Showing papers on "RNA published in 1981"
TL;DR: In this article, a dynamic programming algorithm was proposed to fold an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies, based on applied mathematics.
Abstract: This paper presents a new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies. It is based on a dynamic programming algorithm from applied mathematics, and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature. Its power is demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy chain messenger RNA fragment. We go beyond the basic method to show how to incorporate additional information into the algorithm. This includes data on chemical reactivity and enzyme susceptibility. We illustrate this with the folding of two large fragments from the 16S ribosomal RNA of Escherichia coli.
3,202 citations
TL;DR: It is proposed that the H strand is transcribed into a single polycistronic RNA molecule, which is processed later into mature species by precise endonucleolytic cleavages which occur, in most cases, immediately before and after a tRNA sequence.
Abstract: A 3'-end proximal segment of most of the putative mRNAs encoded in the heavy strand of HeLa cell mtDNA has been partially sequences and aligned with the DNA sequence. In all cases, the 3'-end nucleotide of the individual mRNA coding sequences has been found to be immediately contiguous to a tRNA gene or another mRNA coding sequence. These and previous results indicate that the heavy (H) strand sequences coding for the rRNA, poly(A)-containing RNA and tRNA species form a continuum extending over almost the entire length of this strand. We propose that the H strand is transcribed into a single polycistronic RNA molecule, which is processed later into mature species by precise endonucleolytic cleavages which occur, in most cases, immediately before and after a tRNA sequence.
2,185 citations
TL;DR: Comparison of the sequence of λrifd18 with sequences from other isolates of the rrB operon provides direct evidence for structural rearrangements within rRNA operons.
1,683 citations
Patent•
24 Mar 1981TL;DR: New and useful intermediate nucleotides bound to an inorganic polymer support, including the preparation thereof, and processes for the conversion to oligonucleotides which are especially useful for the synthesis of polynucleotide, particularly ribonucleic (RNA) and deoxyribonuclic acids (DNA) are presented in this paper.
Abstract: New and useful intermediate nucleotides bound to an inorganic polymer support, including the preparation thereof, and processes for the conversion to oligonucleotides which are especially useful for the synthesis of polynucleotides, particularly ribonucleic (RNA) and deoxyribonucleic acids (DNA).
1,394 citations
TL;DR: Biotin-labeled polynucleotides, both single and double-stranded, are selectively and quantitatively retained on avidin-Sepharose, even after extensive washing with 8 M urea, 6 M guanidine hydrochloride, or 99% formamide.
Abstract: Analogs of dUTP and UTP that contain a biotin molecule covalently bound to the C-5 position of the pyrimidine ring through an allylamine linker arm have been synthesized. These biotin-labeled nucleotides are efficient substrates for a variety of DNA and RNA polymerases in vitro. Polynucleotides containing low levels of biotin substitution (50 molecules or fewer per kilobase) have denaturation, reassociation, and hybridization characteristics similar to those of unsubstituted controls. Biotin-labeled polynucleotides, both single and double-stranded, are selectively and quantitatively retained on avidin-Sepharose, even after extensive washing with 8 M urea, 6 M guanidine hydrochloride, or 99% formamide. In addition, biotin-labeled polynucleotides can be selectively immunoprecipitated in the presence of antibiotin antibody and Staphylococcus aureus protein A. The unique features of biotin-labeled polynucleotides suggest that they will be useful affinity probes for the detection and isolation of specific DNA and RNA sequences.
1,256 citations
TL;DR: The results strongly suggest that the same two overlapping promoters, which were previously identified by in vitro transcription of gal DNA fragments, also control the expression of the galactose operon in intact cells.
970 citations
TL;DR: The primary structure of the poliovirus genome has been determined and Twelve viral polypeptides have been mapped by amino acid sequence analysis and were found to be proteolytic cleavage products of the polyprotein, cleavages occurring predominantly at Gln-Gly pairs.
Abstract: The primary structure of the poliovirus genome has been determined. The RNA molecule is 7,433 nucleotides long, polyadenylated at the 3' terminus, and covalently linked to a small protein (VPg) at the 5' terminus. An open reading frame of 2,207 consecutive triplets spans over 89% of the nucleotide sequence and codes for the viral polyprotein NCVPOO. Twelve viral polypeptides have been mapped by amino acid sequence analysis and were found to be proteolytic cleavage products of the polyprotein, cleavages occurring predominantly at Gln-Gly pairs.
