Structure and Dynamics of RNA Repeat Expansions That Cause Huntington’s Disease and Myotonic Dystrophy Type 1

Abstract

RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington’s disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson–Crick/Watson–Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson–Crick/Watson–Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.

Design of a small molecule that stimulates vascular endothelial growth factor A enabled by screening RNA fold–small molecule interactions

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“…influences the intramolecular structures that can be adopted by the repeat (e.g. 22), which in turn can influence transcription, translation, and binding to various RNA binding proteins. GC-rich sequences are more prone to adopt highly stable intramolecular folds that bind RNA-binding proteins (eg.…”

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“…To facilitate studying the binding interactions of the RNA motif and AstraZeneca small molecule libraries, we used an approach dubbed AbsorbArray, where the small molecules are absorbed onto agarose-coated microarrays allowing for spatial encoding. 14 The arrays were then probed for binding to radiolabeled RNA motif libraries in the presence of 100-fold excess of unlabeled competitor oligonucleotides that mimic the constant regions in the library (1-5), DNA (6,7), and tRNA (8) (Fig. 1A).…”

“…Previous studies have provided some insight into RNA structural dynamics such as smaller loops are not typically as conformationally dynamic as their larger counterparts and U-rich motifs can have dynamic character. 18,20 We were therefore interested in if the SMIRNAs studied herein had a preference for dynamic or structurally well-defined loops. Fortuitously, a set of structurally related small molecules had overlap in the RNAs that they preferred to bind and those that they discriminated against.…”

“…[3][4] RNA, however, folds into 3dimensional structures that often affect its biology, including causation of disease. [5][6] Thus, SMIRNAs can serve as an alternative approach to target RNA, affording distinct target sites and potential advantages.…”