Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats

Trinucleotide repeats are microsatellite sequences that are polymorphic in length. Their expansion in specific genes underlies a number of neurode-generative disorders. Using ultraviolet-visible, circu-lar dichroism, nuclear magnetic resonance (NMR) spectroscopies and electrospray ionization mass spectrometry, the structural preferences of RNA molecules composed of two and four repeats of AGG, CGG and UGG in the presence of K+, Na+ and NH4+ were analysed. (AGG)2A, (AGG)4A, p(UGG)2U and p(UGG)4U strongly prefer folding into G-quadruplexes, whereas CGG-containing se-quences can adopt different types of structure de-pending on the cation and on the number of re-peats. In particular, the two-repeat CGG sequence folds into a G-quadruplex in potassium buffer. We also found that each G-quadruplex fold is differ-ent: A:(G:G:G:G)A hexads were found for (AGG)2A, whereas mixed G:C:G:C tetrads and U-tetrads were observed in the NMR spectra of G(CGG)2C and p(UGG)2U, respectively. Finally, our NMR study high-lights the influence of the strand sequence on the structure formed, and the influence of the intracellu-lar environment on the folding. Importantly, we high-light that although potassium ions are prevalent in cells, the structures observed in the HeLa cell ex-tract are not always the same as those prevailing in biophysical studies in the presence of K+ ions