Extended Data Figure 5. Effect of breaking the ‘linchpin’ interaction.
a, Small angle X-ray scattering (SAXS) analysis of TYMV TLS RNAs, adapted from Hammond et al. (2010)5. Left: ab initio SAXS reconstruction of the shape of the TLS when the 5′ sequence that interacts with the pseudoknot (Fig. 2) is present. The RNA overall forms an L-shape, illustrated by the black bars (stabilizing long-range interaction in grey). When these 5′ nucleotides are removed (right), the L-shape is lost and the RNA becomes more extended. b, Hydroxyl radical probing of several TYMV TLS RNAs that indicate the effect of disrupting the long-range interaction, adapted from Hammond et al. (2009 & 2010)5,11. Green and red indicate protection from cleavage by radicals and enhanced cleavage by radicals, respectively. Overall, the presence of green and red indicate tightly folded RNA. When the 5′ nucleotides that form the long-range interaction are present, the RNA stably folds (TYMV UUAG, left). Removal of the 5′ nucleotides destabilizes the fold (TYMV 0G, right). The presence of just G4 on the 5′ end partially stabilizes the RNA fold (TYMV 1G, middle), confirming its importance in folding and also indicating that nucleotides adjacent to G4 further stabilize the fold.