Abstract
A DNA triplex is formed through a third strand binding to the major groove of a duplex through hydrogen bonds. Due to the high charge density of a DNA triplex, metal ions are critical for triplex stability. We recently developed the tightly bound ion (TBI) model for ion-nucleic acids interactions. The model accounts for correlation and fluctuations of the ion distribution. We now apply the TBI model to analyze the ion-dependence of thermodynamic stability for DNA triplexes. We investigate the ion-dependent stability for two experimentally studied systems: a 24-bp DNA triplex and a 15-bp triplex with the third strand containing different base sequence. Because a triplex has a higher charge density than a duplex, a triplex attracts more ions and hence causes stronger ion correlation than a duplex. Our results for the number of bound ions indicate that for a DNA triplex in a Mg2+ solution, the TBI model, which accounts for ion correlation, gives much improved predictions than Poisson-Boltzmann Equation (PB), which ignores ion correlation, and the improvement is more significant for a triplex than for a duplex. In addition, we also calculate the stability of a pair of 14-mer triple helices immersed in an ionic solution. The goal is to predict the ion-dependent free energy landscape for different sequences and helix lengths.
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