Attractive Forces between Cation Condensed DNA Double Helices

Abstract

By combining single-molecule magnetic tweezers and osmotic stress on DNA assemblies, we separate attractive and repulsive components of the total intermolecular interaction between multivalent cation condensed DNA. Based on measurements of several different cations, we identify two invariant properties of multivalent cation-mediated DNA interactions: repulsive forces decay exponentially with a 2.3 +/- 0.1 A characteristic decay length and the attractive component of the free energy is always 2.3 +/- 0.2 times larger than the repulsive component of the free energy at force-balance equilibrium. These empirical constraints are not consistent with current theories that attribute DNA-DNA attractions to a correlated lattice of counterions. The empirical constraints are consistent with theories for Debye-Hückel interactions between helical line charges and with the order-parameter formalism for hydration forces. Each of these theories posits exponentially decaying attractions and, if we assume this form, our measurements indicate a cation-independent, 4.8 +/- 0.5 A characteristic decay length for intermolecular attractions between condensed DNA molecules.

Molecular Dynamics Simulation of High Density DNA Arrays

“…In the opposite regime of high DNA densities, the osmotic pressure difference between two different ion types is substantial for both lattices, while the presence of multivalent Spd 3+ results in pronounced lowering of the osmotic pressure. At small DNA separations, our quantitative results compare quite well with the experimentally observed values at 2 mM Spd 3+ [23] for the hex lattice. At larger separations, however, the pressure obtained with simulations while small, is usually overestimated and attributable to the small size of the simulated array as well as to the possible inaccuracies in the force field.…”

“…In the two most recent simulations, the parametrizations were chosen such as to be close to experimental conditions in the osmotic stress experiments [4,23], with either 250 mM or 1 M pure NaCl [73], or with 200/50 mM NaCl-MgCl 2 ionic mixture [51], leading in both cases to the pronounced screening of the electrostatic interactions. On the other hand, the strongly coupled ions were simulated either as a combination of 1 M NaCl and spermidine Spd 3+ , where 6 Spd 3+ molecules are used per each DNA molecule [73] or sub-mM concentration of Sm 4+ and 200 mM NaCl [51].…”

“…The detailed sequence of mesophase ordering on increase of the DNA density has been identified as consisting of isotropic (I) → cholesteric (Ch) → line hexatic (LH) (or hexagonal columnar H) → orthorhombic (OR) phase [3,11,[15][16][17][18], with many details, including the complete DNA length dependence and the demarcation between the line hexatic and hexagonal order, still remaining to be systematically investigated [19]. For multivalent counterions at concentrations above a critical value depending on their identity [20], the EoS exhibits pronounced van der Waals-like density discontinuities that are in general larger then in the case of monovalent salt solutions, signalling a buildup of attractive interactions [21,22], whose details can be inferred from complementary experiments [23], that eventually lead to DNA condensation [24].…”

Divalent counterion-induced condensation of triple-strand DNA

“…Force measurements on dsDNA condensed by a variety of multivalent ions have extensively characterized the attractive and repulsive forces underlying DNA assembly (31). The attraction force varies exponentially with interhelical distance with an approximate 5-Å decay length (35). This force is due to the direct interaction of surfaces through either electrostatic or hydration forces.…”

Quantifying Coulombic and Solvent Polarization-Mediated Forces Between DNA Helices

“…16,25 Furthermore, the theory, which puts many-ion correlation and fluctuation, solvent polarization, and atomistic nucleic acid structures in a consistent framework, has the potential to be extended to treat more complex systems.…”