SEARCH · Search PubMed

Results for “RNA structure”

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.

SourceResearch connectionFrom yearThrough year

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

At least 1,333 records · Page 74Linked to original sources

PubMed2002

An H/ACA guide RNA directs U2 pseudouridylation at two different sites in the branchpoint recognition region in Xenopus oocytes.

U2 is the most extensively modified of all spliceosomal snRNAs. We previously showed that at least some of the internally modified nucleotides in U2 snRNA are required for snRNP biogenesis and pre-mRNA splicing. Recent work from several laboratories suggests that nuclear guide RNAs facilitate U2 snRNA internal modification, including pseudouridylation and 2'-O-methylation. Here, we present a novel approach to identifying guide RNAs for U2 pseudouridylation. Several Xenopus oocyte nuclear RNAs were affinity selected with U2 snRNA substituted with 5-fluorouridine, a pseudouridylation inhibitor that sequesters pseudouridylases. One of these RNAs was sequenced and found to be a novel RNA of 134 nt. This small RNA contains an H/ACA motif and folds into a typical H/ACA RNA structure, and its authenticity as an H/ACA RNA was confirmed by immunoprecipitation analysis. The RNA contains two guide sequences for pseudouridylation (psi) of U2 snRNA at positions 34 and 44 in the branch-site recognition region, and we demonstrate that this RNA indeed guides the formation of psi34 and psi44 in U2 using a Xenopus oocyte reconstitution system. Therefore, this novel RNA was designated pugU2-34/44, for pseudouridylation guide for U2 snRNA U34 and U44. Intranuclear localization analyses indicate that pugU2-34/44 resides within the nucleoplasm rather than nucleoli or Cajal bodies where other guide RNAs have been localized. Our results clarify the mechanism of U2 snRNA pseudouridylation in Xenopus oocytes, and have interesting implications with regard to the intranuclear localization of U2 snRNA pseudouridylation.

Animals↗

PubMed2003

Structure of HCV IRES domain II determined by NMR.

Complex RNA structures regulate many biological processes, but are often too large for structure determination by NMR methods. The 5' untranslated region (5' UTR) of the hepatitis C viral (HCV) RNA genome contains an internal ribosome entry site (IRES) that binds to 40S ribosomal subunits with high affinity and specificity to control translation. Domain II of the HCV IRES forms a 25-kDa folded subdomain that may alter ribosome conformation. We report here the structure of domain II as determined using an NMR approach that combines short- and long-range structural data. Domain II adopts a distorted L-shape structure, and its overall shape in the free form is markedly similar to its 40S subunit-bound form; this suggests how domain II may modulate 40S subunit conformation. The results show how NMR can be used for structural analysis of large biological RNAs.

5' Untranslated Regions↗

PubMed2004

RNA sequence elements required for high affinity binding by the zinc finger domain of tristetraprolin: conformational changes coupled to the bipartite nature of Au-rich MRNA-destabilizing motifs.

Tristetraprolin (TTP) binds AU-rich elements (AREs) encoded within selected labile mRNAs and targets these transcripts for rapid cytoplasmic decay. RNA binding by TTP is mediated by an approximately 70-amino acid domain containing two tandemly arrayed CCCH zinc fingers. Here we show that a 73-amino acid peptide spanning the TTP zinc finger domain, denoted TTP73, forms a dynamic, equimolar RNA.peptide complex with a 13-nucleotide fragment of the ARE from tumor necrosis factor alpha mRNA, which includes small but significant contributions from ionic interactions. Association of TTP73 with high affinity RNA substrates is accompanied by a large negative change in heat capacity without substantial modification of RNA structure, consistent with conformational changes in the peptide moiety during RNA binding. Analyses using mutant ARE substrates indicate that two adenylate residues located 3-6 bases apart within a uridylate-rich sequence are sufficient for high affinity recognition by TTP73 (K(d) <20 nm), with optimal affinity observed for RNA substrates containing AUUUA or AUUUUA. Linkage of conformational changes and binding affinity to the presence and spacing of these adenylate residues provides a thermodynamic basis for the RNA substrate specificity of TTP.

Amino Acid Motifs↗

PubMed1977

[Primary structure of functions of RNA terminals].

