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This study employs simulations based on the Three Interaction Site (TIS) model to investigate the persistence length (lp) of short single-stranded DNA (ssDNA) homopolymers in the presence of polyvalent cations, specifically Mg2+ and Ca2+. The findings reveal that lp for dT30 and dA30 is quantitatively described by a model involving the bare persistence length, a dimensionless constant, and the inverse Debye length, with values of 0.4 nm and 1.1 nm, respectively. Notably, the persistence length shows minimal dependence on tetravalent spermine concentration, challenging existing theoretical frameworks and suggesting a saturation effect in binding dynamics that warrants further experimental validation.
The surprising independence of ssDNA persistence length from tetravalent spermine concentration challenges established theories in polyelectrolyte behavior.
We used simulations of short single stranded DNA (ssDNA) homopolymers, based on the sequence dependent Three Interaction Site (TIS) model, to calculate the persistence length (lp) in polyvalent cations. The TIS model accounts for stacking interactions and electrostatic interactions are treated using the Coulomb potential. We find that lp for dT30 (T is thymine) and dA30 (A is adenine) is quantitatively fit using ( is the bare persistence length, λ is a dimensionless constant, and κ−1 is the inverse Debye length) in the divalent cations Mg2+ and Ca2+. The dependence of lp on κ is surprising because it was derived for long flexible polyelectrolytes in which the charges interact via the Debye-Hückel potential. The values are 0.4 nm and 1.1 nm for polyT and polyA, respectively. Strikingly, lp is almost independent of the tetravalent spermine concentration. There is no clear theoretical explanation although simulations suggest that the number of spermine molecules that bind to the ssDNA saturates at a small value. A qualitative picture, based on the restrictions of access to the phosphate groups due to volume exclusion of the anisotropic structure of Spm4+, rationalizes the simulation results. The predicted dependence of lp in spermine awaits experimental test.
