Improved thrombin binding aptamer analogues containing inversion of polarity sites: structural effects of extra-residues at the ends

In this paper, we report the investigations, based on NMR, molecular modelling, CD measurements and electrophoresis, of thrombin binding aptamer (TBA) analogues containing an extra-residue at the 3′-end or at both the ends of the original TBA sequence, linked through 3′–3′ or 5′–5′ phosphodiester bonds. The data indicate that most of the modified aptamers investigated adopt chair-like G-quadruplex structures very similar to that of the TBA and that stacking interactions occur between the 3′–3′ or 5′–5′ extra residues and the deoxyguanosines of the upper G-tetrad. A comparison of the thermodynamic data of TBA-A and TBA-T containing a 3′–3′ extra residue and their canonical versions clearly indicates that the 3′–3′ phosphodiester bond is fundamental in endowing the modified aptamers with remarkably higher thermal stabilities than the original TBA.