Characterization of parallel and antiparallel G-tetraplex structures by vibrational spectroscopy

Abstract

A series of G-rich oligonucleotides able to form tetraplexes has been studied by FTIR spectroscopy. Characteristic markers of the formation of guanine tetrads are given. Moreover, we propose a new marker discriminating between parallel and antiparallel tetraplexes: the position of the C6 O6 guanine carbonyl stretching vibration. In intermolecular parallel tetrameric structures formed by four separate strands this absorption is observed at 1693 cm −1 while for antiparallel tetrameric structures, either intramolecular or formed by dimerization of hairpins, this vibrational mode is observed at 1682 cm −1. These shifts to higher wavenumbers, when compared to the position of a free guanine C6 O6 carbonyl stretching vibration observed at 1666 cm −1 (Δ ν = 27 cm −1 for parallel tetraplexes and Δ ν = 16 cm −1 for antiparallel tetraplexes) reflect different strand orientations in the structures. This marker has been used to evidence the possibility of an antiparallel–parallel tetraplex reorganization for Oxytricha nova d(G 4T 4G 4) and d((G 4T 4) 3G 4) and human d(G 3T 2AG 3) telomeric sequences induced by Na +/K + or Na +/Ca 2+ ion exchange. Formation of the guanine tetrads, characterization of the phosphate geometries and of the sugar conformations have also been obtained by FTIR for the different tetraplexes.