Showing papers on "RNA published in 1992"
TL;DR: The extent of size reduction within metazoan mitochondrial-transfer RNA (mt-tRNA) gene sets strongly correlates with the degree to which the more variable secondary structure element-forming regions of mt-rRNA genes are lost.
Abstract: Publisher Summary This chapter describes structural features and evolution of metazoan mitochondrial DNA (mtDNA) molecules. Throughout the evolution of metazoa, gene content of mitochondria-genomes is highly conserved, as has the close packing of genes. Most of the occasional sequence expansions that have occurred, by way of either repeated or noncoding unique sequences, are found in the control or putative control region, rather than being dispersed between genes. Of the 13 open reading frames recognized in the human mtDNA molecules, four (COI, COII, COIII, and Cyt b) are originally identified in regard to the proteins they encode, from similarities of their predicted amino acid sequences to known amino acid sequences of bovine proteins, and predicted amino acid sequences of yeast mt-protein genes. Among mtDNAs of vertebrates and higher invertebrates, there are genes that overlap. Some overlaps are among the 3′ ends of two genes that are encoded in opposite strands of the molecule. The extent of size reduction within metazoan mitochondrial-transfer RNA (mt-tRNA) gene sets strongly correlates with the degree to which the more variable secondary structure element-forming regions of mt-rRNA genes are lost.
1,478 citations
TL;DR: A peptide nucleic acid (PNA) as discussed by the authors is a class of compounds that can bind complementary ssDNA and RNA strands more strongly than a corresponding DNA, and it can be used to attach DNA bases to a peptide backbone through a suitable linker.
Abstract: A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.
1,294 citations
TL;DR: Electrophysiological analysis coupled with molecular biology within the same cell will facilitate a better understanding of how changes at the molecular level are manifested in functional properties.
Abstract: We present here a method for broadly characterizing single cells at the molecular level beyond the more common morphological and transmitter/receptor classifications. The RNA from defined single cells is amplified by microinjecting primer, nucleotides, and enzyme into acutely dissociated cells from a defined region of rat brain. Further processing yields amplified antisense RNA. A second round of amplification results in greater than 10(6)-fold amplification of the original starting material, which is adequate for analysis--e.g., use as a probe, making of cDNA libraries, etc. We demonstrate this method by constructing expression profiles of single live cells from rat hippocampus. This profiling suggests that cells that appear to be morphologically similar may show marked differences in patterns of expression. In addition, we characterize several mRNAs from a single cell, some of which were previously undescribed, perhaps due to "rarity" when averaged over many cell types. Electrophysiological analysis coupled with molecular biology within the same cell will facilitate a better understanding of how changes at the molecular level are manifested in functional properties. This approach should be applicable to a wide variety of studies, including development, mutant models, aging, and neurodegenerative disease.
1,029 citations
TL;DR: Analysis of the entire mouse Xist gene supports a role for Xist in X inactivation, possibly as a functional RNA or as a chromatin organizer region.
975 citations
TL;DR: The results strongly suggest that HCV RNA carries an internal ribosome entry site (IRES) and the sequence between nucleotide positions 101 and 332 in the 5' untranslated region ofHCV RNA plays an important role in efficient translation.
Abstract: The mechanism of initiation of translation on hepatitis C virus (HCV) RNA was investigated in vitro. HCV RNA was transcribed from the cDNA that corresponded to nucleotide positions 9 to 1772 of the genome by using phage T7 RNA polymerase. Both capped and uncapped RNAs thus transcribed were active as mRNAs in a cell-free protein synthesis system with lysates prepared from HeLa S3 cells or rabbit reticulocytes, and the translation products were detected by anti-gp35 antibodies. The data indicate that protein synthesis starts at the fourth AUG, which was the initiator AUG at position 333 of the HCV RNA used in this study. Efficiency of translation of the capped methylated RNA appeared to be similar to that of the capped unmethylated RNA. However, a capped methylated RNA showed a much higher activity as mRNA than did the capped unmethylated RNA in rabbit reticulocyte lysates when the RNA lacked a nucleotide sequence upstream of position 267. The results strongly suggest that HCV RNA carries an internal ribosome entry site (IRES). Artificial mono- and dicistronic mRNAs were prepared and used to identify the region that carried the IRES. The results indicate that the sequence between nucleotide positions 101 and 332 in the 5' untranslated region of HCV RNA plays an important role in efficient translation. Our data suggest that the IRES resides in this region of the RNA. Furthermore, an IRES in the group II HCV RNA was found to be more efficient than that in the group I HCV RNA.
