Divalent counterion-induced condensation of triple-strand DNA

Abstract

Understanding and manipulation of the forces assembling DNA/ RNA helices have broad implications for biology, medicine, and physics. One subject of significance is the attractive force between dsDNA mediated by polycations of valence ≥3. Despite extensive studies, the physical origin of the "like-charge attraction" remains unsettled among competing theories. Here we show that triplestrand DNA (tsDNA), a more highly charged helix than dsDNA, is precipitated by alkaline-earth divalent cations that are unable to condense dsDNA. We further show that our observation is general by examining several cations (Mg 2þ , Ba 2þ , and Ca 2þ ) and two distinct tsDNA constructs. Cation-condensed tsDNA forms ordered hexagonal arrays that redissolve upon adding monovalent salts. Forces between tsDNA helices, measured by osmotic stress, follow the form of hydration forces observed with condensed dsDNA. Probing a well-defined system of point-like cations and tsDNAs with more evenly spaced helical charges, the counterintuitive observation that the more highly charged tsDNA (vs. dsDNA) is condensed by cations of lower valence provides new insights into theories of polyelectrolytes and the biological and pathological roles of tsDNA. Cations and tsDNAs also hold promise as a model system for future studies of DNA-DNA interactions and electrostatic interactions in general.DNA condensation | small angle X-ray diffraction H ighly charged DNA helices naturally repel each other under physiological conditions (1). However, cations of valence ≥3 very effectively condense DNA at micromolar concentrations (2). The most studied systems are the condensation of dsDNA with cobalt 3þ hexammine and the biogenic polyamines (spermidine 3þ and spermine 4þ ), whereas polymer-based cations are being exploited as DNA packaging agents for gene delivery (3). In contrast, nonspecifically interacting monovalent and divalent cations [i.e., excluding base-coordinating transition-metal ions (4) such as Mn 2þ , Ni 2þ , and Cu 2þ ], even at molar concentrations, do not condense dsDNA from dilute solution (2). The prominent role of cation valence has promoted electrostatic interaction as the primary candidate to explain this multivalent cation mediated DNA-DNA attraction (1). Whereas it is clear that further considerations must be made beyond the mean field PoissonBoltzmann (PB) treatment, which always predicts like-charge repulsion, the physical basis for DNA condensation is still under intensive debate (5).The multifaceted nature of DNA-ion interactions and of possible DNA-ion-DNA correlations between apposing helices has led to theories that differ greatly in starting assumptions. For instance, counterions have been treated either as continuous ionic "clouds" or as discrete point-like cations of finite radius; the DNA helix has been modeled as a continuously charged rod or to have discretely charged phosphates placed on a helical path around a smooth rod. As a result, a number of competing theories have been proposed to explain cation mediated DNA-DNA attraction....

Electrostatic interactions in biological DNA-related systems

“…ES forces between these periodic arrays of charges might turn from repulsion to attraction for well-neutralized DNA duplexes. Attractive DNA-DNA forces have been systematically measured in solutions of some di-and many tri-valent cations at E1 nm between DNA surfaces, [46][47][48]55 Fig. 2, while purely repulsive ES forces are detected in solutions of monovalent salts.…”

RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics

“…(2) For a system of loop-tethered short helices, the SAXS experiments suggested a possible weak side-side helix-helix attraction in a Mg 2+ solution of high concentration (*0.6 M) [68]. (3) The experiments showed that the PB theory underestimates the efficiency of Mg 2+ in RNA structural collapse by over 10 times [184]. (4) In trivalent ion solution, short DNA duplexes can become condensed while RNA duplexes keep soluble [185].…”

“…(4) In trivalent ion solution, short DNA duplexes can become condensed while RNA duplexes keep soluble [185]. (5) Mg 2+ cannot condense long DNA duplexes while could condense short DNA triplex in aqueous solution [181,184].…”

Short-Range Disorder and Electrostatic Interactions in Macromolecules

“…A SC analysis seems potentially compatible and could provide some rational basis to the effective parameters of the KL theory [51,8,55,48,56].…”