Journal of Physical Chemistry B, Vol.104, No.31, 7496-7501, 2000
Spectroscopic characterization of the G*G center dot C triplet in triple helix structures
Intramolecular triple helices have been obtained by twice folding back oligonucleotides formed by decamers bound by nonnucleotide linkers: 5'd(G)(10)-L-d(C)(10)-L-d(G)(10)-3' and S'd(C)(10)-L-d(G)(10)-L-d(G)(10)-3' (L = pO(CH2CH2O)(6)p). We have thus prepared two triple helices with forced third strand orientation, respectively parallel and antiparallel with respect to the guanosine strand of the Watson-Crick duplex. The stability of the parallel tripler is found to be lower than that of the antiparallel, and the sugar conformations determined by infrared spectroscopy are different for both triplexes. Only S-type sugars are found in the antiparallel tripler, whereas both S- and N-type sugars are present in the parallel one. In-plane normal-mode frequencies have been calculated for G*G . C triplet by using a valence force field that incorporates transition dipole coupling for guanine C=O groups in the Hoogsteen triplet structure. This coupling mechanism is shown to give a reasonable explanation of the nu C=O splitting observed for the Hoogsteen G*G . C triplet, unlike the nu C=O spectral profile of the reverse Hoogsteen structure, where this couplings is absent. It is, therefore, now possible to distinguish with confidence between these triplet structures, and their characteristic spectral features can be applied to get structural information of nucleic acid triplexes.