5-Hydroxymethyl-2′-Deoxyuridine Residues in the Thrombin Binding Aptamer: Investigating Anticoagulant Activity by Making a Tiny Chemical Modification

In this article we report an investigation concerning analogues of the thrombin binding aptamer (TBA) in which thymidines have been replaced, one at a time, by the unusual residue 5-hydroxymethyl-2'-deoxyuridine (hmU) that differs from the canonical thymidine only in the presence of an hydroxyl on the 5-methyl group. NMR and CD data clearly indicate that all TBA derivatives preserve the ability to fold in the original ''chair-like'' structure. The presence of the hmU residue doesn't affect notably thermal stability of the modified aptamers compared to the parent one, except the analogue H9 for which a more marked increase of the melting temperature has been observed. Although all TBA analogues have shown decreased affinities to thrombin, derivatives H3, H7 and H9 have proven to possess improved anticoagulant activities in comparison with the parent aptamer. Our data open-up the possibility to enhance the TBA biological properties, just introducing small chemical modifications.