A repulsive field: advances in the electrostatics of the ion atmosphere

Abstract

The large electrostatic repulsion arising from the negatively charged backbone of RNA molecules presents a large barrier to folding. Solution counterions assist in the folding process by screening this electrostatic repulsion. While early research interpreted the effect of these counterions in terms of an empirical ligand-binding model, theories based on physical models have supplanted them and revised our view of the roles that ions play in folding. Instead of specific ion-binding sites, most ions in solution interact inside an 'ion atmosphere'--a fluctuating cloud of nonspecifically associated ions surrounding any charged molecule. Recent advances in experiments have begun the task of characterizing the ion atmosphere, yielding valuable data that have revealed deficiencies in Poisson-Boltzmann theory, the most widely used theory of the ion atmosphere. The continued development of experiments will help guide the development of improved theories, with the ultimate goal of understanding RNA folding and function and nucleic acid/protein interactions from a quantitative perspective.

Figure 1

This figure depicts “snapshots” of the ion atmosphere around a 24 base pair DNA duplex (net charge: -46e) as Na⁺ is titrated into a fixed 5 mM Mg²⁺ background (with Cl⁻ co-ions). The sizes of the ions have been exaggerated for clarity. Charged objects in solution achieve charge neutrality by attracting cations (Mg²⁺, red; Na⁺, blue) or excluding anions (Cl⁻, pale green). A) At 10 mM Na+, the ion atmosphere is composed almost entirely of excess Mg²⁺ (21 excess Mg²⁺, 2 excess Na⁺, and 2 excluded Cl⁻). B) At 100 M Na⁺, the increasing availability of Na⁺ in the bulk increases its presence in the ion atmosphere (10 Mg²⁺, 19 Na⁺, 7 excluded Cl⁻). C) At 1M Na⁺ swamps out Mg²⁺. Under these conditions, the charge neutralization is due essentially to 30 excess Na⁺ and 16 excluded Cl⁻. (Data adapted from reference [28])

Figure 2

Left: The tethered duplex consists of two 12 base pair DNA duplexes joined by a polyethylene glycol tether and is an analog of the ubiquitous helix-junction-helix motifs found in all structured RNAs. Middle: Under low salt conditions, the large electrostatic repulsion forces the helices into mostly extended conformers. Right: At higher salt concentrations, the electrostatic penalty is screened, allowing a greater range of conformers, including conformers where the helices adopt a side-by-side arrangement.

Figure 3

Structural relaxation of a simple tethered duplex in Na⁺ (A) and Mg²⁺ (B). Fraction relaxed represents the degree of relaxation as measured by SAXS experiments (solid lines) and predicted by PB theory (dashed lines). Reproduced with permission from [42]. Copyright 2008 American Chemical Society.