Characterization by Raman spectroscopy of conformational changes on guanine-cytosine and adenine-thymine oligonucleotides induced by aminooxy analogues of spermidine

The interactions between aminooxy analogues of the biogenic polyamine spermidine and selected 15-mer oligodeoxyribonucleotides with alternating purine-pyrimidine base sequences, adenine-thymine (AT) and guanine-cytosine (GC), have been studied using Raman spectroscopy. These analogues resulted from the substitution of the two terminal aminomethylene groups of spermidine, +NH3CH2, by an aminooxy one, H2NO. Since this biogenic polyamine has no centre of symmetry, there are two different isosteric molecules, which have been named AOEPUT and APAPA. However, the pK(a) of an aminooxy group (about 5) is not high enough to be protonated at neutral pH. Therefore, under physiological conditions, these analogues have a positive charge less than spermidine, which makes them suitable models to investigate the roles of both charge and structure in the polyamine-DNA interactions. Raman spectra of solutions containing different concentrations of the analogues, from 10 to 75 mm, and either a GC and an AT oligonucleotide, at a fixed concentration 60 mm (in phosphate), were recorded. The spectra demonstrated the existence of strong differences in the oligonucleotide-analogue interactions depending on the base sequences. In the presence of the aminooxy analogues, a 15-mer GC oligonucleotide adopted a highly ordered tertiary structure (aggregate state or T-DNA) and, at the same time, it changed its secondary structure (from B to Z-DNA). Evidence of macromolecular transitions was not achieved from the Raman spectra of a 15-mer AT oligonucleotide. However, the assignments of the Raman bands indicated that both H2NO groups of the aminooxy analogues and exocyclic NH2 groups of the oligonucleotides could act as preferential binding sites. However, different spectral features were observed between AOEPUT and APAPA in the presence of the oligonucleotides. This fact supports the idea that the two amino terminal groups of spermidine could have different roles in the interaction of this biogenic polyamine with DNA. Our results also confirm that the aminooxy analogues of biogenic polyamines could act as stabilizers of non-viral transfection vectors, thus improving the efficiency of gene therapy protocols. Copyright (C) 2004 John Wiley Sons, Ltd.