Improved RE31 analogues containing modified nucleic acid monomers: thermodynamic, structural and biological effects.

RE31 is a 31-nt DNA aptamer, consisting of the G quadruplex and a duplex domain, which is able to effectively prolong thrombin time. In this paper, we report on our investigations into the influence of certain modified nucleotide residues on thermal stability, folding topology and biological properties of RE31. In particular, the effect of single incorporation of canonical nucleosides in UNA, LNA or β-L-RNA series, was evaluated. The studies presented herein show that all modified residues can efficiently modulate G-quadruplex thermal and biological stability - and that the effect is strongly position dependent. The aptamers modified simultaneously with UNAs at the T15 position and LNAs in the duplex part, possess the highest value of melting temperature and a two-fold higher anticoagulant effect. Importantly, RE31 variants containing the modified nucleotide residues are characterized by unchanged G quadruplex folding topology. Crucially, introduction of any of the modified residues into RE31 causes prolongation of aptamer stability in human serum.