Central non-Pur·Pyr sequences in oligo(dG·dC) tracts and metal ions influence the formation of intramolecular DNA triplex isomers

The effect of the central non-Pur·Pyr sequences in oligo(dG·dC) inserts on determining the type of intramolecular DNA triplex isomers formed in negatively supercoiled plasmids was investigated. Different triplex types (H- r3, H-r5, and H-y3), revealed by a combination of chemical probing and Maxam- Gilbert sequencing reactions, were adopted by the oligo(dG·dC) tracts depending on the length and composition of the central non-Pur·Pyr sequences (0, 3, or 5 base pairs) and the kind of metal ions. The H-r3 triplex conformer, one isomer of a Pur·Pur·Pyr structure, was formed in the (C)₂₀ and (C)₁₀GCG(C)₁₀ inserts in plasmids in the presence of certain metal ions. Interestingly, H-r5, the other isomer of the Pur·Pur·Pyr triplex which had not been detected previously, was formed in a (C)₉GAATT(C)₉ insert in the presence of either Mg²⁺ or Ca²⁺. Alternatively, H-y3, one isomer of a Pyr·Pur·Pyr triplex, was formed in the (C)₉GAATT(C)₉ insert in the absence of metal ions. Thus, central non-Pur·Pyr sequences and metal ions play a role as determinants of the types of intramolecular triplexes formed; they also reduce the requirement of longer Pur·Pyr repeat sequences to form intramolecular triplexes. Furthermore, the effects of MgCl₂ concentration and pH on the formation of triplex isomers were examined. The Pur·Pur·Pyr conformations (H-r3 and H-r5) may be the favored conformations in the cellular milieu, since they are stable at physiological pH and metal ion concentration.