An RNA hairpin to G-quadruplex conformational transition

Abstract

RNA molecules can fold into noncanonical structures such as the four-stranded structures known as G-quadruplexes. G-quadruplexes in the transcriptome have recently emerged as relevant regulatory elements of gene expression. Conformational transitions in RNA molecules offer an important way to regulate their biological functions. Here we report on the competition between a canonical hairpin structure and a G-quadruplex structure within an RNA molecule. We show that the conformational preference strongly depends on the relative amounts of mono- and divalent metal ions present in solution. In our system, the G-quadruplex, whose formation is not predicted by available predictive RNA folding programs, is the major conformer at physiologically relevant K(+) and Mg(2+) concentrations. Furthermore, we show that a synthetic small molecule can displace the structural dynamic equilibrium in favor of the hairpin conformer. This work highlights a new and important level of complexity in RNA folding that could be relevant to the biological functions and targeting of RNAs comprising G-quadruplex motifs.

Figure 1

A bistable RNA conformational switch (HpQd) under cation-mediated control.

Figure 2

Influence of the K⁺ and Mg²⁺ concentrations on the thermal stabilities of the hairpin (Hp′) and G-quadruplex (Qd′) RNA structures. Denaturation studies were performed in 10 mM sodium cacodylate (pH 7.0) supplemented with (a) increasing amounts of KCl (K⁺ dependence) and (b) 1 mM KCl and increasing amounts of MgCl₂ (Mg²⁺ dependence).

Figure 3

¹H NMR titrations of the HpQd sequence with increasing amounts of (a) KCl and (b) MgCl₂. The initial spectra were acquired in 10 mM PBS (pH 7.0) in the absence of added KCl or MgCl₂. Signals labeled with red stars and blue circles correspond to the Qd and Hp structures, respectively.

Figure 4

¹H NMR titrations of the HpQd sequence with increasing amounts of (a) MgCl₂ and (b) KCl. The initial spectra were acquired in 10 mM PBS (pH 7.0) in the presence of (a) 100 mM KCl and no MgCl₂ and (b) 3 mM MgCl₂ and no KCl. Signals labeled with red stars and blue circles correspond to the Qd and Hp structures, respectively.

Figure 5

¹H NMR titration of the HpQd sequence with increasing amounts of 1. The initial spectrum was recorded in 10 mM PBS (pH 7.0) containing 10 mM KCl and 200 μM MgCl₂.