Competition between the purine and pyrimidine triple helix motifs in an oligonucleotide system

Bibliography: p. 86-109.Triple helices are classified into two groups according to the composition and orientation of the third strand, namely the pyrimidine motif and the purine motif. These motifs constitute two separate fields of research. It was proposed, based on the alternative design rules, that the two motifs can in fact lead to competing structures. An oligonucleotide system has been designed to demonstrate this competition. Systematic variation of its components give insight into the requirements for optimal binding of a third strand. A palindromic, homopyrimidine oligonucleotide of 22 bases was designed to form an overlapping 9-base, Watson-Crick (WC), duplex with a partly complementary 22-base purine-rich oligonucleotide. This leaves two free 3' extensions under conditions when only the duplex is stable. If the conditions, however, favour triplex formation the pyrimidine tail can compete with the purine-rich tail as third strand for the duplex forming Hoogsteen or reverse-Hoogsteen hydrogen bonding respectively with the purines in the WC double strand. The underlying triplexes and core duplex were synthesised and characterised as controls

Protonated pyrimidine-purine-purine triplex.

We have studied a protonated pyrimidine-purine-purine (Py-Pu-Pu) triplex, which is formed between the d(C)nd(G)n duplex and the d(AG)m oligonucleotide as the third strand and carries the CG*A+ protonated base-triads. We have observed such an intermolecular complex between a plasmid carrying the d(C)18 d(G)18 insert and the d(AG)5 oligonucleotide without bivalent cations in 200 mM of Na+ at pH4.0. Bivalent cations additionally stabilize the complex. We propose the structures for nearly isomorphous base-triads TA*A, CG*G and CG*A+. To identify the H-DNA-like structure, which includes the triplex between d(C)n d(G)n duplex and the AG-strand, we have cloned in a superhelical plasmid the insert: G10TTAA(AG)5. The data on photofootprinting and chemical modification with diethyl pyrocarbonate, potassium permanganate and dimethyl sulfate demonstrate that the H-like structure with triplex carrying CG*G and CG*A+ base triads is actually formed under acid conditions. In the course of this study we have come across unexpected results on probing of Py-Pu-Pu triplexes by dimethyl sulfate (DMS): the protection effect is observed not only for guanines entering the duplex but also for guanines in the third strand lying in the major groove. We have demonstrated this effect not only for the case the novel protonated Py-Pu-Pu triplex but also for the traditional non-protonated Py-Pu-Pu intramolecular triplex (H*-DNA) formed by the d(C)37 d(G)37 insert in supercoiled plasmid in the presence of Mg2+ ions