Structure and Stability of Sodium and Potassium Complexes of dT₄G₄ and dT₄G₄T

The ends of eukaryotic chromosomes contain specialized structures that include DNA with multiple tandem repeats of simple sequences containing clusters of G on one strand, together with proteins which synthesize and bind to these sequences. The unit repeat in the protozoan Oxytricha with the cluster dT₄G₄can form structures containing tetrads of guanine residues, referred to G₄DNA, in the presence of metal ions such as Na⁺or K⁺. We show here that, in the presence of Na⁺, dT₄G₄forms a tetramer with parallel strands by means of a UV cross-linking assay. In the presence of K⁺, two further interactions are observed: at low temperature, higher order complexes are formed, provided the 3ʹ end of the strand is G; a single 3ʹT inhibits this association in dT₄G₄T. At high temperature, these complexes dissociate, leading to a tetramer with a different ordered structure that melts only at very high temperatures. These results suggest that the cohesive properties of DNA containing G clusters might depend on associative interactions driven by a free 3ʹG terminus in the presence of K⁺, as well as by connecting antiparallel G hairpins as has been postulated.