Relevant bibliographies by topics / Conserved RNA Structures

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Conserved RNA Structures'

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Published: 4 June 2021
Last updated: 3 February 2022

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Journal articles on the topic "Conserved RNA Structures"

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Shepard, P. J., and K. J. Hertel. "Conserved RNA secondary structures promote alternative splicing." RNA 14, no. 8 (June 20, 2008): 1463–69. http://dx.doi.org/10.1261/rna.1069408.

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Kiening, Ochsenreiter, Hellinger, Rattei, Hofacker, and Frishman. "Conserved Secondary Structures in Viral mRNAs." Viruses 11, no. 5 (April 29, 2019): 401. http://dx.doi.org/10.3390/v11050401.

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RNA secondary structure in untranslated and protein coding regions has been shown to play an important role in regulatory processes and the viral replication cycle. While structures in non-coding regions have been investigated extensively, a thorough overview of the structural repertoire of protein coding mRNAs, especially for viruses, is lacking. Secondary structure prediction of large molecules, such as long mRNAs remains a challenging task, as the contingent of structures a sequence can theoretically fold into grows exponentially with sequence length. We applied a structure prediction pipeline to Viral Orthologous Groups that first identifies the local boundaries of potentially structured regions and subsequently predicts their functional importance. Using this procedure, the orthologous groups were split into structurally homogenous subgroups, which we call subVOGs. This is the first compilation of potentially functional conserved RNA structures in viral coding regions, covering the complete RefSeq viral database. We were able to recover structural elements from previous studies and discovered a variety of novel structured regions. The subVOGs are available through our web resource RNASIV (RNA structure in viruses; http://rnasiv.bio.wzw.tum.de).
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Witwer, C. "Conserved RNA secondary structures in Picornaviridae genomes." Nucleic Acids Research 29, no. 24 (December 15, 2001): 5079–89. http://dx.doi.org/10.1093/nar/29.24.5079.

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Thurner, Caroline, Christina Witwer, Ivo L. Hofacker, and Peter F. Stadler. "Conserved RNA secondary structures in Flaviviridae genomes." Journal of General Virology 85, no. 5 (May 1, 2004): 1113–24. http://dx.doi.org/10.1099/vir.0.19462-0.

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Presented here is a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This virus family consists of the three genera Flavivirus, Pestivirus and Hepacivirus and the group of GB virus C/hepatitis G virus with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered separately: the genus Flavivirus, with its type I cap structure at the 5′ untranslated region (UTR) and a highly structured 3′ UTR, and the remaining three groups, which exhibit translation control by means of an internal ribosomal entry site (IRES) in the 5′ UTR and a much shorter less-structured 3′ UTR. The main findings of this survey are strong hints for the possibility of genome cyclization in hepatitis C virus and GB virus C/hepatitis G virus in addition to the flaviviruses; a surprisingly large number of conserved RNA motifs in the coding regions; and a lower level of detailed structural conservation in the IRES and 3′ UTR motifs than reported in the literature. An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements.
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Mironov, A. A. "New method to predict conserved RNA structures." Molecular Biology 41, no. 4 (August 2007): 642–49. http://dx.doi.org/10.1134/s0026893307040188.

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Hooks, Katarzyna B., and Sam Griffiths-Jones. "Conserved RNA structures in the non-canonical Hac1/Xbp1 intron." RNA Biology 8, no. 4 (July 2011): 552–56. http://dx.doi.org/10.4161/rna.8.4.15396.

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Freidhoff, Paul, and Michael F. Bruist. "In silico survey of the central conserved regions in viroids of the Pospiviroidae family for conserved asymmetric loop structures." RNA 25, no. 8 (May 23, 2019): 985–1003. http://dx.doi.org/10.1261/rna.070409.119.

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LE, SHU-YUN, JACOB V. MAIZEL, and KAIZHONG ZHANG. "FINDING CONSERVED WELL-ORDERED RNA STRUCTURES IN GENOMIC SEQUENCES." International Journal of Computational Intelligence and Applications 04, no. 04 (December 2004): 417–30. http://dx.doi.org/10.1142/s1469026804001409.