Primary structure of tRNA, rRNA, nRNA, mRNA and viral RNA terminals has been studied. Various RNAs responsible for similar functions have been shown to possess some common features. Previously obtained data on the functional role of RNA terminal sequences, mechanisms of their biosynthesis, the stabilizing role of 5'- and 3'-sequences for the molecules of translated eukaryotic RNAs and some viral RNAs are reviewed.

Base Sequence↗

PubMed1999

Quantifying the energetic interplay of RNA tertiary and secondary structure interactions.

To understand the RNA-folding problem, we must know the extent to which RNA structure formation is hierarchical (tertiary folding of preformed secondary structure). Recently, nuclear magnetic resonance (NMR) spectroscopy was used to show that Mg2+-dependent tertiary interactions force secondary structure rearrangement in the 56-nt tP5abc RNA, a truncated subdomain of the Tetrahymena group I intron. Here we combine mutagenesis with folding computations, nondenaturing gel electrophoresis, high-resolution NMR spectroscopy, and chemical-modification experiments to probe further the energetic interplay of tertiary and secondary interactions in tP5abc. Point mutations predicted to destabilize the secondary structure of folded tP5abc greatly disrupt its Mg2+-dependent folding, as monitored by nondenaturing gels. Imino proton assignments and sequential NOE walks of the two-dimensional NMR spectrum of one of the tP5abc mutants confirm the predicted secondary structure, which does not change in the presence of Mg2+. In contrast to these data on tP5abc, the same point mutations in the context of the P4-P6 domain (of which P5abc is a subdomain) shift the Mg2+ dependence of P4-P6 folding only moderately, and dimethyl sulfate (DMS) modification experiments demonstrate that Mg2+ does cause secondary structure rearrangement of the P4-P6 mutants' P5abc subdomains. Our data provide experimental support for two simple conclusions: (1) Even single point mutations at bases involved only in secondary structure can be enough to tip the balance between RNA tertiary and secondary interactions. (2) Domain context must be considered in evaluating the relative importance of tertiary and secondary contributions. This tertiary/secondary interplay is likely relevant to the folding of many large RNA and to bimolecular snRNA-snRNA and snRNA-intron RNA interactions.

Animals↗

PubMed1995

NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures.

Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation in each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA and RNA duplex structures.

Base Composition↗

PubMed2007

Structure-function analysis of the ribosomal frameshifting signal of two human immunodeficiency virus type 1 isolates with increased resistance to viral protease inhibitors.

Expression of the pol-encoded proteins of human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshift at the junction of the gag and pol coding sequences. Frameshifting takes place at a heptanucleotide slippery sequence, UUUUUUA, and is enhanced by a stimulatory RNA structure located immediately downstream. In patients undergoing viral protease (PR) inhibitor therapy, a p1/p6(gag) L449F cleavage site (CS) mutation is often observed in resistant isolates and frequently generates, at the nucleotide sequence level, a homopolymeric and potentially slippery sequence (UUUUCUU to UUUUUUU). The mutation is located within the stimulatory RNA downstream of the authentic slippery sequence and could act to augment levels of pol-encoded enzymes to counteract the PR deficit. Here, RNA secondary structure probing was employed to investigate the structure of a CS-containing frameshift signal, and the effect of this mutation on ribosomal frameshift efficiency in vitro and in tissue culture cells was determined. A second mutation, a GGG insertion in the loop of the stimulatory RNA that could conceivably lead to resistance by enhancing the activity of the structure, was also tested. It was found, however, that the CS and GGG mutations had only a very modest effect on the structure and activity of the HIV-1 frameshift signal. Thus the increased resistance to viral protease inhibitors seen with HIV-1 isolates containing mutations in the frameshifting signal is unlikely to be accounted for solely by enhancement of frameshift efficiency.

Drug Resistance, Viral↗

PubMed2001

Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus.

