FT-IR Spectroscopic Study of the Poly(amino²dA-dT) Duplex in Mg²⁺-Containing Solution and in Films

Abstract

The alternative structures of the synthetic poly(amino²dA-dT) duplex have been studied using infrared spectroscopy in films and in solution (D₂O and H₂O) in the presence and in the absence of magnesium salt. In solution without magnesium salt, the polynucleotide exists in a B genus conformation with some of the sugar puckers possibly in the C3′-endo/anti geometry. In magnesium-containing solution (66 mM MgCl₂, however, we report infrared spectra of Mg²⁺-poly(amino²dA-dT) which have characteristic marker bands of the A form. Film samples in 70% relative humidity (RH) give similar infrared spectra to those of the polynucleotide obtained using Mg²⁺. Thus, when analyzed in comparison with previously reported infrared spectra of other oligo and polynucleotides, our data show that double helical poly(amino²dA-dT) goes into the same (or very closely related) conformation in dehydrated films as in solutions containing Mg²⁺.

The infrared spectra reported here in the conditions described are compatible with an Aform for the poly(amino²dA-dT) double helix both in films of low relative humidity (70%) and in Mg²⁺-containing solution. Fourth derivative spectrophotometry in the UV region has also been used as a complementary tool to obtain further information regarding the structural features of the polynucleotide in the studied conditions. The role of amino group in position 2 of the adenine residues in the structural transitions of poly(amino²dA-dT) is discussed in view of previous studies of this polynucleotide.