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Recent advances in RNA studies show that the well-ordered, structured RNAs perform a broad functions in various biological mechanisms. Included among these functions are regulations of gene expression at multiple levels by diversified ribozymes and various RNA regulatory elements. The discovered microRNAs (miRNAs) with a distinct stem-loops are a new class of RNA regulatory elements. The prediction of those well-ordered folding sequences (WFS) associated with the RNA regulatory elements in genomic sequences is very helpful for our understandings of RNA-based gene regulations. We present here a new computational method in searching for the conserved WFS in genomes. In the method, the WFS is assessed by a quantitative measure E diff that is defined as the difference of free energies between the computed optimal structure (OS) and its corresponding optimal restrained structure where all the previous base pairings in the OS are forbidden. From those WFS with high E diff scores, the conserved WFS is determined by computing the maximal similarity score (MSS) between the two compared structures. In practice, we first search for those distinct WFS with high statistical significance in genomic sequences and then seek for those conserved WFS with high MSS. The potential and implications of our discoveries in the genome of Caenorhabditis elegans are discussed.
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Asturias, F. J., Y. W. Jiang, L. C. Myers, C. M. Gustafsson, and R. D. Kornberg. "Conserved Structures of Mediator and RNA Polymerase II Holoenzyme." Science 283, no. 5404 (February 12, 1999): 985–87. http://dx.doi.org/10.1126/science.283.5404.985.

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Hofacker, I. L., P. F. Stadler, and R. R. Stocsits. "Conserved RNA secondary structures in viral genomes: a survey." Bioinformatics 20, no. 10 (July 1, 2004): 1495–99. http://dx.doi.org/10.1093/bioinformatics/bth108.

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Dissertations / Theses on the topic "Conserved RNA Structures"

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Hershan, Almonther A. "Identification and analysis of conserved structures in RNA viruses." Thesis, University of Essex, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.572803.

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The family Picornaviridae includes many important human pathogens. RNA structures play important roles in picornavirus molecular biology and recent evidence suggests that these are more extensive than previously thought. In this project we identified a number of potential RNA structures in picornavirus genomes and started to analyse one of these structures. The work focussed on human parechoviruses (HPe V). The structure of the HPe V 5' untranslated region (UTR) was analysed by obtaining several new sequences and using an alignment of 60 sequences to identify covariant changes. This allowed the previously predicted structure to be confirmed and refined. Aligned sequences representing most picornavirus species were then analysed for suppression of synonymous codon variation (SSCV). Strong SSCV was seen in several cases and this was often related to the presence of RNA structures including the Cre and novel potential structures. Patterns of conserved dinucleotides were also used to identify regions of importance in the picornavirus genome. A new program, Dinucleotider (1.0) was developed and used, which allows a graphical output of conserved dinucleotides in aligned sequences. CG was found to be the most informative dinucleotide and could be used to identify regions of the picornavirus genome, which corresponded to the 5'UTR, 3'UTR and Cre, as well as further new structures. Genetic analysis of a predicted structure in the 3D-encoding region of HPe V s, was carried out by making two mutants, with 3 or 6 mutations in one of the structural domains. Both sets of mutations had little effect on virus growth in cultured cells, suggesting that the structure does not play a critical role in replication and other possible roles need to be identified. Overall, this project has allowed several RNA structures to be identified in picornaviruses. These are conserved between related viruses and presumably play important roles in the biology of picornaviruses. They need to be studied further in order to improve understanding of how picornaviruses infect cells, which is required to improve diagnosis and control of these pathogens.
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Zhu, Jing Yun Alice. "Beyond the one-sequence-one-structure dogma : predicting and analysing transient and alternative RNA secondary structures that are evolutionarily conserved." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/54739.

