Triple helix formation by alpha-oligodeoxynucleotides: a vibrational spectroscopy and molecular modeling study

Abstract

The structures of triple helices alpha dT6.beta dAn.beta dTn, alpha dT12.beta dAn.beta dTn, alpha dC12+.beta dGn.beta dCn, and alpha dC12+.beta rGn.beta rCn have been studied by Fourier transform infrared spectroscopy, Raman spectroscopy, and molecular mechanics calculations. The sugar conformations in these triplexes have been determined by vibrational spectroscopy. Our results show the existence of only S-type sugars in the alpha dT12.beta dAn.beta dTn triple helix. Both S- and N-type sugar infrared and Raman markers have been detected in the spectra of alpha dC12+.beta dGn.beta dCn. Molecular mechanics refinements taking into account vibrational spectroscopy data constraints allow us to propose third strand hydrogen-bonding schemes and third strand polarities in triple helix models. For alpha dT12.beta dA12.beta dT12 the third strand forms reverse Hoogsteen hydrogen bonds with the beta dA12 strand and therefore is parallel to the purine strand. In contrast, for alpha dC12+.beta dG12.beta dC12 calculations show that only a model in which the third strand is Hoogsteen base paired and antiparallel to the purine strand of the Watson-Crick duplex is compatible with spectroscopic data.