Predicting and Modeling RNA Architecture

Westhof, Éric; Masquida, Benoı̂t; Jossinet, Fabrice

doi:10.1101/cshperspect.a003632

Cited by 36 publications

(23 citation statements)

References 118 publications

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“…Non-Watson-Crick basepairing predominates in RNA 3D structure, forming motifs that facilitate RNA-RNA interactions and bind ligands (Leontis et al 2002;Westhof et al 2011). The phi29 3WJ crystal structure (Zhang et al 2013) revealed the formation of a cis base pair between the Watson-Crick edges of U29 and U72 as well as base stacking between U29 and U74 ( Fig.…”

Section: Structure-energetics Relationships In the Prna 3wjmentioning

confidence: 99%

Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA

Hill

Schroeder

2017

RNA

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The thermodynamic stabilities of four natural prohead or packaging RNA (pRNA) three-way junction (3WJ) nanomotifs and seven phi29 pRNA 3WJ deletion mutant nanomotifs were investigated using UV optical melting on a three-component RNA system. Our data reveal that some pRNA 3WJs are more stable than the phi29 pRNA 3WJ. The stability of the 3WJ contributes to the unique self-assembly properties of pRNA. Thus, ultrastable pRNA 3WJ motifs suggest new scaffolds for pRNA-based nanotechnology. We present data demonstrating that pRNA 3WJs differentially respond to the presence of metal ions. A comparison of our data with free energies predicted by currently available RNA secondary structure prediction programs shows that these programs do not accurately predict multibranch loop stabilities. These results will expand the existing parameters used for RNA secondary structure prediction from sequence in order to better inform RNA structure-function hypotheses and guide the rational design of functional RNA supramolecular assemblies.

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Section: Structure-energetics Relationships In the Prna 3wjmentioning

confidence: 99%

Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA

Hill

Schroeder

2017

RNA

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“…RNA function depends on its structure-it is the seemingly limitless variety of structures that allows so many diverse functions. We can now predict RNA secondary structure quite well (Mathews et al 2010) and see much progress on predicting 3D structure (Westhof et al 2010). Remarkably, we can now watch molecules of RNA fold and unfold and switch from one state to another in "singlemolecule experiments" (Tinoco et al 2010).…”

Section: The World Of Rna Technology and Medical Applicationsmentioning

confidence: 99%

The RNA Worlds in Context

Cech

2011

Cold Spring Harbor Perspectives in Biology

188

136

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SUMMARYThere are two RNAworlds. The first is the primordial RNAworld, a hypothetical era when RNA served as both information and function, both genotype and phenotype. The second RNA world is that of today's biological systems, where RNA plays active roles in catalyzing biochemical reactions, in translating mRNA into proteins, in regulating gene expression, and in the constant battle between infectious agents trying to subvert host defense systems and host cells protecting themselves from infection. This second RNA world is not at all hypothetical, and although we do not have all the answers about how it works, we have the tools to continue our interrogation of this world and refine our understanding. The fun comes when we try to use our secure knowledge of the modern RNAworld to infer what the primordial RNAworld might have looked like.

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“…To compensate for the difficulty in determination of threedimensional structures, various methods are being devised to model them from sequence. The methods include homology modeling aided by human intuition (Martinez et al 2008;Westhof et al 2010), and/or knowledge-based course force fields (Malhotra and Harvey 1994;Tan et al 2006;Das and Baker 2007;Ding et al 2008;Parisien and Major 2008;Jonikas et al 2009;Parisien et al 2009;Das et al 2010;Pasquali and Derreumaux 2010), and/or lowresolution experimental data, and/or bioinformatics data (Gherghe et al 2009;Flores and Altman 2010;Yang et al 2010;Seetin and Mathews 2011). There are relatively few benchmarks available, however, for testing and optimizing these methods, especially all atom methods.…”

Section: Introductionmentioning

confidence: 99%

NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

Lerman

Kennedy²,

Shankar³

et al. 2011

RNA

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The NMR solution structure is reported of a duplex, 59GUGAAGCCCGU/39UCACAGGAGGC, containing a 4 @ 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 59GAA/39AGG, 59GAG/39AGG, 59GAA/39AAG, and 59AAG/39AGG. The structural information is compared with predictions made with the MC-Sym program.

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Predicting and Modeling RNA Architecture

Cited by 36 publications

References 118 publications

Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA

Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA

The RNA Worlds in Context

NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

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