The molecular systematics of Quercus (Fagaceae) was recently assessed by two teams using independently generated ITS sequences. Although the results disagreed in several remarkable features, the phylogenetic trees for either hypothesis were highly supported by bootstrap resampling. We have reanalyzed the ITS sequences used by both teams (eight taxa) to reveal the underlying patterns of this divergence. Within species, conspicuous length and G + C% divergence were evident in most sequence comparisons. In addition, a high rate of substitutions and deletions involving highly conserved motifs in both ITS spacers were present in a set of sequences. This was coupled with a less thermodynamic stability in the RNA structure, lacking conserved hairpins that are putatively involved in the processing of the RNA transcripts. Compelling evidence suggests that the divergent ITS alleles reported by one team are pseudogenes, i.e., nonfunctional paralogous loci. The hypothesis that the contrasting phylogenetic histories drawn from Quercus using ITS data are not strictly related to technical differences between laboratories, but that they have rather been generated from the analysis of paralogous sequences, best reconciles the available data. The risk of incorporating ITS paralogues in plant evolutionary studies which can distortion the phylogenetic signal should caution molecular systematists. Without a detailed inspection of some basic features of the sequence, including the integrity of the conserved motifs and the thermodynamic stability of the secondary structures of the RNA transcripts, errors in evolutionary inferences could be easily overlooked.

Base Composition↗

PubMed2006

Association of RNA helicase a with human immunodeficiency virus type 1 particles.

RNA helicase A (RHA) belongs to the DEAH family of proteins that are capable of unwinding double-stranded RNA structure. In addition to its involvement in the metabolism of cellular RNA, RHA has been shown to stimulate RNA transcription from the long terminal repeat promoter of human immunodeficiency virus type 1 (HIV-1) as well as to enhance Rev/Rev response element-mediated gene expression. In this study, we provide evidence that RHA associates with HIV-1 Gag in an RNA-dependent manner. This interaction results in specific incorporation of RHA into HIV-1 particles. Knockdown of endogenous RHA in virus producer cells leads to generation of HIV-1 particles that are less infectious in part as a result of restricted reverse transcription. Therefore, RHA represents the first example of cellular RNA helicases that participate in HIV-1 particle production and promote viral reverse transcription.

Autoantigens↗

PubMed2005

The contributions of dsRNA structure to Dicer specificity and efficiency.

Dicer processes long double-stranded RNA (dsRNA) and pre-microRNAs to generate the functional intermediates (short interfering RNAs and microRNAs) of the RNA interference pathway. Here we identify features of RNA structure that affect Dicer specificity and efficiency. The data presented show that various attributes of the 3' end structure, including overhang length and sequence composition, play a primary role in determining the position of Dicer cleavage in both dsRNA and unimolecular, short hairpin RNA (shRNA). We also demonstrate that siRNA end structure affects overall silencing functionality. Awareness of these new features of Dicer cleavage specificity as it is related to siRNA functionality provides a more detailed understanding of the RNAi mechanism and can shape the development of hairpins with enhanced functionality.

Base Sequence↗

PubMed2003

Structures of trinucleotide repeats in human transcripts and their functional implications.

Among the goals of RNA structural and functional genomics is determining structures and establishing the functions of a rich repertoire of simple sequence repeats in transcripts. These repeats are present in transcripts from their 'birth' in the nucleus to their 'death' in cytoplasm and have the potential of being involved in many steps of RNA regulation. The knowledge of their structural features and functional roles will also shed more light on the postulated mechanisms of RNA pathogenesis in a growing list of neurological diseases caused by simple sequence repeat expansions. Here, we discuss several different lines of research to support the hypothesis that the mechanism of RNA pathogenesis may be a more common phenomenon triggered or modulated also by abundant long normal repeats. We propose structures of the repeat regions in transcripts of genes involved in Triplet Repeat Expansion Diseases. We have classified the polymorphic repeat alleles of these genes according to their ability to form hairpin structures in transcripts, and describe the distribution of different structural forms of the repeats in the human population. We have also reported the results of a systematic survey of the human transcriptome to identify mRNAs containing triplet repeats and to classify them according to structural and functional criteria. Based on this knowledge, we discuss the putative wider role of triplet repeat RNA hairpins in human diseases. A hypothetical model is proposed in which long normal RNA hairpins formed by the repeats may also be involved in pathogenesis.

Alleles↗

PubMed1993

Structural analysis by energy dot plot of a large mRNA.

