FTIR STUDY OF A NONCLASSICAL DT(10)ASTERISK-DA(10)-DT(10) INTRAMOLECULAR TRIPLE-HELIX

Many early investigations on triple helices have been devoted to the study of the tripler formed by dT*dA-dT base triplets in which the third strand is oriented parallel to the dA strand. We now describe an intramolecular triple helix with dT*dA-dT base triplets in which the pyrimidine third strand is oriented antiparallel, formed by folding back twice the tridecamer dT(10)-linker-dA(10)-linker-dT(10) (linker = pO(CH2CH2O)3p). Third-strand base pairing to the target strand, sugar conformation, and thermal denaturation of the tripler have been studied by Fourier transform infrared spectroscopy. Our results confirm that when the third-strand orientation is reversed from parallel to antiparallel with respect to the target strand, the third-strand hydrogen-bonding scheme is changed from Hoogsteen to reverse Hoogsteen. The sugar conformation in this triple helix is of the S type (C2'endo/anti, B family form) for all strands. Our results are discussed with respect to models for triplexes proposed as intermediates in homologous recombination [Zhurkin, V. B., Raghunathan, G., Ulyanov, N. B., Camerini-Otero, R. D., & Jernigan, R. L. (1994) J. Mol. Biol. 239, 181-200].