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 s tudy of the tripler formed by dTdA-dT base triplets in which the thir d strand is oriented parallel to the dA strand. We now describe an int ramolecular triple helix with dTdA-dT base triplets in which the pyri midine third strand is oriented antiparallel, formed by folding back t wice the tridecamer dT(10)-linker-dA(10)-linker-dT(10) (linker = pO(CH 2CH2O)3p). Third-strand base pairing to the target strand, sugar confo rmation, 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 antiparalle l with respect to the target strand, the third-strand hydrogen-bonding scheme is changed from Hoogsteen to reverse Hoogsteen. The sugar conf ormation 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 mode ls 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].