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State-of-the-art methods in RNA secondary structure prediction focus on predicting the final, functional structure. However, ample experimental and statistical evidence indicates that structure formation starts immediately during transcription and this co-transcriptional folding influences the resultant final RNA structure. Thus, identifying the transient structures that are formed co-transcriptionally may bring insight into understanding how co-transcriptional folding leads to the final conformation in vivo. As RNA secondary structures are currently best predicted by comparative approaches, we therefore investigated whether homologous RNA genes not only assume the same final structure, but also share structural features during the co-transcriptional folding in vivo. For this, we compiled a non-redundant data set of 32 transcripts deriving from six different RNA families which constitutes the most comprehensive data set with experimentally confirmed transient and alternative RNA structures so far. We present statistical evidence that homologous RNA genes from related organisms fold co-transcriptionally in a similar way. In particular, we show that some transient structures are highly conserved with levels similar to those of the final, functional structure. Moreover, we find that the predicted co-transcriptional folding pathways of homologous sequences encounter similar transient structure features, which often coincide with known transient features. We thus also predict candidates for these evolutionarily conserved transient features of co-transcriptional folding pathways in silico. We further expand 4 alignments from the aforementioned dataset by searching via covariance model and manual curation in order to share them with the RNA community. These alignments either update the existing Rfam datasets with annotation of transient structures, or introduce new RNA family: (1) Trp operon leader, where alternative structures are coordinated to regulate the operon transcription in response to tryptophan abundance (2) HDV ribozyme, where the self-cleavage activity is modulated via transient structures involving the extended 5’ flanking sequence (3) 5’ UTR of Levivirus maturation protein, where a transient structure temporarily postpones the formation of the final structure that inhibits the translation of maturation protein (4) SAM riboswitch, where the downstream gene expression is regulated by alternative structures upon binding of SAM.
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Wiebe, Nicholas J. P. "Transat : a method for detecting evolutionarily conserved helices in alignments of RNA sequences and its application in identifying transient or alternative RNA structures." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/28813.

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The secondary structure of RNA molecules is often critical to their proper functioning, and so prediction of those structures has been a focus of bioinformatics research for many years. RNA folds as it is transcribed, and it has lately become apparent that the sequences of structures that an RNA adopts (its folding path) is vitally important for the RNA to fold into its proper structure. Analysis of the evolution of a group of related RNAs is useful for identifying conserved and therefore functionally important secondary structures. In theory, functional but transient secondary structures which play a role in the folding pathway should also be detectable in this way. Moreover, folding may be affected by a variety of factors in the cellular environment, which presents a challenge to the existing methods of RNA pathway prediction via simulation. Evolutionarily conserved helices are implicitly the ones formed in vivo, and so is a useful means of accounting for this problem. Here we present TRANSAT, a method of identifying evolutionarily conserved elements of RNA secondary structure, including transient structures, from an alignment of related RNAs. We evaluate TRANSAT’s performance on a wide variety of alignments, present some examples of its predictions, and show how its predictions may be useful for predicting folding pathways. We also present a method of generating simulated alignments, and use these alignments to examine TRANSAT’s performance in ways that are challenging with alignments of real sequences.
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Casas-Vila, Núria [Verfasser]. "Applications of mass spectrometry-based proteomics: the developmental proteome of D. melanogaster and the RNA-fold interactome of conserved RNA structures in yeast / Núria Casas-Vila." Mainz : Universitätsbibliothek der Johannes Gutenberg-Universität Mainz, 2020. http://d-nb.info/122489653X/34.

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O'Farrell, Heather Colleen. "The KsgA methyltransferase: Characterization of a universally conserved protein involved in robosome biogenesis." VCU Scholars Compass, 2007. http://scholarscompass.vcu.edu/etd/962.

