DETERMINATION OF G-ASTERISK-G.C TRIPLE-HELIX STRUCTURE BY MOLECULAR MODELING AND VIBRATIONAL SPECTROSCOPY

A structural study has been performed on dG(n)*dG(n).dC(n) and rG(n)*dG(n).dC(n) triple helices by molecular modeling, Fourier transform infrared spectroscopy, and Raman spectroscopy. Triple-helix geometries have been obtained by molecular mechanics calculations. Stereochemically reasonable structures in agreement with vibrational spectroscopy data and models of third-strand base pairing and third-strand orientation can be proposed from these simulations. Our results show the existence of both S- and N-type sugars and of an anti glycosidic torsion angle conformation. The dC(n) strand has S-type sugars, the dG(n) strand of the Watson-Crick duplex N-type sugars, and the third strand either N-type sugars (rG(n) strand) or S-type sugars (dG(n) strand). The orientation of the third strand is parallel with respect to the homopurine strand involved in Hoogsteen hydrogen bonding.