Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule.
The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C3), unlocked nucleic acid (UNA) and 3'-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties.
Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.|Institute for Plant Biology and Biotechnology, Westphalian Wilhelms University Münster, Schlossgarten 3, 48149, Münster, Germany.
Lukas J
LJ
Aaldering
Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
Vasanthanathan
V
Poongavanam
Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
Niels
N
Langkjaer
Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology (KTH), 10691, Stockholm, Sweden.
N Arul
NA
Murugan
Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
Per Trolle
0000-0003-3932-5921
PT
Jørgensen
Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
Jesper
0000-0001-9835-1009
J
Wengel
Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.|Centre for Comparative Genomics, Murdoch University, Murdoch, Perth, 6150, Australia.|Western Australian Neuroscience Research Institute, Murdoch, Perth, 6150, Australia.|School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia.
Rakesh N
0000-0003-2192-9532
RN
Veedu
D052157:Aptamers, Nucleotide / Q000138:chemical synthesis* / Q000737:chemistry*; D001777:Blood Coagulation; D054856:G-Quadruplexes; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D013269:Stochastic Processes
D052157:Aptamers, Nucleotide; C000622616:TBA-SP7 aptamer; C081676:thrombin aptamer
G-quadruplex; aptamers; modified DNA; thrombin; unlocked nucleic acid