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The KsgA enzymes comprise an ancient family of methyltransferases that are intimately involved in ribosome biogenesis. Ribosome biogenesis is a complicated process, involving numerous cleavage, base modification and assembly steps. All ribosomes share the same general architecture, with small and large subunits made up of roughly similar rRNA species and a variety of ribosomal proteins. However, the fundamental assembly process differs significantly between eukaryotes and eubacteria, not only in distribution and mechanism of modifications but also in organization of assembly steps. Despite these differences, members of the KsgA/Dim1 methyltransferase family and their resultant modification of small-subunit rRNA are found throughout evolution, and therefore were present in the last common ancestor. The first member of the family to be described, KsgA from Escherichia coli, was initially shown to be the determining factor for resistance/sensitivity to the antibiotic kasugamycin and was subsequently found to dimethylate two adenosines in 16S rRNA during maturation of the 30S subunit. Since then, numerous other members of the family have been characterized in eubacteria, eukaryotes, archaea and in eukaryotic organelles. The eukaryotic ortholog, Dim1, is essential for proper processing of the pre-rRNA, in addition to and separate from its methyltransferase function. The KsgA/Dim1 family bears sequence and structural similarity to a larger group of S-adenosyl-L-methionine dependent methyltransferases, which includes both DNA and RNA methyltransferases. In this document we report that KsgA orthologs from archaea and eukaryotes are able to complement for KsgA function in bacteria, both in vivo and in vitro. This indicates that all of these enzymes can recognize a common ribosomal substrate, and that the recognition elements must be largely unchanged since the evolutionary split between the three domains of life. We have characterized KsgA structurally, and discuss aspects of KsgA's activity in light of the structural data. We also propose a model for KsgA binding to the 30S subunit, based on solution probing data. This model sheds light on KsgA's unusual regulation and on the dual function of the Dim1 enzymes.
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Townsend, Hannah Leanne. "A phylogenetically conserved RNA structure within the poliovirus 3C ORF competitively inhibits the antiviral ribonuclease L /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2008.

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Thesis (Ph.D. in Microbiology) -- University of Colorado Denver, 2008.
Typescript. Includes bibliographical references (leaves 126-147). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;
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King, John. "NMR studies of the structure of a conserved RNA motif of 23S ribosomal RNA and its interaction with peptidyl transferase antibiotics." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/nmr-studies-of-the-structure-of-a-conserved-rna-motif-of-23s-ribosomal-rna-and-its-interaction-with-peptidyl-transferase-antibiotics(79f020db-7357-44bb-8984-6ebfb540e11a).html.

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In this project a number of peptidyl transferase antibiotics were studied, specifically a group of aminohexose cytosine nucleoside antibiotics and their interaction with a selected number of highly conserved ribonucleic acid (RNA) motifs, designed to represent their possible binding site within the ribosome. This group of antibiotics shows a wide range of interesting properties, including antiviral and anti-tumour activity, and as they bind to a particularly conserved region in the ribosome, they are likely to be difficult for microorganisms to develop resistance to. It is hoped that once the mechanism of action of these antibiotics is better understood, that modifications to the antibiotics can be effectively made to create new or hybrid antibiotics with more selective antibacterial, or indeed antiviral or anti-tumour properties. The nuclear magnetic resonance (NMR) structure of the RNA binding, peptidyl tranferase inhibitor antibiotics amicetin, blasticidin S and gougerotin, in their native solution states, have been successfully determined. The structures all exhibit a stable conformation, stabilised by intramolecular hydrogen bonds. Amicetin was observed to be folded, distinctly different from the linear, extended conformation of amicetin previously determined by X-ray crystallography. The structure of blasticidin S was found to be very similar to its X-ray crystal structure. Gougerotin was shown to form a similar conformation to blasticidin S, save that the end chain of gougerotin was bent at right angles to the rest of the molecule, forming a structure similar to that of the major bound X-ray crystal structure of blasticidin S. All the solution structures showed a similar conformation in the analogous regions of their chemical structure, suggesting that hybrid antibiotics could be produced.Two highly conserved RNA motifs of Halobacterium halobium (H. h.) and Escherichia coli (E. coli) 23S ribosomal RNAs were chosen to investigate their interaction with amicetin. The NMR structure of the H. h. and E. coli. 29-mer RNA motifs have been determined; the motifs both form well folded A-form RNA conformations. The E. coli NMR structure differs from the X-ray crystal structure of the motif contained within the ribosome, as a highly conserved adenine residue, which resides in a bulge strongly implicated with amicetin binding, folds into the helix as opposed to being flipped out. Instead, an adjacent cytosine residue partially flips out; whereas in the crystal structure, it is folded within the helix. The NMR stuctures of the H. h. motif differs from the X-ray crystal structure of the motif, contained within the ribosome, as none of the bases are flipped out and a number of non-canonical base pairs are formed in the solution structure. To continue this study, a fully 13C and 15N isotopically labelled version of the H. h. RNA sample has been partially assigned, and an initial structure determination has been performed, using ultra high field 1 GHz spectroscopy.Addition of amicetin to both the H. h. and E. coli 29-mer RNA samples were accompanied by discrete changes to the spectra, suggesting weak interaction between the two components. These can be qualitatively interpreted to changes induced in the local conformation of the RNA motifs and the amicetin arising from the formation of a complex, between the amicetin and the bulge region of the particular motif.
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Nareen, Misbah. "NMR structural studies of the binding of peptidyl transferase antibiotics to conserved secondary structural motifs of 23S ribosomal RNA." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/nmr-structural-studies-of-the-binding-of-peptidyl-transferase-antibiotics-to-conserved-secondary-structural-motifs-of-23s-ribosomal-rna(6666811e-1fe0-49ba-9da6-5999bc9ec93e).html.

