure is rapid, sensitive, and specific. In addition, it does not depend on the existence of an in vitro remodification system or any radiochemical labeling of the tRNA. By varying the extraction technique, the method could be applied to procaryotic or eukaryotic cell lines. The existence of antibodies specific for other nucleoside modifications makes this a system that is potentially applicable to a variety of deficiencies in the modification of both tRNA and rRNA.

Antibodies↗
PubMedDate not supplied

Stimulation of protein, RNA, and nucleotide synthesis in lymphocytes after abdominal surgery is not affected by postoperative amino acid supply.

The effects of abdominal surgery on protein, RNA, and de novo purine nucleotide synthesis in lymphocytes, and modification of these changes by postoperative amino acid supply, were investigated in 24 patients undergoing cholecystectomy (n = 12) or removal of gastric cancer (n = 12). Mono-nuclear cells were isolated from the peripheral venous blood and incubated with radioactive tracers in vitro. Protein and RNA synthesis, as measured using [14C] glycine and [3H]uridine, respectively, increased postoperatively. Nucleotide synthesis determined by the incorporation of radioactivity from [14C] glycine into nucleotides increased simultaneously. The concentration of 5-phosphoribosyl 1-pyrophosphate (PRPP) estimated by the incorporation of [14C]adenine into nucleotides also increased. These changes were greater and of longer duration in patients with cancer operation than in those with cholecystectomy. In neither case were they affected by the amount of amino acid intake, or increases in energy intake. These results suggest that abdominal surgery stimulates protein and ribonucleic acid (RNA) synthesis in lymphocytes. Increased RNA synthesis may be ensured by increased synthesis of nucleotides, and increased PRPP concentrations appear to regulate the rate of nucleotide synthesis. The responses are apparently dependent upon the severity of surgery, but unrelated to the amount of amino acid supplied postoperatively.

Adult↗
PubMed1987

Enhancement of the chemical transformation of Chinese hamster embryo cells in vitro by 7-methylguanine.

The RNA catabolite 7-methylguanine has been shown to inhibit queuine modification of tRNA in Chinese hamster embryo cells under conditions leading to in vitro transformation. Phorbol ester tumor promoters also induce queuine hypomodification of tRNA in normal human cells, and this effect was reported to be correlated directly to the appearance of an altered (transformed) cell phenotype. Based on this common macromolecular alteration, 7-methylguanine was evaluated for its ability to enhance the chemically induced transformation of cultured cells. Two-stage initiation-promotion experiments were undertaken with Chinese hamster embryo cells in vitro to compare the effects of 7-methylguanine to known tumor promoters subsequent to initiation with 3-methylcholanthrene. 7-Methylguanine was able to increase significantly the expression of type III foci as well as anchorage-independent growth, thereby confirming that it can act as a promoting agent in vitro. Methylated guanines that do not induce queuine hypomodification of tRNA were not capable of enhancing these characteristics of in vitro transformation. The results suggest that 7-methylguanine may be a natural, endogenous promoting agent, and that changes in queuine modification of tRNA may play a fundamental role in the promotion of carcinogenesis.

Animals↗
PubMed1994

Pseudouridine formation in U2 small nuclear RNA.

U2 small nuclear RNA contains 13 pseudouridine (psi) nucleotides, of which 11 are clustered in 5' regions involved in base-pairing interactions with other RNAs in the spliceosome. As a first step toward understanding the psi formation pathway in U2 RNA, we investigated psi formation on unmodified human U2 RNA in a HeLa cell extract system. Psi formation was found to occur specifically within only those RNase T1 oligonucleotide fragments of U2 RNA known to contain psi in vivo. Using 5-fluorouridine (FUrd)-containing U2 RNAs as specific inhibitors of psi formation in non-FUrd-substituted substrate U2 RNA, we found that wild-type FUrd-containing U2 RNA as well as several FUrd-containing mutant U2 RNAs completely inhibited psi formation. In contrast, certain other mutant U2 RNAs containing FUrd displayed reduced inhibitory capacity. In these cases psi modifications occurred in specific RNase T1 fragments of the substrate U2 RNA only if the FUrd-containing competitor RNA was mutated at or near this site. Formation of psi at one site in U2 RNA appeared to be neither dependent on prior psi formation at another site or sites nor required for subsequent psi formation elsewhere in the molecule. This autonomous mode of psi formation may be driven by multiple psi synthase enzymes acting independently at different sites in U2 RNA.

Animals↗
PubMed2004

Synthesis, Purification and Crystallization of Guanine-rich RNA Oligonucleotides.