865 citations
TL;DR: It is proposed that Tetrahymena pre-rRNA splicing occurs by a phosphoester transferase mechanism where the guanosine cofactor provides the free 3' hydroxyl necessary to initiate a series of three transfers that results in splicing of the pre- rRNA and cyclization of the excised IVS.
820 citations
TL;DR: It is shown that virions and purified viral cores contain a unique endonuclease that cleaves RNAs containing a 5' methylated cap structure preferentially at purine residues 10 to 14 nucleotides from the cap, generating fragments with 3'-terminal hydroxyl groups.
716 citations
TL;DR: Bacterial operons concerned with the biosynthesis of amino acids are often controlled by a process of attenuation, where the amino acid in short supply means translation is stalled at the relevant codons of the transcript long enough for the succeeding segment of the transcripts to form secondary structures that allow the transcribing RNA polymerase molecule to proceed through a site that otherwise dictates termination of transcription.
Abstract: Bacterial operons concerned with the biosynthesis of amino acids are often controlled by a process of attenuation. The translation product of the initial segment of the transcript of each operon is a peptide rich in the amino acid that the particular operon controls. If the amino acid is in short supply translation is stalled at the relevant codons of the transcript long enough for the succeeding segment of the transcript to form secondary structures that allow the transcribing RNA polymerase molecule to proceed through a site that otherwise dictates termination of transcription. This site is the attenuator; the process is attenuation.
684 citations
TL;DR: The complete 7410 nucleotide sequence of poliovirus type I genome was obtained from cloned cDNA was synthesized and inserted into the Pst I site of plasmid pBR322, and three clones were derived that together provided DNA copies of the entire poliov virus genome.
Abstract: The complete 7410 nucleotide sequence of poliovirus type I genome was obtained from cloned cDNA. Double-stranded poliovirus cDNA was synthesized and inserted into the Pst I site of plasmid pBR322, and three clones were derived that together provided DNA copies of the entire poliovirus genome. Two of the clones contained inserts of 2.5 and 6.5 kilobases and represented all but the 5' 115 bases of poliovirus RNA. A third clone was generated from primer-extended DNA and contained sequences from the 5' end of the viral RNA. An open reading frame that was identified in the nucleotide sequence starting 743 bases from the 5' end of the RNA and extending to a termination codon 71 bases from the 3' end contained known poliovirus polypeptide sequence.
TL;DR: In this article, Epstein-Barr virus (EBV) encodes two small RNAs, EBER 1 and EBER 2, which are associated with protein(s) allowing their specific precipitation by the systemic lupus erythematosus-associated antibody anti-La.
Abstract: Primate cells harboring the Epstein-Barr virus (EBV) genome synthesize large amounts of two small RNAs:EBER 1 and EBER 2 (EBV-encoded RNA). These RNAs are approximately 180 nucleotides long, possess 5' pppA termini, and lack poly(A). They have different T1 and pancreatic RNase digestion fingerprints. They are not found in normal B lymphocytes, in transformed B lymphocytes that lack EBV DNA, in T lymphocytes transformed by Herpesvirus ateles, or in a variety of other nonlymphoid mammalian cells. Hybridization analyses indicate that EBER 1 and EBER 2 are encoded by the EcoRI-J fragment of EBV (B95-8) DNA. In vivo both RNAs are associated with protein(s), allowing their specific precipitation by the systemic lupus erythematosus-associated antibody anti-La. The La antigen in uninfected mammalian cells consists of a heterogeneous class of small ribonucleoprotein particles, some of whose RNA components exhibit sequence homology with a highly repetitive, interspersed class of human DNA designated the Alu family. Possible functions for EBER 1 and EBER 2 in infection and cell transformation by EBV and their potential relationship to the pathogenesis of systemic lupus erythematosus are discussed.
TL;DR: The RNP and Sm antigens recognized by lupus erythematosus antibodies are located on discrete particles containing single small nuclear RNA's complexed with proteins, while ribonucleoproteins with La contain a striking highly banded spectrum of small RNA's from uninfected cells as well as virus-associated RNA from adenovirus-infected cells.
