Frayed Wires: A Thermally Stable Form of DNA with Two Distinct Structural Domains

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Abstract
In aqueous solutions containing mono- and divalent cations, the oligodeoxyribonucleotide d(A15G15) readily self-assembles into high-molecular weight species that resolve as discrete bands on native and denaturing electrophoresis gels. The complexes consist of an integer number of strands of d(A15G15), the number of strands range from one (the monomer) to greater than nine. The complexes form within a few minutes even at low concentrations (2 μM strands) of d(A15G15). The relative concentration of species is determined by the solvent conditions. The complexes are resistant to standard denaturation conditions, 50% formamide heated to 95 °C for 2 min followed by electrophoresis in 7 M urea at 55 °C. In the proposed model for the oligomers and polymers of d(A15G15), several molecules of d(A15G15) interact via a stem of tetraplex structure formed by the guanine residues. The 15 guanine residues in the stem account for its high stability. The 5‘ end adenines form single-stranded arms that are displaced from the guanine-containing stem. The arms can participate in the formation of Watson−Crick base pairs with dT10 and other partially complementary oligodeoxyribonucleotides such as d(CT15). Engagement of the arms in interactions with other strands does not affect the distribution of the species between different conformations. On the other hand, the addition of the fully complementary oligodeoxyribonucleotide d(C15T15) to the polymer leads to the disappearance of the high-molecular weight complexes and results in the formation of a canonical Watson−Crick base-paired duplex. The type and concentration of the cation present in solution determine which conformation d(A15G15) will adopt. Divalent cations at millimolar concentrations lead to the formation of the polymer, while the presence of the monovalent cations stabilizes lower-molecular weight complexes consisting of two to six strands of d(A15G15).