Guanine-rich RNA oligonucleotides display many novel structural motifs in recent crystal structures. Here we describe the procedures of the chemical synthesis and the purification of such RNA molecules that are suitable for X-ray crystallographic studies. Modifications of the previous purification methods allow us to obtain better yields in shorter time. We also provide 24 screening conditions that are very effective in crystallization of the guanine-rich RNA oligonucleotides. Optimal crystallization conditions are usually achieved by adjustment of the concentration of the metal ions and pH of the buffer. Crystals obtained by this method usually diffract to high resolution.

Journal Article↗
PubMed1997

Identification of functional domains in the self-cleaving Neurospora VS ribozyme using damage selection.

Varkud Satellite (VS) RNA contains a small self-cleaving RNA motif that is distinct in its sequence and secondary structure from the hammerhead, hairpin, and hepatitis delta virus ribozymes, which are found in other natural RNAs. We have used a base specific chemical damage selection (modification interference) assay to identify functionally important nucleotides and structural elements in VS RNA. Many modified bases interfered with self-cleavage and most of these clustered at helix junctions, certain internal loops, and in a long-range pseudoknot; these correspond to previously determined sites of magnesium-dependent protection from chemical modification. The clustering suggests that these bases are important not only for a large number of individual interactions, but because they form a smaller number of structural elements that are important for activity. Modification of bases in other single-stranded regions, which did not exhibit magnesium-dependent protection, generally did not interfere with activity, suggesting that some of these regions might be dispensable for function. Surprisingly, we found a separate cluster of bases whose modification significantly enhanced cleavage. These bases appear to form a structural element that naturally attenuates the self-cleavage reaction. In natural VS RNA this attenuator structure may affect the cleavage/ligation equilibrium by inhibiting circle re-opening, thereby helping to maintain the RNA in a circular form, which is the predominant form of VS RNA in vivo. Taken together, the results of the damage selection experiments localize the catalytic core of VS RNA to a small subset of the previously determined minimal contiguous sequence.

Base Sequence↗
PubMed1993

Similarity of the 5' and 3'-TAR secondary structures in HIV-1.

The structure of the TAR RNA element transcribed at the 5' end of the R region of the human immunodeficiency virus is compared to the structure of its duplicate sequence in the 3' R region of the viral genome. Based on the 5'-TAR secondary structure already described, we assessed by RNase T1 primer extension assay the degree of similarity between the 5'-TAR and the 3'-TAR RNA secondary structures. We also analysed the influence of modifications in the flanking sequences. We show that the secondary structures of the 5'-TAR and the 3'-TAR are very similar and are not influenced by the flanking sequences.

Base Composition↗
PubMed1992

Exploiting the chemical synthesis of RNA.

A number of nucleotide phosphoramidites are now available that permit the chemical synthesis of RNA, modified RNA and RNA-DNA chimeric oligonucleotides. Since the chemical strategy allows the introduction of a particular modification at any given site in a nucleotide polymer, very subtle and specific questions regarding structure-function relationships in RNA may be addressed.

Base Sequence↗
PubMed1985

Widespread distribution of a 7S RNA in archaebacteria.

An RNA of nonribosomal origin was found in the extreme halophilic bacteria. This novel small RNA was found to be a homogeneous species by RNA fingerprinting. Analysis of the ribonuclease T1 oligonucleotides gave no evidence of the presence of posttranscriptional modifications. Comparisons of electrophoretic mobility with other RNAs of known size suggest that this is a 7S RNA containing 325-375 nucleotides. An RNA of similar mobility was found in all major divisions of the archaebacteria. Insufficient sequence information is available to determine whether these RNAs are homologs of any other known small RNA.

Archaea↗
PubMed1977

[T2 DNA, modified by 2,2,6,6-tetramethyl-4-bromoacetooxypiperidine-i-oxyl as a template for RNA polymerase from E. coli B].

T2-DNA was modified by 2,2,6,6-tetramethyl-4-bromoacetooxypiperidine-1-oxyl (I) at different NaCl concentrations (10(-1) M NaCl--10(-4) M NaCl). Modified DNA were investigated as templates for the RNA-polymerase from E. coli B. It was shown that T2-DNA modified I in 0,1 M NaCl completely preserves the native secondary structure, has a low degree modification (1 molecule I per 1000-2000 nucleotide pairs), but is a noneffective template for the RNA-polymerase from E. coli B (20%-40% as compared with unmodified T2-DNA). Under these conditions the modification occurs probably at the "weakest" (readily melting) sites of DNA. The role of these "weak" sites on DNA as promotors is discussed. The modification of T2-DNA by reagnet I has a stronger inhibitory effect on the total RNA synthesis than on the RNA-synthesis stable to rifampicin. Possible existence of two kinds of "early" promotors on T2-DNA is assumed.

