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Automated 3D structure composition for large RNAs
Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessingExpand
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RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures
TLDR
We present and discuss RNA FRABASE 2.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. Expand
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RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, representedExpand
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The bulge region of HIV-1 TAR RNA binds metal ions in solution.
Binding of Mg2+, Ca2+ and Co(NH3)6(3+) ions to the HIV-1 TAR RNA in solution was analysed by 19F NMR spectroscopy, metal ion-induced RNA cleavages and Brownian dynamics (BD) simulations. ChemicallyExpand
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High salt solution structure of a left-handed RNA double helix.
Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure ofExpand
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RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
TLDR
The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. Expand
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Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions.
Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5"Expand
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Z‐RNA: The solution NMR structure of r(CGCGCG)
Left‐handed double‐helical Z‐RNA has been studied using the ribohexanucleotide pentaphosphate r(CpGpCpGpCpG). One‐dimensional proton nmr experiments were used to probe the structural details of theExpand
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The Apical Loop of the HIV-1 TAR RNA Hairpin Is Stabilized by a Cross-loop Base Pair*
The TAR hairpin of the HIV-1 RNA genome is indispensable for trans-activation of the viral promoter and virus replication. The TAR structure has been studied extensively, but most attention has beenExpand
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Automated RNA 3D Structure Prediction with RNAComposer.
TLDR
This chapter provides guidance for using RNAComposer and discusses points that should be considered when predicting 3D RNA structure. Expand
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