Compact intermediates in RNA folding

Abstract

Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

Figure 1.. Folding of hairpin ribozyme.

Internal loops A and B dock in the native state (72). Rapid fluctuations of the four-way junction (4WJ) produces a compact intermediate; conformational changes in loops A and B lead to the native docked state. Docking is slower when the 4WJ is replaced by a two helix junction (2WJ). Adapted from (65, 88, 110).

Figure 2.. Tertiary interactions increase the cooperativity of helix assembly.

A loop mutation (GAAA to GUAA) in the Azoarcus ribozyme (1) makes pairing of core helices less concerted, as revealed by partial digestion with ribonuclease T1 (WT, black lines; mutant, red lines). As helix assembly becomes less specific, the fraction of slow folding RNA folding rises. Adapted from (17).

Figure 3.. Specificity of collapse from equilibrium SAXS.

The Azoarcus ribozyme collapses to native-like intermediates (I_C) while the Tetrahymena ribozyme collapses to an ensemble of non-native intermediates (I’s) (16, 23, 74). In both RNAs, specific transitions to a native-like fold are sensitive to counterion charge density. Redrawn from (53).