We have predicted the secondary structure of the entire 4217 nucleotide sequence of the genomic RNA of coliphage Q beta in one computer run using the computer program MFOLD that computes RNA structures within any prescribed increment of the computed minimum free energy. The results are presented in the form of an "energy dot plot" that shows both an optimal folding as well as the superposition of all base-pairs that can form in slightly suboptimal foldings. The plot reveals five large, well-determined, independent structural domains that cover approximately 50% of the viral genome. The predicted structural domains are consistent with and provide support for five large structural domains identified previously by quantitative electron microscopy in Q beta RNA. The dot plot also contains cluttered regions that indicate large numbers of alternative foldings within or between segments of an RNA molecule. These reflect the impossibility of accurate structure prediction and/or the biological reality of more than one folding. Weaker, long range structures, that are observed by electron microscopy in two alternate competing conformations, are located in the regions of the Q beta sequence that correspond to cluttered regions of the dot plot. The potential biological significance of these secondary structures is discussed.

Coliphages↗

PubMed1989

Structural differences between active and inactive mammalian 60S ribosomal subunits. Circular dichroism and electric birefringence studies.

The structure and conformation of different active and inactive forms of the 60S rat liver ribosomal subunits have been analyzed by electric birefringence and circular dichroism. These studies show the following: 1) When a phosphate buffer is used instead of a triethanolamine buffer, there are major changes in RNA stacking, RNA-protein interactions, and particle orientation and conformation with no concomitant loss in ribosome activity. 2) The inactivated subunits by K(+)-depletion exhibit the same electro-optical and near-UV CD behaviour than the active subunits in phosphate buffer. 3) Inactivation by EDTA-treatment leads to drastic changes in RNA structure, RNA-protein interactions and subunit conformation; the 60S particles behave like free RNA, indicating the absence of any stabilization of rRNA by ribosomal proteins. 4) The inactivation of subunits by depletion of either monovalent or divalent cations is accompanied by a net decrease of the alpha-helicity of the ribosomal proteins. 5) The transition from active to inactive form of 60S subunits may involve protein modifications, likely dependent on a specific array of cations. 6) RNA has a certain degree of liberty within the subunits and one can suppose that this property is responsible for the flexible structure of ribosome.

Animals↗

PubMed2025

Discovery of functional factorless internal ribosome entry site-like structures through virome mining.

All viruses must co-opt the host translational machinery for viral protein synthesis. The dicistrovirus intergenic region internal ribosome entry site (IGR-IRES) utilizes the most streamlined translation mechanism by adopting a triple pseudoknot structure that directly recruits and binds within the intersubunit space of the ribosome and initiates translation from a non-AUG codon. The origin of this unprecedented mechanism is not known. Using a bioinformatics pipeline to examine the diversity and function of IRESs across RNA viromes, we searched for IRES-like RNA structures using RNA covariance models for multiple IRES sub-types, and tested functional IRES by using a dual-fluorescent lentiviral library reporter screen. We identified over >4,700 dicistro-like genomes with ~32% containing putative IRES structures, including novel viral genome arrangements with multiple IRESs and IRESs embedded within open-reading frames (ORFs). Predicted IRESs bound directly to purified ribosomes and supported internal ribosome entry activity in vitro and in vivo. Moreover, internal IRESs embedded within an ORF of monocistronic genomes were functional and operated simultaneously to produce the downstream ORF. We also identified IRES-like structures within non-dicistrovirus viral genomes, including in the families Tombusviridae and Narnaviridae that bound to ribosomes directly and a subset can direct internal ribosome entry. This study provides a framework to map the origin of factorless IRES mechanisms and study the diverse viral strategies utilizing RNA-based mechanisms.

Internal Ribosome Entry Sites↗

PubMed1988

In vivo and in vitro structural analysis of the rplJ mRNA leader of Escherichia coli. Protection by bound L10-L7/L12.