967 citations
TL;DR: A set of ligand-binding DNA sequences are isolated from a large pool of random sequence DNAs by selection and amplification in vitro, revealing that ligand binding is DNA-specific; RNAs of identical sequence could not interact with the same ligands.
Abstract: We have isolated a set of ligand-binding DNA sequences from a large pool of random sequence DNAs by selection and amplification in vitro, using similar methods to those described for the isolation of ligand-binding RNAs The ligand-DNA interactions are both sequence- and ligand-specific, and are dependent on proper folding of the single-stranded DNA Some ligands led to the isolation of more DNA sequences than RNA sequences, and vice versa Analysis of individual sequences reveals that ligand binding is DNA-specific; RNAs of identical sequence could not interact with the same ligands Ligand-binding DNAs might be more suitable than RNAs as potential pharmacological reagents because of the greater stability of DNA The apparent primacy of RNA in the early evolution of life may have been due to its availability rather than to its functional superiority
820 citations
TL;DR: Fingerprinting of RNA populations was achieved using an arbitrarily selected primer at low stringency for first and second strand cDNA synthesis and PCR amplification was then used to amplify the products.
Abstract: Fingerprinting of RNA populations was achieved using an arbitrarily selected primer at low stringency for first and second strand cDNA synthesis. PCR amplification was then used to amplify the products. The method required only a few nanograms of total RNA and was unaffected by low levels of genomic double stranded DNA contamination. A reproducible pattern of ten to twenty clearly visible PCR products was obtained from any one tissue. Differences in PCR fingerprints were detected for RNAs from the same tissue isolated from different mouse strains and for RNAs from different tissues from the same mouse. The strain-specific differences revealed are probably due to sequence polymorphisms and should be useful for genetic mapping of genes. The tissue-specific differences revealed may be useful for studying differential gene expression. Examples of tissue-specific differences were cloned. Differential expression was confirmed for these products by Northern analysis and DNA sequencing uncovered two new tissue-specific messages. The method should be applicable to the detection of differences between RNA populations in a wide variety of situations.
636 citations
TL;DR: Nuclear microinjection of cells constitutively expressing SV40 large T antigen with either a 15-mer or 20-mer PNA targeted to the T Ag messenger RNA suppressed T Ag expression, and Binding of PNAs to RNA resulted in site-specific termination of both reverse transcription and in vitro translation.
Abstract: Peptide nucleic acids (PNAs) are polyamide oligomers that can strand invade duplex DNA, causing displacement of one DNA strand and formation of a D-loop. Binding of either a T10 PNA or a mixed sequence 15-mer PNA to the transcribed strand of a G-free transcription cassette caused 90 to 100 percent site-specific termination of pol II transcription elongation. When a T10 PNA was bound on the nontranscribed strand, site-specific inhibition never exceeded 50 percent. Binding of PNAs to RNA resulted in site-specific termination of both reverse transcription and in vitro translation, precisely at the position of the PNA.RNA heteroduplex. Nuclear microinjection of cells constitutively expressing SV40 large T antigen (T Ag) with either a 15-mer or 20-mer PNA targeted to the T Ag messenger RNA suppressed T Ag expression. This effect was specific in that there was no reduction in beta-galactosidase expression from a coinjected expression vector and no inhibition of T Ag expression after microinjection of a 10-mer PNA.
624 citations
TL;DR: It is reported that the first residue in the HRIGRXXR region is involved in ATP hydrolysis and that the SAT region is essential for RNA unwinding.
