ArticleJournal of the American Chemical Society2008
NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.
Article in Journal of the American Chemical Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 47 citations in OpenAlex.
- Article
- Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.Frontiers in genetics · 2017Review
- Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.Biochemistry · 2015Article
- Microarrays for identifying binding sites and probing structure of RNAs.Nucleic acids research · 2015Review
- Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions.RNA (New York, N.Y.) · 2014Article
- Article
- Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.Biochemistry · 2012Article
- RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts.Journal of biomolecular NMR · 2012Article
- NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.RNA (New York, N.Y.) · 2011Article
- Secondary structure of the HIV reverse transcription initiation complex by NMR.Journal of molecular biology · 2011Article
- Computational approaches for RNA energy parameter estimation.RNA (New York, N.Y.) · 2010Article
- Folding and finding RNA secondary structure.Cold Spring Harbor perspectives in biology · 2010Review
- Article
- RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.Biochemistry · 2010Article
- Evaluation of the information content of RNA structure mapping data for secondary structure prediction.RNA (New York, N.Y.) · 2010Article
- RNAstructure: software for RNA secondary structure prediction and analysis.BMC bioinformatics · 2010Article
- RNA pseudoknots: folding and finding.F1000 biology reports · 2010Article
- Fluorescence competition assay measurements of free energy changes for RNA pseudoknots.Biochemistry · 2010Article
- 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.Nucleic acids research · 2009Article
- Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.Journal of molecular biology · 2009Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
As the rate of functional RNA sequence discovery escalates, high-throughput techniques for reliable structural determination are becoming crucial for revealing the essential features of these RNAs in a timely fashion. Computational predictions of RNA secondary structure quickly generate reasonable models but suffer from several approximations, including overly simplified models and incomplete knowledge of significant interactions. Similar problems limit the accuracy of predictions for other self-folding polymers, including DNA and peptide nucleic acid (PNA). The work presented here demonstrates that incorporating unassigned data from simple nuclear magnetic resonance (NMR) experiments into a dynamic folding algorithm greatly reduces the potential folding space of a given RNA and therefore increases the confidence and accuracy of modeling. This procedure has been packaged into an NMR-assisted prediction of secondary structure (NAPSS) algorithm that can produce pseudoknotted as well as non-pseudoknotted secondary structures. The method reveals a probable pseudoknot in the part of the coding region of the R2 retrotransposon from Bombyx mori that orchestrates second-strand DNA cleavage during insertion into the genome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.