Coliphages↗
PubMed1995

The tetrodotoxin-insensitive sodium current in rat dorsal root ganglia is unlikely to involve the expression of the tetrodotoxin-resistant sodium channel, SkM2.

Tetrodotoxin-insensitive (TTX-I) sodium currents have been recorded from newborn and adult rat sensory neurons, but the sodium channel gene(s) responsible for the TTX-I current are unknown. Because SkM2, one of six voltage-sensitive sodium channel genes cloned from rat, encodes the only cloned channel that is relatively resistant to tetrodotoxin, we sought to test whether the TTX-I current in rat sensory neurons is due to the SkM2 channel. We hypothesized that the TTX-I current might be generated from (1) an RNA splicing variant of SkM2, (2) post-translational modification of the SkM2 protein, or (3) interaction with alternate additional channel subunits. SkM2 mRNA expression was examined in newborn rat dorsal root ganglia (DRG) by RNase protection assay. No SkM2 expression was detected. Therefore, we conclude that the TTX-I sodium current in DRG is unlikely to result from the expression of the SkM2 gene.

Alternative Splicing↗
PubMed2000

Recognition of a conserved class of RNA tetraloops by Saccharomyces cerevisiae RNase III.

Ribonucleases III are double-stranded RNA (dsRNA) endonucleases required for the processing of a large number of prokaryotic and eukaryotic transcripts. Although the specificity of bacterial RNase III cleavage relies on antideterminants in the dsRNA, the molecular basis of eukaryotic RNase III specificity is unknown. All substrates of yeast RNase III (Rnt1p) are capped by terminal tetraloops showing the consensus AGNN and located within 13-16 bp to Rnt1p cleavage sites. We show that these tetraloops are essential for Rnt1p cleavage and that the distance to the tetraloop is the primary determinant of cleavage site selection. The presence of AGNN tetraloops also enhances Rnt1p binding, as shown by surface plasmon resonance monitoring and modification interference studies. These results define a paradigm of RNA loops and show that yeast RNase III behaves as a helical RNA ruler that recognizes these tetraloops and cleaves the dsRNA at a fixed distance to this RNA structure. These results also indicate that proteins belonging to the same class of RNA endonucleases require different structural elements for RNA cleavage.

Bacteriophage T7↗
PubMed2004

Deoxyribozymes: DNA catalysts for bioorganic chemistry.

Deoxyribozymes are DNA molecules with catalytic activity. For historical and practical reasons, essentially all reported deoxyribozymes catalyze reactions of nucleic acid substrates, although this is probably not a fundamental limitation. In vitro selection strategies have been used to identify many deoxyribozymes that catalyze RNA cleavage, RNA and DNA ligation, and a variety of covalent modification reactions of nucleic acid substrates. Many deoxyribozymes are capable of catalysis with substantial rate enhancements reaching up to 10(10)-fold over background, and their very high selectivities would often be difficult or impossible to achieve using traditional organic synthesis approaches. This report summarizes the current utility and potential future applications of deoxyribozymes from the bioorganic chemistry perspective.

Catalysis↗
PubMed2002

The relationship of preventable opportunistic infections, HIV-1 RNA, and CD4 Cell counts to chronic mortality.

BACKGROUND: Both HIV-1 RNA and absolute CD4 cell counts have been identified as important predictors of HIV-1 disease progression and mortality. The independent impact of opportunistic infections on the risk of chronic mortality, defined as death beyond 30 days of an opportunistic infection, has not been studied when controlling for HIV-1 RNA. Our objective was to determine the relationship between a history of any of five preventable opportunistic infections (Pneumocystis carinii pneumonia, Mycobacterium avium complex, toxoplasmosis, cytomegalovirus, and candida esophagitis) and chronic mortality. METHODS: Using the Multicenter AIDS Cohort Study (MACS) public use data set of 2193 HIV-infected men in four U.S. cities, we employed a Cox regression model to estimate the impact of a history of preventable opportunistic infection on chronic mortality while controlling for maximum HIV-1 RNA, CD4 cell count, use of antiretroviral drugs, and age. FINDINGS: The chronic mortality rate among individuals with a history of preventable opportunistic infection was 66.7 per 100 person-years compared with 2.3 per 100 person-years for those without a history of preventable opportunistic infection (RR = 28.4, 95% CI: 24.7-32.8). In the adjusted analysis, the relative hazard of death for those with a history of preventable opportunistic infections was 7.0 (5.8-8.3), whereas antiretroviral therapy was associated with a decreased risk of death (0.37 [0.30-0.44]). We found no association between maximum HIV-1 RNA and chronic mortality. There was statistically significant effect modification between preventable opportunistic infections and CD4 cell count (p <.0001). INTERPRETATION: Preventable opportunistic infections cause not only short-term mortality in HIV-1 disease but appear to have a major impact on chronic mortality.

