Metal Ion Dependence of Cooperative Collapse Transitions in RNA

Abstract

Positively charged counterions drive RNA molecules into compact configurations that lead to their biologically active structures. To understand how the valence and size of the cations influences the collapse transition in RNA, small angle X-ray scattering was used to follow the decrease in the radius of gyration (Rg) of the Azoarcus and Tetrahymena ribozymes in different cations. Small, multivalent cations induced the collapse of both ribozymes more efficiently than monovalent ions. Thus, the cooperativity of the collapse transition depends on the counterion charge density. Singular value decomposition of the scattering curves showed that folding of the smaller and more thermostable Azoarcus ribozyme is well described by two components, whereas collapse of the larger Tetrahymena ribozyme involves at least one intermediate. The ion-dependent persistence length, extracted from the distance distribution of the scattering vectors, shows that the Azoarcus ribozyme is less flexible at the midpoint of transition in low charge density ions than in high charge density ions. We conclude that the formation of sequence-specific tertiary interactions in the Azoarcus ribozyme overlaps with neutralization of the phosphate charge, while tertiary folding of the Tetrahymena ribozyme requires additional counterions. Thus, the stability of the RNA structure determines its sensitivity to the valence and size of the counterions.

Increased Ribozyme Activity in Crowded Solutions

“…When the burst amplitudes were fit to a three-state model that empirically describes the ribozyme folding transitions in Mg 2ϩ (20,26), we observed a steep transition from inactivity to activity at ϳ1 mM MgCl 2 (Fig. 3a).…”

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

“…Tertiary folding of complex RNAs begins with rapid electrostatic collapse, followed by search for the native state (Thirumalai et al 2001;Russell et al 2002;Moghaddam et al 2009). This occurs on a rough landscape (Woodson 2010;Takamoto et al 2012) wherein misfolds are broken prior to native folding (Thirumalai et al 2001).…”

Methods to Detect and Characterize Metal Ion Binding Sites in RNA

“…Often in combination with other techniques, a rather accurate picture of shape, flexibility and conformational changes dependent on cofactors can be obtained [138][139][140][141]. For example, SAXS has been used to investigate complete solution structures of the VS ribozyme in solution [142], to look at riboswitch conformations [143], to characterize conformational states of ribozymes [144], to follow folding in a time-resolved manner [145], or to investigate the effect of metal ions on the order of transition states of two group I intron ribozymes [146]. Woodson and Thirumalai could show that the Azoarcus group I intron folding is described by two components, whereas the Tetrahymena folding has at least one intermediate [146] (see also Chapter 7).…”