Electrostatic Effects in DNA Triple Helices

Electrostatic effects dominate many aspects of nucleic acid behavior in a sequence independent manner. Sequence dependent electrostatic effects are introduced when a polypyrimidine, which contains one or more protonated cytosines, binds in the major groove (Hoogsteen side) of a complementary Watson-Crick double helix. Depending on the number of cytosines in the third strand (global effect) and on their relative position (local effect), the cytosines either enhance or decrease the binding affinity of the third strand, because adjacent protonated cytosines destabilize the third strand binding compared to cytosines separated by intervening thymines. This local effect (crowding) can reverse the effect of global composition. To investigate the extent of the local and global electrostatic effects further, two families of oligonucleotides have been synthesized. They share as a common design feature that they all fold sequentially into isosterical intramolecular triple helices by way of hairpin intermediates. This is confirmed by P₁ nuclease probing, CD spectroscopy, and UV spectroscopy. The thermal stability of these conformations depends on the sequences, pH, and the ionic strength and can be summarized as follows: The energy of third strand binding depends on the protonated cytosine content in the Hoogsteen strand. It increases with increasing cytosine content (global composition) below pH 7.1 (150 mM Na⁺), decreases above pH 7.1, and is independent of the cytosine content at pH 7.1. At pH 6.75 the energy of binding increases with increasing cytosine content below 400 mM Na⁺, decreases above 400 mM Na⁺, and is independent of the global composition at 400 mM Na⁺.