Interchain base-stacking and spermine bridges govern ssDNA condensation and reentrant transitions

Double-stranded DNA condensation and reentrant transitions are traditionally explained by backbone electrostatics. However, the role of these principles in single-stranded DNA, whose solvent-exposed bases can interact within and between chains to form complex phases, remains unclear. To address this, researchers employed both simulations and experiments to explore the mechanisms at play.

Their findings revealed that the tetravalent cation spermine (Spm4+) triggers two equilibrium transitions in poly(dT) and poly(dA). The commencement of phase separation, leading to a thermodynamic equilibrium between the dispersed low-density phase and high-density coacervate, happens at a low sequence-independent concentration of Spm4+. This transition is primarily driven by the charge balance between phosphate groups and Spm4+.

Interestingly, the condensed phases are stabilized by a maximum of 1.5 bridging Spm4+ molecules per chain in poly(dT) and 2.5 in poly(dA). Despite this minimal bridging, the ssDNA chains condense to form fluid-like networks without collapsing. The fluidity of these chains in the dense phases is corroborated by fluorescence recovery after photobleaching experiments.

Both simulations and experiments confirmed that the range of spermine concentration over which phase coexistence persists is sequence-dependent. Notably, this range is nearly three times wider in poly(dA) compared to poly(dT). At higher spermine concentrations within the sequence-dependent range, a reentrant phase emerges, characterized by the dissolution of the coacervates. This transition occurs when the number of bridging Spm4+ molecules vanishes at high spermine concentrations.

The integrated results from experiments and simulations demonstrate that the two phase transitions in ssDNA are governed by the interplay of stacking and electrostatic interactions.