Utilizing the GAAA Tetraloop/Receptor To Facilitate Crystal Packing and Determination of the Structure of a CUG RNA Helix

Coonrod, Leslie A.; Lohman, Jeremy R.; Berglund, J. Andrew

doi:10.1021/bi300829w

Cited by 36 publications

(49 citation statements)

References 44 publications

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“…The modifications were targeted to the uridines because these were proposed as dynamic mismatches (23). (CUG) 4 was synthesized with one, two and four Ψs in place of uridines (Figure 1B).…”

Section: Resultsmentioning

confidence: 99%

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

deLorimier

Coonrod

Copperman

et al. 2014

Nucleic Acids Research

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CUG repeat expansions in the 3′ UTR of dystrophia myotonica protein kinase (DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2′-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2′-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecular dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.

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Section: Resultsmentioning

confidence: 99%

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

deLorimier

Coonrod

Copperman

et al. 2014

Nucleic Acids Research

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“…The most recent report regarding the CUG series presents the crystal structure of an RNA construct containing a tandem GAAA tetraloop and its receptor that form the tip and the upper part of a hairpin, respectively, while the lower part of the stem is a double-helical segment of two CUG repeats (Figure 1F, PDB code 4fnj) (69). The combination of the tetraloop with the receptor facilitated crystallisation, which enabled the examination of yet another instance of two consecutive CUG repeats.…”

Section: X-ray Crystallographic Studiesmentioning

confidence: 99%

Structural studies of CNG repeats

Kiliszek

Rypniewski

2014

Nucleic Acids Res

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CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date.

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“…The model consists of three CCUG repeats attached to an RNA motif containing a tetraloop and a tetraloop receptor. Elements of the tetraloop system associate in solution, facilitating crystallization (Coonrod et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Watson–Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation

Rypniewski

Banaszak

Kuliński

et al. 2015

RNA

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RNA transcripts that include expanded CCUG repeats are associated with myotonic dystrophy type 2. Crystal structures of two CCUG-containing oligomers show that the RNA strands associate into slipped duplexes that contain noncanonical C-U pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual Watson-Crick-like pairing. The overhanging ends of the duplexes interact forming U-U pairs, which also show tautomerism. Duplexes consisting of CCUG repeats are thermodynamically less stable than the trinucleotide repeats involved in the TRED genetic disorders, but introducing LNA residues increases their stability and raises the melting temperature of the studied oligomers by ∼10°C, allowing detailed crystallographic studies. Quantum mechanical calculations were performed to test the possibility of the tautomeric transitions or protonation within the noncanonical pairs. The results indicate that tautomeric or ionic shifts of nucleobases can manifest themselves in biological systems, supplementing the canonical "rules of engagement."

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Utilizing the GAAA Tetraloop/Receptor To Facilitate Crystal Packing and Determination of the Structure of a CUG RNA Helix

Cited by 36 publications

References 44 publications

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

Structural studies of CNG repeats

Watson–Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation

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