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 (Δν=27 cm⁻¹ for parallel tetraplexes and Δν=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(G₄T₄G₄) and d((G₄T₄)₃G₄) and human d(G₃T₂AG₃) telomeric sequences induced by Na⁺/K⁺ or Na⁺/Ca²⁺ 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.