Charge and Size Dependent Effects of Cations on Triplex DNA Stabilization

Triplex DNA stabilization is affected by the microenvironment, including the presence of monovalent and divalent cations. We used melting temperature (Tm) measurements and circular dichroism spectroscopy to assess the stability and conformation of poly(dA)·2poly(dT). Monovalent cations (Li+, Na+, K+, Rb+, Cs+ and NH4+) promoted triplex DNA at concentrations ≥ 150 mM. The triplex DNA melting temperature varied from 49.8°C in the presence of 150 mM Li+ to 30.6°C in the presence of 150 mM K+. Among ammonium compounds, NH4+ was the most effective ion in stabilizing triplex DNA and its efficacy decreased with increasing substitution of the hydrogen atoms with bulky alkyl groups. Divalent cations were ∼1000-fold more efficacious than monovalent ions in stabilizing triplex DNA. Circular dichroism spectroscopic studies showed distinct conformational changes in triplex DNA stabilized by alkali metal and ammonium ions. These data demonstrate charge- and size-dependent effects of cations on triplex DNA stability.