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The peptidyl transferase centre (PTC) of 23S ribosomal RNA is the target for a number of antibiotics which inhibit protein synthesis. The precise mode of binding of these antibiotics is largely unknown and hence is an active area of research in structural biology. The NMR solution structures of three PT antibiotics, bamicetin, sparsomycin and anisomycin have been successfully characterised using a range of two-dimensional NMR techniques and restrained molecular dynamics. The NMR structures of the these antibiotics provided valuable first hand insight into their conformations, since no X-ray crystal structures of the antibiotics in their free states have been determined so far. Bamicetin adopts a folded conformation possibly held by intramolecular hydrogen bonds and similar to the published NMR structure of amicetin. These antibiotics generate spontaneous single nucleotide mutants upon prolonged exposure and bamicetin and sparsomycin are universal PT inhibitors, interacting with all three evolutionary domains of 23S rRNAs. The amicetin antibiotic produces a spontaneous single mutation U2457C in the Halobacterium halobium (H.hal) 23S rRNA and the binding site is predicted to be very close to this nucleotide. The similarity in chemical structure with amicetin, suggests bamicetin to target the same binding site on the 23S rRNA. Both bamicetin and sparsomycin show exchange retarded amide proton resonances in the NMR spectrum, akin to other amicetin family antibiotics, indicating the retarded exchange to be a characteristic feature in the native solution state. The Bacillus subtilis (B.subtilis) 70S ribosomes have strong affinity for bamicetin and so a highly conserved 27mer RNA motif containing the possible binding site was selected for NMR structure determination and bamicetin binding studies. The greater number of imino proton resonances observed together with the high quality of the determined structure of the motif proved that B.subtilis rRNA is more stable than E.coli and H.hal rRNAs. The B.subtilis 27mer rRNA-bamicetin interaction studies revealed a fast exchange, weak binding system and careful analysis of line width and chemical shifts indicated changes at the local conformation of the RNA after binding. To probe the cross-hypersensitivity phenomenon, a 25mer RNA corresponding to the thiostrepton-resistant mutant (G1159) residing in the domain II of H.hal 23S rRNA was chosen for NMR structure determination and amicetin binding. Discrete chemical shift changes and NOESY experiments using ultrahigh field 1GHz NMR revealed weak interactions. The structures of the antibiotics and analysis of their dynamics as well as interactions with the RNA motifs of different organisms have yielded important information in understanding their binding and inhibitory activities at the atomic level. The results can be used for generating new or hybrid antibiotics to tackle the escalating problem of antibiotic resistance.
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Mohammed, Sadia. "NMR studies of the structure, dynamics and interactions of the conserved RNA motifs of the EMCV picornavirus." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/nmr-studies-of-the-structure-dynamics-and-interactions-of-the-conserved-rna-motifs-of-the-emcv-picornavirus(2cc0fa5b-f80d-48f2-a918-44b7bf5a2429).html.

