Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages

Abstract

A series of DNA aptamers bearing triazole internucleotide linkages that bind to thrombin was synthesized. The novel aptamers are structurally analogous to the well-known thrombin-inhibiting G-quadruplexes TBA15 and TBA31. The secondary structure stability, binding affinity for thrombin and anticoagulant effects of the triazole-modified aptamers were measured. A modification in the central loop of the aptamer quadruplex resulted in increased nuclease resistance and an inhibition efficiency similar to that of TBA15. The likely aptamer-thrombin binding mode was determined by molecular dynamics simulations. Due to their relatively high activity and the increased resistance to nuclease digestion imparted by the triazole internucleotide linkages, the novel aptamers are a promising alternative to known DNA-based anticoagulant agents.

Keywords: Anticoagulants; CD; DNA aptamers; EDTA; EMSA; G-Quadruplexes; HPLC; HR ES MS; MALDI TOF MS; MD; MST; TBA; TLC; TT; Thr; Thrombin inhibition; Triazole internucleotide linkages; X-ray diffraction analysis; XDA; circular dichroism; electrophoretic mobility shift assay; ethylendiamine tetraacetic acid; high performance liquid chromatography; high-resolution electrospray ionization mass spectrometry; matrix-assisted laser desorption/ionization-time of flight mass spectrometry; microscale thermophoresis; molecular dynamics; thin layer liquid chromatography; thrombin; thrombin binding aptamer; thrombin time.