Parallel and antiparallel A*A-T intramolecular triple helices

Intramolecular triple helices have been obtained by folding back twice oligonucleotides formed by decamers bound by non-nucleotide linkers: dA(10)-linkers-dA(10)-linker-dT(10) and dA(10)-linker-dT(10)-linker-dA(10). We have thus prepared two triple helices with forced third strand orientation, respectively antiparallel (apA*A-T) and parallel (pA*A-T) with respect to the adenosine strand of the Watson-Crick duplex, The existence of the triple helices has been shown by FTIR, UV and fluorescence spectroscopies, Similar melting temperatures have been obtained in very different oligomer concentration conditions (micromolar solutions for thermal denaturation classically followed by UV spectroscopy, milimolar solutions in the case of melting monitored by FTIR spectroscopy) showing that the triple helices are intramolecular, The stability of the parallel tripler is found to be slightly lower than that of the antiparallel (Delta T-m = 6 degrees C). The sugar conformations determined by FTIR are different for bath triplexes, Only South-type sugars are found in the antiparallel tripler whereas both South- and North-type sugars are detected in the parallel tripler, In this case, thymidine sugars have a South-type geometry, and the adenosine strand of the Watson-Crick duplex has North-type sugars, For the antiparallel tripler the experimental results and molecular modeling data are consistent with a reverse-Hoogsteen like third-strand base pairing and South-type sugar conformation, An energetically optimized model of the parallel A*A-T triple helix with a non-uniform distribution of sugar conformations is discussed.