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The conserved secondary structural RNA motifs of EncephaloMyoCarditis Virus (EMCV) have been well characterised biochemically and shown to play an important role in translation initiation by a novel cap-independent mechanism called Internal Ribosomal Entry Site (IRES). However, the three dimensional structure and interactions of these conserved motifs are not known, and hence the mechanism is not fully understood. The NMR results described in this thesis have provided, for the first time, new structural knowledge on the conformation of these motifs, their affinity for Mg2+ and their intermolecular interactions. RNA motifs selected from two separate domains (I and J) of the IRES structure were investigated using a range of 2D and 3D NMR techniques. The apical ‘hammerhead’ region of the I domain contains a highly conserved 16mer RNA which hosts a stable and mutationally sensitive G547CGA550 tetraloop. Sequence specific assignments were carried out on this motif, along with its Mg2+ complex, and a large number of NMR experimental constraints were generated for the RNA structure determination. Similarly, high resolution NMR structures of a distal 17mer RNA, which has been predicted to be a potential receptor for the GCGA tetraloop, and its Mg2+ complex were also produced. Thus, we were able to demonstrate that Mg2+ stabilises the RNA tertiary structure via non-specific interactions. Since the largest changes were induced at the tetraloop motif, we propose that Mg2+ stabilises the 16mer into an optimum conformation which is essential for IRES function. The determination of the structures of the above motifs led us to investigate the 16mer-17mer binary (1:1) complex at 1 GHz, in the presence of Mg2+. Significant changes were observed in the 1H and 31P chemical shift, NOE intensity and line width, clearly demonstrating RNA-RNA interactions taking place between the two components. The most interesting result to emerge was the distinct absence of NOEs from G547{NH} of the stable tetraloop, thus highlighting an important structural role for this functionally critical residue. Since no previous work has shown a clear interaction between the two RNAs, the results obtained in this project provide the first direct experimental evidence for intramolecular interactions in the I domain of EMCV IRES.Finally, we show how isotopically labelled RNAs can be successfully used as an aid in NMR assignment, analysis and structure determination. The J domain of EMCV IRES binds to eIF4GII protein and is essential for translation initiation. A suite of 3D NMR techniques were carried out on a highly enriched and uniformly 13C, 15N-labelled 39mer RNA. Several key features of the RNA, which may be involved in protein recognition, were identified. Further, a selectively 19F-labelled 16mer RNA from the I domain, was also studied to show how fluorine NMR can be used to probe RNA structure, dynamics and interactions. The RNA motifs of the EMCV IRES were shown to exhibit high stabilities, which are brought about by the complex folding of the various secondary structural elements involving RNA- Mg2+, RNA-RNA and RNA-protein tertiary interactions. It is these vital interactions that enable the IRES to recruit the ribosome in the translation initiation step of protein synthesis, and have laid a strong foundation for further NMR investigation of the whole IRES.
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Eno-Ibanga, Cheryl K. "The analysis of a conserved RNA structure in the 3D polymerase encoding region of human parechovirus 1." Thesis, University of Essex, 2016. http://repository.essex.ac.uk/19097/.

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Picornaviruses are important causes of human illness and it is necessary to understand more about how these viruses function. Human parechoviruses (HPeV) are common pathogens and studies have shown that 95% of people become infected with HPeV at a very early age, usually with symptoms such as mild diarrhoea and fever. However, one virus type HPeV3, is implicated in much more serious cases of neonatal disease and so it is important to understand HPeVs to increase the opportunity to develop drugs or vaccines against the infection. The HPeV1 genome encodes a single polyprotein that is cleaved into structural and non-structural proteins. Analysis of one region of the genome (encoding the polymerase, 3Dpol) shows that some codons are perfectly conserved, suggesting functions in addition to protein coding. This region seems to fold into an RNA secondary structure made up of three stem-loops and a tertiary structure “kissing” interaction. The structure was validated by comparing all the available HPeV sequences and found to be highly conserved. To investigate if the structure has a role in RNA stability, an EGFP fluorescent assay was used. Sequences containing the structure was added to the 3’ UTR of the EGFP gene. A mutant with 21 mutations which completely destroys the RNA structure was also used. A FACS-based method was used to measure expression levels of EGFP. The results showed that there was a significant reduction in fluorescence from the mutant construct. The effect of the structure was also investigated in infected cells and in cells exposed to different stresses which could mimic virus infection. The results suggest that the structure can positively affect RNA stability/translation. Further investigation on other possible roles such as RNA replication and translation should be performed to improve the understanding of the biology of the structure in HPeVs and a Renilla Luciferase reporter gene system was assembled to facilitate the studies in the future.
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Books on the topic "Conserved RNA Structures"

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Almehdi, Mirza A. The function and structural characteristics of conserved regions within Escherichia Coli small subunit ribosomal RNA. 1991.

