TRIPLE-HELIX FORMATION BY ALPHA-OLIGODEOXYNUCLEOTIDES - A VIBRATIONAL SPECTROSCOPY AND MOLECULAR MODELING STUDY

The structures of triple helices alphadT6.betadA(n).betadT(n), alphadT12.betadA(n).betadT(n), alphadC-12+.betadG(n)betadC(n), and alphadC-12+.betarG(n).betarC(n) 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 alphadT12.betadA(n).betadT(n) triple helix. Both S- and N-type sugar infrared and Raman markers have been detected in the spectra of alphadC-12+.betadG(n).betadC(n). 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 alphadT12.betadA12.betadT12 the third strand forms reverse Hoogsteen hydrogen bonds with the betadA12 strand and therefore is parallel to the purine strand. In contrast, for alphadC-12+.betadG12.betadC-12 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.