Improving Structural Stability and Anticoagulant Activity of a Thrombin Binding Aptamer by Aromatic Modifications

Chembiochem. 2022 Mar 18;23(6):e202100670. doi: 10.1002/cbic.202100670. Epub 2022 Jan 31.

Abstract

The thrombin binding aptamer (TBA) is a 15-mer DNA oligonucleotide (5'-GGT TGG TGT GGT TGG-3'), that can form a stable intramolecular antiparallel chair-like G-quadruplex structure. This aptamer shows anticoagulant properties by interacting with one of the two anion binding sites of thrombin, namely the fibrinogen-recognition exosite. Here, we demonstrate that terminal modification of TBA with aromatic fragments such as coumarin, pyrene and perylene diimide (PDI), improves the G-quadruplex stability. The large aromatic surface of these dyes can π-π stack to the G-quadruplex or to each other, thereby stabilizing the aptamer. With respect to the original TBA, monoPDI-functionalized TBA exhibited the most remarkable improvement in melting temperature (ΔTm ≈+18 °C) and displayed enhanced anticoagulant activity.

Keywords: G-quadruplexes; anticoagulants; aptamers; supramolecular chemistry; π-π stacking.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anticoagulants / chemistry
  • Anticoagulants / pharmacology
  • Aptamers, Nucleotide* / chemistry
  • Binding Sites
  • G-Quadruplexes*
  • Thrombin / metabolism

Substances

  • Anticoagulants
  • Aptamers, Nucleotide
  • Thrombin