Abstract: eIF-4A is a translation initiation factor that exhibits bidirectional RNA unwinding activity in vitro in the presence of another translation initiation factor, eIF-4B and ATP. This activity is thought to be responsible for the melting of secondary structure in the 5' untranslated region of eukaryotic mRNAs to facilitate ribosome binding. eIF-4A is a member of a fast growing family of proteins termed the DEAD family. These proteins are believed to be RNA helicases, based on the demonstrated in vitro RNA helicase activity of two members (eIF-4A and p68) and their homology in eight amino acid regions. Several related biochemical activities were attributed to eIF-4A: (i) ATP binding, (ii) RNA-dependent ATPase and (iii) RNA helicase. To determine the contribution of the highly conserved regions to these activities, we performed site-directed mutagenesis. First we show that recombinant eIF-4A, together with recombinant eIF-4B, exhibit RNA helicase activity in vitro. Mutations in the ATPase A motif (AXXXXGKT) affect ATP binding, whereas mutations in the predicted ATPase B motif (DEAD) affect ATP hydrolysis. We report here that the DEAD region couples the ATPase with the RNA helicase activity. Furthermore, two other regions, whose functions were unknown, have also been characterized. We report that the first residue in the HRIGRXXR region is involved in ATP hydrolysis and that the SAT region is essential for RNA unwinding. Our results suggest that the highly conserved regions in the DEAD box family are critical for RNA helicase activity.
618 citations
TL;DR: The cloning and sequencing of a cDNA encoding the hnRNP U protein is described, the determination of its amino acid sequence and the delineation of a region in this protein that confers RNA binding are described, and an RNA binding activity is identified within the C‐terminal glycine‐rich 112 amino acids.
Abstract: Heterogeneous nuclear ribonucleoproteins (hnRNPs) are thought to influence the structure of hnRNA and participate in the processing of hnRNA to mRNA. The hnRNP U protein is an abundant nucleoplasmic phosphoprotein that is the largest of the major hnRNP proteins (120 kDa by SDS-PAGE). HnRNP U binds pre-mRNA in vivo and binds both RNA and ssDNA in vitro. Here we describe the cloning and sequencing of a cDNA encoding the hnRNP U protein, the determination of its amino acid sequence and the delineation of a region in this protein that confers RNA binding. The predicted amino acid sequence of hnRNP U contains 806 amino acids (88,939 Daltons), and shows no extensive homology to any known proteins. The N-terminus is rich in acidic residues and the C-terminus is glycine-rich. In addition, a glutamine-rich stretch, a putative NTP binding site and a putative nuclear localization signal are present. It could not be defined from the sequence what segment of the protein confers its RNA binding activity. We identified an RNA binding activity within the C-terminal glycine-rich 112 amino acids. This region, designated U protein glycine-rich RNA binding region (U-gly), can by itself bind RNA. Furthermore, fusion of U-gly to a heterologous bacterial protein (maltose binding protein) converts this fusion protein into an RNA binding protein. A 26 amino acid peptide within U-gly is necessary for the RNA binding activity of the U protein. Interestingly, this peptide contains a cluster of RGG repeats with characteristic spacing and this motif is found also in several other RNA binding proteins. We have termed this region the RGG box and propose that it is an RNA binding motif and a predictor of RNA binding activity.
604 citations
TL;DR: The high frequency and widespread nature of RNA recombination indicate that this phenomenon plays a more significant role in the biology of RNA viruses than was previously recognized.
TL;DR: The messenger RNAs of human immunodeficiency virus-1 (HIV-1) have an RNA hairpin structure, TAR, at their 5' ends that contains a six-n nucleotide loop and a three-nucleotide bulge that stabilizes arginine hydrogen bonding to G26 and phosphates.
