Structural and Functional Characterization of Thrombin Binding Aptamer Minor Loop

Giuseppe Marson(1*), Manlio Palumbo(2), Claudia Sissi(3)

(1) Dept. of Pharmaceutical Sciences, v. Marzolo 5, 35131 Padova, Italy, Italy
(2) Dept. of Pharmaceutical Sciences, v. Marzolo 5, 35131 Padova, Italy, Italy
(3) Dept. of Pharmaceutical Sciences, v. Marzolo 5, 35131 Padova, Italy, Italy
(*) Corresponding author

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The thrombin binding aptamer (29hTBA), identified with a SELEX approach, shows a significant affinity for the coagulation factor thrombin by recognizing the protein  Exosite II (heparin binding site). The structure of 29hTBA consists of a G-quadruplex core flanked by two partially paired terminal strands. Literature data underline that the structure and stability of intramolecular G-quadruplexes can be profoundly influenced by the length and composition of the loops. Here, we investigated the role of the minor loop (10-11) composition by introducing a single A-T mutation at position 11. A comparative structural investigation of the wild type and the mutant aptamers evidenced that this loop is not largely impairing the folding of the G-quadruplex core. Additionally, thrombin binding analysis suggested that this loop is not directly involved in protein binding at exosite II
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Thrombin; Aptamer; G-quadruplex

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