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Book chapters on the topic "Conserved RNA Structures"

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Xu, Zhenjiang Zech, and David H. Mathews. "Prediction of Secondary Structures Conserved in Multiple RNA Sequences." In RNA Structure Determination, 35–50. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6433-8_3.

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Pervouchine, Dmitri, Ekaterina Khrameeva, Marina Pichugina, Olexii Nikolaienko, Mikhail Gelfand, Petr Rubtsov, and Andrei Mironov. "Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures." In Lecture Notes in Computer Science, 199. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-29627-7_20.

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Chen, Qingfeng, Baoshan Chen, and Chengqi Zhang. "Modeling Conserved Structure Patterns for Functional Noncoding RNA." In Intelligent Strategies for Pathway Mining, 151–73. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-04172-8_7.

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Greenbaum, Nancy L. "Role of a conserved pseudouridine in U2 snRNA on the structural and electrostatic features of the spliceosomal pre-mRNA branch site." In Fine-Tuning of RNA Functions by Modification and Editing, 205–21. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/b106846.

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Cech, Thomas R. "Conserved sequences and structures of group I introns: building an active site for RNA catalysis — a review." In RNA: Catalysis, Splicing, Evolution, 191–203. Elsevier, 1989. http://dx.doi.org/10.1016/b978-0-444-81210-0.50023-3.

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Wong, Thomas K. F., and S. M. Yiu. "Structural Alignment of RNAs with Pseudoknots." In Handbook of Research on Computational and Systems Biology, 550–71. IGI Global, 2011. http://dx.doi.org/10.4018/978-1-60960-491-2.ch024.

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Non-coding RNAs (ncRNAs) are found to be critical for many biological processes. However, identifying these molecules is very difficult and challenging due to the lack of strong detectable signals such as opening read frames. Most computational approaches rely on the observation that the secondary structures of ncRNA molecules are conserved within the same family. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, the problem becomes more difficult if the secondary structure contains pseudoknots. Only until recently, many of the existing approaches could not handle structures with pseudoknots. This chapter reviews the state-of-the-art algorithms for different types of structures that contain pseudoknots including standard pseudoknot, simple non-standard pseudoknot, recursive standard pseudoknot, and recursive simple non-standard pseudoknot. Although none of the algorithms is designed for general pseudoknots, these algorithms already cover all known ncRNAs in both Rfam and PseudoBase databases. The evaluation of the algorithms also shows that the approach is useful in identifying ncRNA molecules in other species, which are in the same family of a known ncRNA.
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Athanasiadis, Alekos, Diana Placido, Stefan Maas, Bernard A. Brown, Ky Lowenhaupt, and Alexander Rich. "The Crystal Structure of the Zβ Domain of the RNA-editing Enzyme ADAR1 Reveals Distinct Conserved Surfaces Among Z-domains." In The Excitement of Discovery: Selected Papers of Alexander Rich, 249–60. WORLD SCIENTIFIC, 2018. http://dx.doi.org/10.1142/9789813272682_0037.

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Conference papers on the topic "Conserved RNA Structures"

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Haoyue Fu, Dingyu Xue, Xiangde Zhang, and Cangzhi Jia. "Conserved secondary structure prediction for similar highly group of related RNA sequences." In 2009 Chinese Control and Decision Conference (CCDC). IEEE, 2009. http://dx.doi.org/10.1109/ccdc.2009.5194995.

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Fang, Xiaoyong, Zhigang Luo, Bo Yuan, and Zhenghua Wang. "Detecting and Assessing Conserved Stems for Accurate Structural Alignment of RNA Sequences." In 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering. IEEE, 2007. http://dx.doi.org/10.1109/bibe.2007.4375580.

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