Abstract: The RNP and Sm antigens recognized by lupus erythematosus antibodies are located on discrete particles containing single small nuclear RNA's complexed with proteins. The antigens Ro and La are also on ribonucleoproteins. The small RNA's in ribonucleoproteins with Ro are discrete, like those associated with RNP and Sm; in contrast, ribonucleoproteins with La contain a striking highly banded spectrum of small RNA's from uninfected cells as well as virus-associated RNA from adenovirus-infected cells.
TL;DR: The results show that viral gene products are not required for maintenance of neoplastic transformation and suggest that in lymphoid tumors, an ALV provirus is integrated adjacent to a specific cellular gene, and the insertion of the viral promoter adjacent to this gene results in its enhanced expression, leading to neoplasia.
TL;DR: It appears that transcriptional events are primarily responsible for the synthesis of these, and perhaps most, tissue-specific moderately abundant mRNAs.
TL;DR: Re recombinant plasmids containing the entire Escherichia coli rrnB ribosomal RNA operon and segments thereof become a powerful tool for studies such as initiation and termination of transcription, processing of rRNA precursors, and investigations of the structure, function, and assembly of the ribosome itself.
TL;DR: The most frequent ribonuclease L cleavages occur after UA, UG, and UU (A, adenine; U, uracil; and G, guanine) and much less frequent cleavage after CA and AC (C, cytosine).
Abstract: One of the mediators of interferon action is a latent endoribonuclease (ribonuclease L) that is activated by (2'-5')oligoadenylates Among the homopolymers of the four common ribonucleotides, activated ribonuclease L degrades at an appreciable rate only polyuridylic acid In two natural RNA's tested the most frequent ribonuclease L cleavages occur after UA, UG, and UU (A, adenine; U, uracil; and G, guanine) and much less frequent cleavages after CA and AC (C, cytosine)
TL;DR: Small ribonucleic acid (RNA)-protein complexes precipitated by anti-Ro and anti-La antibodies from lupus patients have been examined with emphasis on their RNA components and the possibility that the La protein(s) functions in the transcription or maturation of all RNA polymerase III transcripts is discussed.
Abstract: Small ribonucleic acid (RNA)-protein complexes precipitated by anti-Ro and anti-La antibodies from lupus patients have been examined with emphasis on their RNA components. In both ribonucleoprotein (RNP) classes, the numbers of different RNA molecules and their sequences vary between mouse and human cells. The complex mixtures of La RNAs include two previously sequenced 4.5S RNAs from mouse cells and 5S ribosomal RNA-like molecules from both mouse and human cells. All Ro and La RNAs possess 5-triphosphates. Some La RNAs have internal modifications typical of transfer RNAs. The Ro RNPs are quite stable and are localized by immunofluorescence in the cell cytoplasm, whereas the majority of the La RNPs turn over rapidly and reside in the nucleus. Despite these differences, reconstitution experiments show that the Ro particles carry the La as well as the Ro determinant. Studies using a nuclear transcription system demonstrate that most of the La RNAs are synthesized by RNA polymerase III. The possibility that the La protein(s) functions in the transcription or maturation of all RNA polymerase III transcripts is discussed.
TL;DR: The viral mRNA produced by two of the transformed cell lines was structurally indistinguishable from the normal middle-T mRNA found in productively infected cells, suggesting that RNA splicing is not an essential step in the biogenesis of this messenger.
Abstract: A modified polyoma virus genome has been constructed which can encode the middle-T protein, but not the large-T or small-T proteins. This was achieved, starting with the full length viral DNA inserted into a plasmid vector, by replacing a small genomic restriction fragment spanning the middle-T intervening sequence with the equivalent fragment from a cloned partial cDNA copy of the middle-T protein mRNA. Transfection of the modified viral DNA into cultured rat cells efficiently induced the formation of transformed cell foci which gave rise to cell lines that grew as tumours after injection into Fisher rats. The only viral early-region antigen synthesized by the cell lines was the middle-T protein. Expression of the middle-t protein is therefore sufficient to establish and maintain a transformed state. The viral mRNA produced by two of the transformed cell lines was structurally indistinguishable from the normal middle-T mRNA found in productively infected cells, suggesting that RNA splicing is not an essential step in the biogenesis of this messenger.