Abstract: The messenger RNAs of human immunodeficiency virus-1 (HIV-1) have an RNA hairpin structure, TAR, at their 5' ends that contains a six-nucleotide loop and a three-nucleotide bulge. The conformations of TAR RNA and of TAR with an arginine analog specifically bound at the binding site for the viral protein, Tat, were characterized by nuclear magnetic resonance (NMR) spectroscopy. Upon arginine binding, the bulge changes conformation, and essential nucleotides for binding, U23 and A27.U38, form a base-triple interaction that stabilizes arginine hydrogen bonding to G26 and phosphates. Specificity in the arginine-TAR interaction appears to be derived largely from the structure of the RNA.
TL;DR: Analysis of complexes between dsRNA and DAI suggests that at maximal packing the enzyme interacts with as little as a single helical turn of ds RNA (11 bp) but under conditions that allow activation the binding site protects about 80 bp of duplex.
Abstract: The interferon-induced protein kinase DAI, the double-stranded RNA (dsRNA)-activated inhibitor of translation, plays a key role in regulating protein synthesis in higher cells. Once activated, in a process that involves autophosphorylation, it phosphorylates the initiation factor eIF-2, leading to inhibition of polypeptide chain initiation. The activity of DAI is controlled by RNA regulators, including dsRNA activators and highly structured single-stranded RNAs which block activation by dsRNA. To elucidate the mechanism of activation, we studied the interaction of DAI with RNA duplexes of discrete sizes. Molecules shorter than 30 bp fail to bind stably and do not activate the enzyme, but at high concentrations they prevent activation by long dsRNA. Molecules longer than 30 bp bind and activate the enzyme, with an efficiency that increases with increasing chain length, reaching a maximum at about 85 bp. These dsRNAs fail to activate at high concentrations and also prevent activation by long dsRNA. Analysis of complexes between dsRNA and DAI suggests that at maximal packing the enzyme interacts with as little as a single helical turn of dsRNA (11 bp) but under conditions that allow activation the binding site protects about 80 bp of duplex. When the RNA-binding site is fully occupied with an RNA activator, the complex appears to undergo a conformational change.
TL;DR: This chapter highlights endosymbiont hypothesis, which states that all contemporary genomes ultimately derive from a single genome—the genome of a single, presumably cellular, entity which was the ancestor of all surviving forms of live.
Abstract: Publisher Summary This chapter highlights endosymbiont hypothesis. All contemporary genomes (including those of plastids and mitochondria) ultimately derive from a single genome—the genome of a single, presumably cellular, entity which was the ancestor of all surviving forms of live. The construction and interpretation of phylogenetic trees based on small subunit (SSU, or 16S-like) and large subunit (LSU, or 23S-like) rRNA sequences have proven especially informative in instances where morphological diversity tends to confound traditional methods of phylogenetic analysis. In addition to ribosomal RNA (rRNA) sequence, there are a number of traits that characterize the archaebacteria as a distinct group of organisms, separate from all other prokaryotes. These include (1) cell walls that, when present, lack peptidoglycan and muramic acid; (2) the presence of lipids containing phytanyl side groups in ether linkage; and (3) the presence of RNA polymerases that are distinct from those of eubacteria in subunit composition, response to RNA synthesis inhibitors or stimulators, immunological reactivity, and gene sequence. Two major divisions of archaebacteria include (1) sulfur-dependent, extreme thermophiles; and (2) methane-producers (methanogens) and their relatives, including the extreme halophiles.
TL;DR: In this article, the complete sequence of the liverwort mitochondrial DNA was determined and 94 possible genes in the sequence of 186,608 base-pairs were detected, including genes for three species of ribosomal RNA, 29 genes for 27 species of transfer RNA and 30 open reading frames (ORFs) for functionally known proteins.
TL;DR: The downward alkaline capillary transfer of DNA and RNA from agarose gel to a hybridization membrane was performed using a transfer solution containing 3 M NaCl and 8 mM NaOH to allow for a hybridized efficiency higher than that of the standard blotting protocols performed at neutral pH.
TL;DR: Using a subtraction cloning approach, a set of cDNA clones from mouse neural precursor cells whose respective mRNA levels are down-regulated during the development of mouse brain are isolated and indicate that these genes may play important roles during the embryonic development and differentiation of central nervous system.