The rplJL-rpoBC operon of Escherichia coli is regulated in part at the level of translation by an autogenous mechanism (feedback regulation) that involves ribosomal protein L10-L7/L12. Feedback regulation occurs as the result of L10-L7/L12 binding to a site on the untranslated leader region of the rplJ mRNA that is located more than 100 nucleotides upstream from the translation start site. Previous studies have indicated that the secondary structure of the rplJ leader region is important for efficient translation and feedback regulation. We have done chemical modification experiments to examine the secondary structure of approximately 200 nucleotides of the rplJ leader region, and we propose a secondary structure that is consistent with the experimental data. RNA structure was probed in vitro by treating samples of total cellular RNA with diethyl pyrocarbonate and in vivo by treating log-phase cultures with dimethyl sulfate. Modified bases were detected by primer extension using three different oligonucleotide primers. The proposed structure includes five double-stranded regions designated I to V, separated by single-stranded segments numbered 1 to 5. We have also identified specific nucleotides in the rplJ mRNA leader that are protected by purified L10-L7/L12 from methylation by dimethyl sulfate in vitro. The protected bases are located within a bulge-loop of region IV, a portion of the mRNA that has been shown genetically to be necessary for feedback regulation.

Base Sequence↗

PubMed1997

Substrate structure requirements of the Pac1 ribonuclease from Schizosaccharmyces pombe.

The Pac1 ribonuclease of Schizosaccharomyces pombe is a member of the RNase III family of double-strand-specific ribonucleases. To examine RNA structural features required for efficient cleavage by the Pac1 RNase, we tested a variety of double-stranded and hairpin RNAs as substrates for the enzyme. The Pac1 RNase required substrates that have a minimal helix length of about 20 base pairs. The enzyme cut both strands of the helix at sites separated by two base pairs. However, Pac1 was also able to make a single-stranded cleavage within an internal bulge of an authentic Escherichia coli substrate at the same site chosen by RNase III. Pac1 efficiently degraded the structurally complex adenovirus VA RNA(I), but was inactive against the short HIV-1 TAR RNA hairpin. These results indicate that the Pac1 RNase prefers straight, perfect helices, but it can tolerate internal bulges that do not distort the helix severely. Like its homologue from Saccharomyces cerevisiae, the Pac1 RNase cleaved at two in vivo RNA processing sites in a hairpin structure in the 3' external transcribed spacer of the S. pombe pre-rRNA, suggesting a role for the enzyme in rRNA maturation.

Base Sequence↗

PubMedDate not supplied

[The RNA polymerase structure-activity studies (1962-2001)].

The study of RNA polymerase initiated by R.B. Khesin is conducted for about forty years at the laboratory founded by him (since 1989, in collaboration with A. Goldfarb's laboratory). Genetic methods are used in combination with methods of the specific chemical crosslinks of nucleic acids with proteins. The paper assesses the main results of the study in comparison with the X-ray crystallographic data of high resolution obtained recently. A short comparative summary of the RNA polymerase structure has been done for bacteria, archaebacteria, and eukaryotic organelles and nuclei. A brief history of the RNA polymerase study is also presented.

Crystallography, X-Ray↗

PubMed2000

Optical spectroscopic study of the effects of a single deoxyribose substitution in a ribose backbone: implications in RNA-RNA interaction.

The 2'-OH group in the ribose sugars of an RNA molecule plays an important role in guiding tertiary interactions that stabilize different RNA structural motifs. Deoxyribose, or 2'-OH by 2'-H, substitution in both the single-stranded and the duplex part of an RNA backbone has been routinely used to evaluate what role the 2'-OH plays in different tertiary interactions that guide an RNA-RNA contact. A deoxyribose substitution not only has the effect of removing a hydrogen bond donating group, but also introduces a sugar moiety with a preference for C2'-endo pucker in a backbone of predominantly C3'-endo sugars. This study evaluates the effects of a single deoxyribose substitution in both single-stranded and double-helical forms of RNA oligomers. A single-stranded, nonrepetitive 7-mer oligoribonucleotide (7-mer RNA) and four different variants having the same base sequence but with a single deoxyribose sugar at different positions in the strands have been studied by ultraviolet (UV) absorption, circular dichroism (CD), and Fourier transform infrared (FTIR) spectroscopy. Duplexes were formed by association with the complementary strand of the 7-mer RNA. The results show that both RNA and DNA single strands have preorganized conformations with spectral properties resembling those of A- and B-form helices, respectively, with RNA being more heterogeneous than its DNA counterpart. A single deoxyribose substitution perturbs the structure of the RNA backbone, with the effect being more pronounced in the single-stranded than in the duplex structure. The perturbation depends on the position of the 2'-H substitution in the strand.

Base Composition↗