TL;DR: Experiments with recombinant plasmids show the region that determines the specificity of response to RNA I to be greater than 300 base pairs upstream of the origin of DNA replication, which indicates the inhibition of primer formation by RNA I is incompatibility specific.
Abstract: Transcription of ColE1 DNA by RNA polymerase in vitro starts at two sites in a region required for maintenance of the plasmid. Certain transcripts that start at one of the sites can be cleaved by RNase H and then act as primers for DNA replication. Transcription from the other site produces a RNA approximately 108 nucleotides long (species I or RNA I). Transcripts analogous to the primer and RNA I of ColE1 are produced when p15A or small derivatives of two other ColE1-compatible plasmids, CloDF13 and RSF1030, are used as template. If purified RNA I is added to the transcription reaction containing RNase H, formation of primer is inhibited. Each RNA I can inhibit primer formation by the plasmid that specifies it but has no effect on primer formation by heterologous templates. Thus, the inhibition of primer formation by RNA I is incompatibility specific. Because RNA I does not inhibit initiation or propagation of transcription or the processing of preformed precursors, the step that is sensitive to inhibition is probably formation of the hybrid between the primer precursor and the template. This hybrid is the required substrate for RNase H. Experiments with recombinant plasmids show the region that determines the specificity of response to RNA I to be greater than 300 base pairs upstream of the origin of DNA replication.
TL;DR: A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli, Bacillus stearothermophilis, human and mouse mitochondria and several partial sequences.
Abstract: A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli. Bacillus stearothermophilis, human and mouse mitochondria and several partial sequences. The model has been tested extensively with single strand-specific chemical and enzymatic probes. Long range base-paired interactions organize the molecule into six major structural domains containing over 100 individual helices in all. Regions containing the sites of interaction with several ribosomal proteins and 5S RNA have been located. Segments of the 23S RNA structure corresponding to eucaryotic 5.8S and 25 RNA have been identified, and base paired interactions in the model suggest how they are attached to 28S RNA. Functionally important regions, including possible sites of contact with 30S ribosomal subunits, the peptidyl transferase center and locations of intervening sequences in various organisms are discussed. Models for molecular 'switching' of RNA molecules based on coaxial stacking of helices are presented, including a scheme for tRNA-23S RNA interaction.
TL;DR: Both mRNAs contain 10-15 heterogeneous nonviral nucleotides at their 5' ends that appear to be derived from cellular RNAs used for priming the transcription of viral RNAs.
Abstract: RNA segment 7 of the influenza A virus genome codes for at least two proteins, M1 and M2, which are synthesized from separate mRNA species. Sequence analysis of the M2 mRNA has shown that it contains an interrupted sequence of 689 nucleotides. The approximately 51 virus-specific nucleotides comprising the 5'-end leader sequence of the M2 mRNA are the same as those found at the 5' end of the colinear M1 mRNA. Following the leader sequence of the M2 mRNA, where is a 271-nucleotide body region that is 3' coterminal with the M1 mRNA. Another small potential mRNA (mRNA3) related to RNA segment 7 has been found. mRNA3 has a leader sequence of approximately 11 virus-specific nucleotides that are the same as the 5' end of the M1 and M2 mRNAs, followed by an interrupted sequence of 729 nucleotides, and then a body region of approximately 271 nucleotides that is the same as that of the M2 mRNA. The nucleotide sequences found at the junctions of the interrupted sequences in M2 mRNA and mRNA3 are similar to those found at the splicing points of intervening sequences in eukaryotic mRNAs. In addition, both mRNAs contain 10-15 heterogeneous nonviral nucleotides at their 5' ends that appear to be derived from cellular RNAs used for priming the transcription of viral RNAs. Because the 5'-end sequences of the M1 mRNA and the M2 mRNA are the same and share the 5'-proximal initiation codon for protein synthesis, the first nine amino acids would be the same in the M1 and M2 protein and then the sequences would diverge. The approximately 271-nucleotide body region of the M2 mRNA can be translated in the +1 reading frame, and the sequence indicates that M1 and M2 overlap by 14 amino acids. The coding potential of the mRNA3 is for only nine amino acids, and these would be identical to the COOH-terminal region of the membrane protein (M1).
