Abstract
We are interested in the interactions of monovalent cations with duplex DNA as observed by capillary electrophoresis. Here we compare the interactions of Na+ and of tetraalkylammonium+ (TXA+) with a model hairpin oligonucleotide having the sequence GA5C4T5C. As the size of the monovalent cation increases, its association with the coil conformation is enhanced and its association with the hairpin conformation is diminished. These changes can be ascribed to the hydrophobic surface of TXA+, increasingly attracted to the hydrophobic coil conformation and increasingly rejected by the hydrophilic hairpin conformation. Thus TXA+ acts as a denaturant, markedly lowering the melting temperatures of duplex DNA.
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