TL;DR: Because complex quasispecies populations of RNA viruses arise probabilistically and differentially in every host, their compositions and exact roles in disease pathogenesis are indeterminate and their directions of evolution are unpredictable.
Abstract: This chapter discusses the high mutation frequencies and rapid evolution potential of RNA viruses. The concepts discussed are applicable to all “ordinary” RNA viruses (riboviruses), viroids and satellite RNAs; to retroviruses; and to viruses (such as the hepadnaviruses) with DNA genomes which replicate via RNA transcripts. Because DNA virus polymerases can have proofreading (Kornberg 1974), their mutation frequencies can be much lower than those of RNA viruses. For example, the mutation rate of bacteriophage T4 approximates 10−8 per base pair per replication (Drake 1969). However, some DNA viruses may avoid high-fidelity replication mechanisms (Drake et al. 1969; Hall et al. 1984) to gain the evolutionary advantages of high mutation frequencies (Smith and Inglis 1987).
TL;DR: Analysis of the kinetics of processive synthesis suggested that the initial binding of dNTP leads to a faster rate of dissociation of DNA from the enzyme, and further investigation supported a two-step dN TP binding mechanism with the formation of an initial E.DNA.dNTP complex.
TL;DR: A review of putative RNA helicases from different organisms ranging from Escherichia coli to humans and viruses involved in diverse cellular functions such as RNA splicing, ribosome assembly, initiation of translation, spermatogenesis, embryogenesis, and cell growth and division.
Abstract: RNA metabolism plays a central role in cell growth It is essential to regulate RNA synthesis, processing, stability and degradation Conformational changes in RNA are key elements in regulating cellular processes Recently, an increasing number of putative RNA helicases from different organisms ranging from Escherichia coli to humans and viruses have been identified They are involved in diverse cellular functions such as RNA splicing, ribosome assembly, initiation of translation, spermatogenesis, embryogenesis, and cell growth and division Based on sequence homologies these proteins were grouped in a family, the D-E-A-D box protein family (D-E-A-D = Asp-Glu-Ala-Asp) Some of the better characterized members have been shown to possess ATP-binding and hydrolysing activities as well as ATP-dependent RNA helicase activities Most of the genes encoding such proteins have been isolated from yeast, on which we will focus in this review From sequence data, three of the members form a subfamily, the D-E-A-H subfamily
TL;DR: It is demonstrated that at least one of the ligands inhibits cDNA synthesis by HIV reverse transcriptase but fails to inhibit other reverse transcriptases, highlighting the power of SELEX to yield highly specific ligands that reduce the activity of target proteins.
Abstract: High-affinity ligands of the reverse transcriptase of human immunodeficiency virus type 1 (HIV-1) were isolated by the SELEX procedure (systematic evolution of ligands by exponential enrichment) from RNA populations randomized at 32 positions. Analysis of these ligands revealed a pseudoknot consensus with primary sequence bias at some positions. We demonstrated that at least one of the ligands inhibits cDNA synthesis by HIV reverse transcriptase but fails to inhibit other reverse transcriptases. These experiments highlight the power of SELEX to yield highly specific ligands that reduce the activity of target proteins. Such ligands may provide therapeutic reagents for viral and other diseases.
TL;DR: Observations show that HEV, RubV, and BNYVV encompass partially conserved arrays of distinctive putative functional domains, suggesting that these viruses constitute a distinct monophyletic group within the alpha-like supergroup of positive-strand RNA viruses.
