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 MgC12, 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. © 1992 Adenine press.