RNA pseudoknots: folding and finding

RNA pseudoknots are important for function. Three-dimensional structural information is available, insights into factors affecting pseudoknot stability are being reported, and computer programs are available for predicting pseudoknots.

• Publication year

  2010

• Venue

  F1000 Biology Reports

• Publication date

  2010-01-27

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.3410/B2-8PMID 20495679PMCID 2873773
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase

  2009cited by this paper
• Predicting structures and stabilities for H-type pseudoknots with interhelix loops.

  2009cited by this paper
• Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of –1 ribosomal frameshifting

  2009cited by this paper
• The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain*♦

  2009cited by this paper
• Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots†

  2009cited by this paper
• Predicting ribosomal frameshifting efficiency

  2008cited by this paper
• PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots

  2008influential reference
• Solution structure and dynamics of the wild-type pseudoknot of human telomerase RNA.

  2008cited by this paper
• NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon

  2008cited by this paper
• Structure of the SAM-II riboswitch bound to S-adenosylmethionine

  2008cited by this paper
• Crystal Structure of a Self-Spliced Group II Intron

  2008cited by this paper
• Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding

  2007cited by this paper
• Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting

  2007cited by this paper
• Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA.

  2007cited by this paper
• Characterization of the Mechanical Unfolding of RNA Pseudoknots

  2007cited by this paper
• Viral RNA pseudoknots: versatile motifs in gene expression and replication

  2007cited by this paper
• Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity.

  2007cited by this paper
• Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions.

  2007cited by this paper
• SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

  2007cited by this paper
• Structural Basis for Ribosome Recruitment and Manipulation by a Viral IRES RNA

  2006cited by this paper
• The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical.

  2006cited by this paper
• NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation

  2006cited by this paper
• A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting

  2006cited by this paper
• Structural Basis of glmS Ribozyme Activation by Glucosamine-6-Phosphate

  2006cited by this paper
• Predicting RNA pseudoknot folding thermodynamics

  2006cited by this paper
• Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function.

  2005influential reference
• Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif.

  2005cited by this paper
• Inaugural Article: Functional analysis of the pseudoknot structure in human telomerase RNA

  2005cited by this paper
• HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.

  2005influential reference
• A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting.

  2005influential reference
• Crystal structure of a phage Twort group I ribozyme–product complex

  2005cited by this paper
• Prediction of consensus RNA secondary structures including pseudoknots

  2004cited by this paper
• Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

  2004cited by this paper
• Crystal structure of a self-splicing group I intron with both exons

  2004cited by this paper
• An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots

  2004cited by this paper
• Classifying RNA pseudoknotted structures

  2004cited by this paper
• Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site.

  2004cited by this paper
• Telomerase RNA structure and function: implications for dyskeratosis congenita.

  2004cited by this paper
• Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA

  2003cited by this paper
• A partition function algorithm for nucleic acid secondary structure including pseudoknots

  2003cited by this paper
• Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution

  2002cited by this paper
• A molecular switch underlies a human telomerase disease

  2002cited by this paper
• Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot.

  2002cited by this paper
• Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting1

  2001cited by this paper
• RNA Pseudoknot Prediction in Energy-Based Models

  2000cited by this paper
• Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots

  2000cited by this paper
• Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme.

  2000cited by this paper
• Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot.

  2000cited by this paper
• Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

  1999cited by this paper
• An RNA folding method capable of identifying pseudoknots and base triples

  1998cited by this paper
• Structure of the 3′‐hairpin of the TYMV pseudoknot: preformation in RNA folding

  1998cited by this paper
• A dynamic programming algorithm for RNA structure prediction including pseudoknots.

  1998cited by this paper
• Crystal structure of a hepatitis delta virus ribozyme

  1998cited by this paper
• NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA.

  1998cited by this paper
• Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.

  1998cited by this paper
• A mutant RNA pseudoknot that promotes ribosomal frameshifting in mouse mammary tumor virus.

  1997cited by this paper
• Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus.

  1996cited by this paper
• The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus.

  1995cited by this paper
• An APL-programmed genetic algorithm for the prediction of RNA secondary structure.

  1995cited by this paper
• Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: loop lengths and stability of the stem regions.

  1995cited by this paper
• Identification and analysis of the pseudoknot-containing gag-pro ribosomal frameshift signal of simian retrovirus-1.

  1994cited by this paper

• AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction

  2025cites this paper
• Using the RNAstructure Software Package to Predict Conserved RNA Structures

  2024cites this paper
• Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.

  2024cites this paper
• SQUARNA - an RNA secondary structure prediction method based on a greedy stem formation model

  2024cites this paper
• RNA Secondary Structure Analysis Using RNAstructure

  2023cites this paper
• Linear-Time Algorithms for RNA Structure Prediction.

  2023cites this paper
• Computational approaches for RNA structure ensemble deconvolution from structure probing data.

  2022cites this paper
• Knotify: An Efficient Parallel Platform for RNA Pseudoknot Prediction Using Syntactic Pattern Recognition

  2022cites this paper
• Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots.

  2021cites this paper
• Computational approaches for the discovery of splicing regulatory RNA structures.

  2019cites this paper
• Scans of the MYC mRNA reveal multiple stable secondary structures—including a 3′ UTR motif, conserved across vertebrates, that can affect gene expression

  2019cites this paper
• A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.

  2019cites this paper
• RNA structural analysis of the MYC mRNA reveals conserved motifs that affect gene expression

  2019cites this paper
• How to benchmark RNA secondary structure prediction accuracy.

  2019cites this paper
• Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

  2018cites this paper
• RNA2DMut: a web tool for the design and analysis of RNA structure mutations

  2018cites this paper
• RNA structure prediction including pseudoknots through direct enumeration of states

  2018cites this paper
• A Survey on RNA Alignment Algorithm

  2018cites this paper
• Modeling RNA secondary structure folding ensembles using SHAPE mapping data

  2017cites this paper
• Secondary Structure Prediction of Single Sequences Using RNAstructure.

  2016cites this paper
• Bridging the gap between in vitro and in vivo RNA folding

  2016cites this paper
• In silico discovery and modeling of non-coding RNA structure in viruses.

  2015cites this paper
• Improving RNA secondary structure prediction with structure mapping data.

  2015cites this paper
• A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

  2015cites this paper
• Using the RNAstructure Software Package to Predict Conserved RNA Structures

  2014cites this paper
• RNA Secondary Structure Analysis Using RNAstructure

  2014cites this paper
• Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C

  2014cites this paper
• Stochastic Models of –1 Programmed Ribosomal Frameshifting

  2014cites this paper
• Local structural and environmental factors define the efficiency of an RNA pseudoknot involved in programmed ribosomal frameshift process.

  2014cites this paper
• RNA families in Epstein–Barr virus

  2014cites this paper
• Bioinformatics of prokaryotic RNAs

  2014cites this paper
• Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS.

  2013cites this paper
• Molecular dynamics simulation of RNA pseudoknot unfolding pathway

  2013cites this paper
• Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

  2013cites this paper
• Bacterial Regulatory RNA

  2012cites this paper
• TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots

  2012cites this paper
• Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction.

  2012cites this paper
• RNA structure prediction: an overview of methods.

  2012cites this paper
• IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

  2011cites this paper
• RNA Secondary Structure Analysis Using RNAstructure

  2006cites this paper