Reversible Metal-Dependent Destabilization and Stabilization of a Stem-Chelate-Loop Probe Binding to an Unmodified DNA Target

Herein, we report the discovery of a novel DNA probe with a stem-chelate-loop structure, wherein the stability of the probe target duplex can be modulated lower or higher using a narrow concentration range of dilute transition metal ions (0.1-10 mu M). Oligonucleotide probes containing two terpyridine (TPY) ligands separated by 15 bases of single-stranded DNA, with or without a flanking 5 base self-complementary DNA stem, were tested in thermal transition studies with linear target DNA and varying amounts of ZnCl2. Without the stem, addition of Zn2+ resulted only in reversible destabilization of the probe target duplex, consistent with assembly (up to 1 equiv Zn2+) and disassembly (excess Zn2+) of the intramolecular Zn2+-(TPY)(2) chelate. Surprisingly, probes including both the intramolecular chelate and the stem gave a probe-target duplex that was reversibly destabilized and stabilized upon addition of Zn2+ by +/- 5-7 degrees C, a phenomenon consistent with assembly and then disassembly of the entire stem-Zn2+-(TPY)(2) motif, including the DNA stem. Stem-chelate-loop probes containing dipicolylamine (DPA) ligands exhibited no metal-dependent stabilization or destabilization. The stem-Zn2+-(TPY)(2) motif is readily introduced with automated synthesis, and may have broad utility in applications where it is desirable to have both upward and downward, reversible metal-dependent control over probe-target stability involving an unmodified DNA target.