AIDS-Related Opportunistic Infections↗
PubMed1996

RNA tertiary structure mediation by adenosine platforms.

The crystal structure of a group I intron domain reveals an unexpected motif that mediates both intra- and intermolecular interactions. At three separate locations in the 160-nucleotide domain, adjacent adenosines in the sequence lie side-by-side and form a pseudo-base pair within a helix. This adenosine platform opens the minor groove for base stacking or base pairing with nucleotides from a noncontiguous RNA strand. The platform motif has a distinctive chemical modification signature that may enable its detection in other structured RNAs. The ability of this motif to facilitate higher order folding provides one explanation for the abundance of adenosine residues in internal loops of many RNAs.

Adenosine↗
PubMed1996

The unique organization of the rpoB region of Spiroplasma citri: a restriction and modification system gene is adjacent to rpoB.

A 6.5-kb DNA fragment containing the gene (rpoB) encoding the RNA polymerase (RNAP) beta subunit, from the mollicute Spiroplasma citri (Sc), was cloned and sequenced. The classical eubacterial organization, with the genes (rplK, A, J and L) encoding ribosomal proteins L11, L1, L10 and L12 located immediately upstream from rpoB, was not found in the Sc DNA. Instead, an open reading frame (hsdS) potentially encoding a component of a type I restriction and modification system was identified upstream from rpoB, and sequences showing similarities with insertion elements were found between hsdS and rpoB.

Amino Acid Sequence↗
PubMed2001

A tobacco nuclear extract supporting transcription, processing, splicing and modification of plant intron-containing tRNA precursors.

Nuclear tRNA genes are transcribed by RNA polymerase III (Pol III) and pre-tRNAs are processed into mature tRNAs via complex processes in the nucleus. We have developed an in vitro Pol III-dependent transcription system derived from tobacco cultured cells, which supports efficiently not only transcription of a variety of plant tRNA genes but also 5'-and 3'-end processing, nucleotide modification and splicing of intron-containing pre-tRNAs. The structures of in vitro transcripts have been confirmed by primer extension analysis and by RNase T1 fingerprinting. The optimal Mg2+ concentration differed for each step so that each reaction can be controlled by adjusting the Mg2+ concentration. At 1 mm Mg2+, only transcription occurs so that pre-tRNAs accumulate. The splicing reaction can be initiated by raising Mg2+ ions (> 5 mm) and enhanced by adding 1 mm hexamminecobalt chloride. Using the optimized system for the Nicotiana intron-containing tRNATyr gene, the precise initiation and termination sites of transcription and the splice sites were determined. The presence of 1 mm NAD+ in the reaction mixture leads to the removal of the 2' phosphate at the splice junction of tRNATyr, demonstrating the activity of a 2'-phosphotransferase in the tobacco nuclear extract. Many modified nucleosides such as m2G, m22G, m1A, phi27 and phi35 are introduced in either of the studied transcripts. As shown in other systems, the conversion of U35 to phi requires an intron-containing substrate.

Base Sequence↗
PubMed1992

Partial purification of somatotropin receptors from pig liver: they arise from a single somatotropin receptor messenger RNA transcript.

Specific binding sites for porcine somatotropin (pST) have been identified in pig liver microsomal membranes. Little information, however, is available about the size and number of ST receptor (ST-R) forms present. Therefore, the present study was conducted to characterize ST-R in pig liver using two approaches. In the first set of experiments, cross-linking of [125I]bST (bovine ST) to microsomal membranes, followed by gel electrophoresis under reducing conditions, revealed the presence of a predominant protein of 107 kDa and four other proteins of 71, 52, 40, and 26 kDa. In a second set of experiments, ST-R were partially purified using affinity chromatography. Binding studies indicated that there was an approximately 1,800-fold purification compared to liver homogenate. Two specific proteins of 107 and 40 kDa were detected after crosslinking of [125I]bST to partially purified ST-R. Northern blot analysis revealed that these proteins arise by posttranslational modification of a single 4.2-kilobase somatotropin receptor messenger RNA transcript. Although the present study indicates that several forms of ST-R are present in pig liver, it is not clear what physiological role these different ST-R play in mediating the hepatic effects of pST. It is evident, however, that the smaller proteins are generated from the 107-kDa protein, which is the predominant isoform present in liver microsomal membranes.

Animals↗