The stabilities of oligodeoxyribonucleotide triplexes containing a single pyrimidine-purine base pair, which interrupts an otherwise purine-pyrimidine base pair motif, were studied by UV melting experiments. The oligomer systems consisted of an oligodeoxyribonucleotide target duplex d-GAAGAAAAAAYAAAA/d-TTTTZTTTTTTCTTC, I•II(Y-Z), or d-GAAG AAAAAGUGAAA/d-TTTCACTTTTTCTTC, IV•V(U•A), where Y•Z is C•G, T•A, or U•A and U is deoxyuridine. The third strand oligodeoxyribopyrimidine was d-CTTCTTTTTTXTTTT, III(X), or d-CTTCTTTTTCXCTTT, VI(X), where C is 5-methyldeoxycytidine. Triplexes were observed in the system III•I•II(X-C-G) when X was T or U. This may involve formation of T• or U•C•G triads in which the 4-carbonyl of T or U serves as a hydrogen bond acceptor for the N4-amino group of C. Triplex formation between III(X) and I•II(T•A) was only observed when X was G. In contrast to T•A or C•G, it appears a U•A base pair in the duplex target is a much more versatile participant in triad formation. Thus, stable triplexes were observed in III•I•II(X•U•A) and in VI•IV•V(X•U•A) when X was C, C, T, or U. The formation of a T•U•A or U•U•A triad can occur if the T or U of III translates approximately 1.4 A into the major groove, thereby allowing the 3-NH of T or U to donate a hydrogen bond to the 4-carbonyl oxygen of U in the duplex. Formation of C• or C•U•A base triads could involve formation of a single hydrogen bond between the third strand N4-amino group of C or C and the 4-carbonyl group of U of the target. Alternatively, a hydrogen bonding scheme similar to that proposed for the T• or U•U•A triads can be drawn in which protonation of C or C at N-3 could provide a hydrogen bond to the 4-carbonyl of U of the duplex. The latter hydrogen bonding scheme is supported by the observed greater reduction in stability with increasing pH of the III•I•II(C• or C•U•A) triplexes compared to that of the III•I•II(T•U•A) triplex. The observations that III•I•II(G•U•A) does not form a stable triplex suggests that factors in addition to the availability of a 4-carbonyl hydrogen bond acceptor group influence the formation of G•T•A versus G•U•A triads.
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