Ligand-induced formation of nucleic acid triple helices

Abstract

We demonstrate that ligand binding can be used to induce the formation of triplex structures that would not otherwise form. Specifically, we show that binding of berenil or 4',6-diamidino-2-phenylindole (DAPI) induces formation of the poly(rA)·poly(rA)·poly(dT) triplex, providing an example of an RNA(purine)·RNA(purine)·DNA(pyrimidine) triplex. We also show that binding of berenil, DAPI, ethidium, or netropsin can induce formation of the poly(dT)·poly(rA)·poly(dT) triplex, thereby overcoming a practical limitation to the formation of DNA·RNA·DNA triplexes with a purine RNA strand. Based on the enhanced thermal stabilities of the drug-bound poly(dT)·poly(rA)·poly(dT) complexes at 18 mM Na+, we define the relative triplex-inducing efficiencies of these four ligands to be: berenil > DAPI > ethidium > netropsin. Our results demonstrate that ligand binding can be used to induce the formation of triplex structures that do not form in the absence of the ligand. This triplex-inducing capacity has potentially important implications in the design of novel antisense, antigene, and diagnostic strategies.