Cargando…

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

RNA secondary structure prediction is widely used for developing hypotheses about the structures of RNA sequences, and structure can provide insight about RNA function. The accuracy of structure prediction is known to be improved using experimental mapping data that provide information about the pai...

Descripción completa

Detalles Bibliográficos
Autores principales:	Spasic, Aleksandar, Assmann, Sarah M, Bevilacqua, Philip C, Mathews, David H
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2018
Materias:	RNA and RNA-protein complexes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758915/ https://www.ncbi.nlm.nih.gov/pubmed/29177466 http://dx.doi.org/10.1093/nar/gkx1057

Ejemplares similares

Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects
por: Zuber, Jeffrey, et al.
Publicado: (2022)

Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel
por: Kolář, Michal H, et al.
Publicado: (2022)

In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding
por: Incarnato, Danny, et al.
Publicado: (2017)

Revealing the distinct folding phases of an RNA three-helix junction
por: Plumridge, Alex, et al.
Publicado: (2018)

How to fold and protect mitochondrial ribosomal RNA with fewer guanines
por: Hosseini, Maryam, et al.
Publicado: (2018)

Tuning RNA folding and function through rational design of junction topology
por: Daher, May, et al.
Publicado: (2017)

Activation of viral transcription by stepwise largescale folding of an RNA virus genome
por: Chkuaseli, Tamari, et al.
Publicado: (2020)

Alu RNA fold links splicing with signal recognition particle proteins
por: Borovská, Ivana, et al.
Publicado: (2023)

The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity
por: Voigt, Christin, et al.
Publicado: (2018)

rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles
por: Biesiada, Marcin, et al.
Publicado: (2022)

In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells
por: Sieg, Jacob P, et al.
Publicado: (2023)

Stability of local secondary structure determines selectivity of viral RNA chaperones
por: Bravo, Jack P K, et al.
Publicado: (2018)

Theoretical basis for stabilizing messenger RNA through secondary structure design
por: Wayment-Steele, Hannah K, et al.
Publicado: (2021)

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs
por: Simon, Lisa Marie, et al.
Publicado: (2019)

A transient α-helix in the N-terminal RNA recognition motif of polypyrimidine tract binding protein senses RNA secondary structure
por: Maris, Christophe, et al.
Publicado: (2020)

The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements
por: Hohmann, Katharina F, et al.
Publicado: (2021)

Monitored eCLIP: high accuracy mapping of RNA-protein interactions
por: Hocq, Rémi, et al.
Publicado: (2018)

Mapping domains of ARS2 critical for its RNA decay capacity
por: Melko, Mireille, et al.
Publicado: (2020)

Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis
por: Płociński, Przemysław, et al.
Publicado: (2019)

YB-1 unwinds mRNA secondary structures in vitro and negatively regulates stress granule assembly in HeLa cells
por: Budkina, Karina, et al.
Publicado: (2021)

High-resolution RNA 3′-ends mapping of bacterial Rho-dependent transcripts
por: Dar, Daniel, et al.
Publicado: (2018)

rRNA expansion segment 27Lb modulates the factor recruitment capacity of the yeast ribosome and shapes the proteome
por: Shankar, Vaishnavi, et al.
Publicado: (2020)

Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN
por: Romero, Manuel, et al.
Publicado: (2018)

NMR-derived secondary structure of the full-length Ox40 mRNA 3′UTR and its multivalent binding to the immunoregulatory RBP Roquin
por: Tants, Jan-Niklas, et al.
Publicado: (2022)

Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures
por: Castandet, Benoît, et al.
Publicado: (2019)

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time
por: Hori, Naoto, et al.
Publicado: (2023)

Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation
por: Micic, Jelena, et al.
Publicado: (2022)

A structural map of oncomiR-1 at single-nucleotide resolution
por: Chakraborty, Saikat, et al.
Publicado: (2017)

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal
por: Glasser, Eliezra, et al.
Publicado: (2022)

Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome
por: Tosar, Juan Pablo, et al.
Publicado: (2020)

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements
por: Watters, Kyle E, et al.
Publicado: (2018)

Synthesis of RNA-cofactor conjugates and structural exploration of RNA recognition by an m(6)A RNA methyltransferase
por: Meynier, Vincent, et al.
Publicado: (2022)

Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing
por: Chan, Dalen, et al.
Publicado: (2021)

Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA–protein complexes
por: Baulin, Eugene, et al.
Publicado: (2020)

A conserved RNA structure is essential for a satellite RNA-mediated inhibition of helper virus accumulation
por: He, Lu, et al.
Publicado: (2019)

Identification of new high affinity targets for Roquin based on structural conservation
por: Braun, Johannes, et al.
Publicado: (2018)

In vivo structure of the Ty1 retrotransposon RNA genome
por: Andrzejewska, Angelika, et al.
Publicado: (2021)

Structural characterization of the ANTAR antiterminator domain bound to RNA
por: Walshe, James L, et al.
Publicado: (2022)

Structural identification of conserved RNA binding sites in herpesvirus ORF57 homologs: implications for PAN RNA recognition
por: Tunnicliffe, Richard B, et al.
Publicado: (2019)

De novo discovery of structural motifs in RNA 3D structures through clustering
por: Ge, Ping, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_e8e2gnq5426h583f9qamh6ffep