Abstract: Computer-assisted comparison of the nonstructural polyprotein of hepatitis E virus (HEV) with proteins of other positive-strand RNA viruses allowed the identification of the following putative functional domains: (i) RNA-dependent RNA polymerase, (ii) RNA helicase, (iii) methyltransferase, (iv) a domain of unknown function ("X" domain) flanking the papain-like protease domains in the polyproteins of animal positive-strand RNA viruses, and (v) papain-like cysteine protease domain distantly related to the putative papain-like protease of rubella virus (RubV). Comparative analysis of the polymerase and helicase sequences of positive-strand RNA viruses belonging to the so-called "alpha-like" supergroup revealed grouping between HEV, RubV, and beet necrotic yellow vein virus (BNYVV), a plant furovirus. Two additional domains have been identified: one showed significant conservation between HEV, RubV, and BNYVV, and the other showed conservation specifically between HEV and RubV. The large nonstructural proteins of HEV, RubV, and BNYVV retained similar domain organization, with the exceptions of relocation of the putative protease domain in HEV as compared to RubV and the absence of the protease and X domains in BNYVV. These observations show that HEV, RubV, and BNYVV encompass partially conserved arrays of distinctive putative functional domains, suggesting that these viruses constitute a distinct monophyletic group within the alpha-like supergroup of positive-strand RNA viruses.
TL;DR: From morphological and biochemical properties of the virus, this virus is identified as a new member of the family of Nodaviridae and designated it striped jack nervous necrosis virus.
TL;DR: Splicing of the modified pre-messenger RNA's in vitro revealed that, although a 2'-hydroxyl is not absolutely required at either splice site, the 2'-Hydroxyl at the 3' splicing site is important for the second step of splicing.
Abstract: A simple and efficient method for synthesizing long, site-specifically modified RNA molecules was developed whereby segments of RNA were joined with the use of bacteriophage T4 DNA ligase. A single hydrogen or O-methyl group was substituted for the 2'-hydroxyl group at either splice site of a nuclear pre-messenger RNA substrate. Splicing of the modified pre-messenger RNA's in vitro revealed that, although a 2'-hydroxyl is not absolutely required at either splice site, the 2'-hydroxyl at the 3' splice site is important for the second step of splicing. These results are compared to previous studies of analogous 2'-hydroxyl groups in the self-splicing Tetrahymena group I intron.
TL;DR: A large conserved stem-loop structure within the 3' 200 bases of the 5'NTRs of both HCV and pestiviruses which corresponds to the ribosomal landing pad of hepatitis A virus, suggesting that these functionally similar structures may have evolved independently.
Abstract: The RNA genomes of human hepatitis C virus (HCV) and the animal pestiviruses responsible for bovine viral diarrhea (BVDV) and hog cholera (HChV) have relatively lengthy 5' nontranslated regions (5'NTRs) sharing short segments of conserved primary nucleotide sequence. The functions of these 5'NTRs are poorly understood. By comparative sequence analysis and thermodynamic modeling of the 5'NTRs of multiple BVDV and HChV strains, we developed models of the secondary structures of these RNAs. These pestiviral 5'NTRs are highly conserved structurally, despite substantial differences in their primary nucleotide sequences. The assignment of similar structures to conserved segments of primary nucleotide sequence present in the 5'NTR of HCV resulted in a model of the secondary structure of the HCV 5'NTR which was refined by determining sites at which synthetic HCV RNA was cleaved by double- and single-strand specific RNases. These studies indicate the existence of a large conserved stem-loop structure within the 3' 200 bases of the 5'NTRs of both HCV and pestiviruses which corresponds to the ribosomal landing pad (internal ribosomal entry site) of HCV. This structure shows little relatedness to the ribosomal landing pad of hepatitis A virus, suggesting that these functionally similar structures may have evolved independently.
TL;DR: The observation that RNA encapsidation and formation of RC-DNA can be genetically separated suggests that the core protein, via its basic C-terminal region, also acts as an essential auxiliary component in HBV replication, possibly like a histone, or like a single-stranded-DNA-binding protein.