TL;DR: Investigation of the sequence specificities of the 2-5A-dependent ribonucleases in extracts of rabbit reticulocytes, mouse ascites tumour cells and human lymphoblastoid cells in conditions of partial digestion using terminally labelled RNA substrates found the enzymes cleaved on the 3′-side of UN sequences to yield UpNp terminated products.
Abstract: The oligonucleotides pppA2'p5'A2'p5'A and related oligomers (2-5A) are synthesized by an enzyme that is widely distributed in a variety of cells, the activity of which varies with interferon treatment, growth and hormone status. Because significant amounts of 2-5A have recently been detected in interferon-treated cells, it has been suggested that the oligonucleotides may be involved in interferon action and in the control of cell metabolism. In both intact cells and cell-free systems 2-5A has been shown to activate a ribonuclease. We report here investigations of the sequence specificities of the 2-5A-dependent ribonucleases in extracts of rabbit reticulocytes, mouse ascites tumour cells and human lymphoblastoid cells in conditions of partial digestion using terminally labelled RNA substrates. The enzymes cleaved on the 3'-side of UN sequences to yield UpNp terminated products. Cleavage was observed predominantly at UA and UU sequences.
TL;DR: The present understanding of negative-strand RNA virus replication is summarized and the replicative event leading to the generation of defective interfering (DI) particles is examined.
TL;DR: It is shown that VAII RNA as well as VAI RNA and the EBERs exist in ribonucleoprotein complexes which are precipitable by anti-La antibodies associated with systemic lupus erythematosus.
Abstract: The nucleotide sequence of the region of the Epstein-Barr virus genome that specifies two small ribonucleic acids (RNAs), EBER 1 and EBER 2, has been determined. Both of these RNAs are encoded by the right-hand 1,000 base pairs of the EcoRI J fragment of EBV deoxyribonucleic acid. EBER 1 is 166 (167) nucleotides long and EBER 2 is 172 +/- 1 nucleotides long; the heterogeneity resides at the 3' termini. The EBER genes are separated by 161 base pairs and are transcribed from the same deoxyribonucleic acid strand. In vitro, both EBER genes can be transcribed by RNA polymerase III; sequences homologous to previously identified RNA polymerase III intragenic transcription control regions are present. Striking similarities are therefore apparent both between the EBERs and the two adenovirus-associated RNAs, VAI and VAII, and between the regions of the two viral genomes that specify these small RNAs. We have shown that VAII RNA as well as VAI RNA and the EBERs exist in ribonucleoprotein complexes which are precipitable by anti-La antibodies associated with systemic lupus erythematosus. Finally, we have demonstrated that the binding of protein(s) from uninfected cells confers antigenicity on each of the four virus-encoded small RNAs.
TL;DR: The structures of the aberrant proviruses and the absence of normal viral RNA in some tumors indicate that expression of viral genes is not required for maintenance of the tumor phenotype, in at least some cases, the mechanism of oncogenesis may involve stimulation of transcription of flanking cellular sequences by a viral promoter.
TL;DR: Recombinant viruses are constructed which, in infected cells, express large quantities of haemagglutinin, which accumulates at the cell surface and displays haemabsorbing activity.
Abstract: By replacing either the early or the late genes of SV40 with a cloned copy of the influenza virus haemagglutinin gene we have constructed recombinant viruses which, in infected cells, express large quantities of haemagglutinin. This glycoprotein, over 108 molecules of which are produced per cell, is identical in molecular weight to authentic influenza virus haemagglutinin, accumulates at the cell surface and displays haemabsorbing activity.
TL;DR: Pancreatic amylase messenger RNA progressively decreases in rats rendered diabetic with streptozotocin, and insulin reverses this effect, inducing a selective decrease in amyl enzyme messenger RNA in the pancreas.
Abstract: Pancreatic amylase messenger RNA progressively decreases in rats rendered diabetic with streptozotocin. Insulin reverses this effect, inducing a selective decrease in amylase messenger RNA in the pancreas. Parotid amylase messenger RNA is not significantly affected by either diabetes or insulin.
TL;DR: The results suggest the necessity for an endonucleolytic cleavage of a primary transcript followed by polyadenylation in the process of creating the 3′ end of this cellular mRNA, as has previously been demonstrated for every virus mRNA so far studied.