Abstract: Assembly of replication-competent hepatitis B virus (HBV) nucleocapsids requires the interaction of the core protein, the P protein, and the RNA pregenome. The core protein contains an arginine-rich C-terminal domain which is dispensable for particle formation in heterologous expression systems. Using transient expression in HuH7 cells of a series of C-terminally truncated core proteins, I examined the functional role of this basic region in the context of a complete HBV genome. All variants containing at least the 144 N-terminal amino acids were assembly competent, but efficient pregenome encapsidation was observed only with variants consisting of 164 or more amino acids. These data indicate that one function of the arginine-rich region is to provide the interactions between core protein and RNA pregenome. However, in cores from the variant ending with amino acid 164, the production of complete positive-strand DNA was drastically reduced. Moreover, almost all positive-strand DNA originated from in situ priming, whereas in wild-type particles, this type of priming not supporting the formation of relaxed circular DNA (RC-DNA) accounted for about one half of the positive strands. Further C-terminal residues to position 173 restored RC-DNA formation, and the corresponding variant did not differ from the full-length core protein in all assays used. The observation that RNA encapsidation and formation of RC-DNA can be genetically separated suggests that the core protein, via its basic C-terminal region, also acts as an essential auxiliary component in HBV replication, possibly like a histone, or like a single-stranded-DNA-binding protein. In contrast to their importance for HBV replication, sequences beyond amino acid 164 were not required for the formation of enveloped virions. Since particles from variant 164 did not contain mature DNA genomes, a genome maturation signal is apparently not required for HBV nucleocapsid envelopment.
TL;DR: The provocative stability of the triplex with an RNA third strand+DNA duplex points to novel antisense strategies and opens the possibility of an in vivo role of these structures.
Abstract: Studies of a series of short oligonucleotide double and triple helices containing either all RNA, all DNA, or a mixture of the two show strand-dependent variation in their stability and structure. The variation in stability for both groups falls over a range of greater than 10 kilocalories per mole. In forming the triple helix, RNA is favored on both pyrimidine strands, whereas DNA is favored on the purine strand. In general, relatively unstable duplexes form particularly stable triplexes and vice versa. Structural data indicate that the strands in hybrid helices adopt a conformation that is intermediate between molecules containing all DNA and all RNA. Thus, RNA-DNA hybrids were not forced into the conformation of the RNA (A-form). The provocative stability of the triplex with an RNA third strand+DNA duplex points to novel antisense strategies and opens the possibility of an in vivo role of these structures. Overall, the data emphasize the fundamental role of sugars in determining the properties of nucleic acid complexes.
TL;DR: These results fail to show evidence for proofreading exonuclease activity associated with the virion replicase of an RNA virus, and suggest that RNA virus replication might generally be error-prone, because RNA replicases base misincorporations are proofread very inefficiently or not at all.
TL;DR: It is shown that the nanos 3' untranslated region, like that of the bicoid RNA, is sufficient for RNA localization, and a role forRNA localization in regulating nanos activity is proposed.
TL;DR: It is hypothesized that this domain may be involved in methylation of the cap during viral RNA maturation, and the motifs typical of the putative methyltransferase domain are universal within the Sindbis-like supergroup of positive-strand RNA viruses.
Abstract: Computer-assisted comparisons of the large proteins involved in the replication of viral RNA have revealed a novel domain located near the N termini of these proteins and conserved throughout the so-called ‘Sindbis-like’ supergroup of positive-strand RNA viruses. This domain encompasses four distinct conserved motifs, with motifs I, II and IV containing an invariant His residue, the AspXXArg signature and an invariant Tyr residue, respectively. Each of the two large groups of viruses within this supergroup, the ‘altovirus’ group (alphaviruses, tobamoviruses, tobraviruses, hordeiviruses, tricornaviruses, furoviruses, hepatitis E virus and probably rubiviruses), and the ‘typovirus’ group (tymoviruses, potexviruses, carlaviruses and apple chlorotic leaf spot virus), can be characterized by additional conserved sequence motifs. Based on the available results of biochemical studies and site-directed mutagenesis of the alphavirus proteins, it is hypothesized that this domain may be involved in methylation of the cap during viral RNA maturation. Unlike the other conserved domains, the RNA-dependent RNA polymerase and the RNA helicase, the motifs typical of the putative methyltransferase domain are universal within the Sindbis-like supergroup but are not found in the proteins of any other viruses, constituting a distinctive hallmark of this supergroup.