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Troisi, R.* ; Napolitano, V. ; Rossitto, E.* ; Osman, W.* ; Nagano, M.* ; Wakui, K.* ; Popowicz, G.M. ; Yoshimoto, K.* ; Sica, F.*

Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide.

Nucleic Acids Res. 51, 8880-8890 (2023)
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Ligand/protein molecular recognition involves a dynamic process, whereby both partners require a degree of structural plasticity to regulate the binding/unbinding event. Here, we present the characterization of the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. M08s-1 is the most active anticoagulant aptamer selected thus far. Circular dichroism and gel electrophoresis analyses indicate that both intramolecular and intermolecular G-quadruplex structures are populated in solution. The presence of thrombin stabilises the antiparallel intramolecular chair-like G-quadruplex conformation, that provides by far the main contribution to the biological activity of the aptamer. The crystal structure of the thrombin-oligonucleotide complex reveals that M08s-1 adopts a kinked structural organization formed by a G-quadruplex domain and a long duplex module, linked by a stretch of five purine bases. The quadruplex motif hooks the exosite I region of thrombin and the duplex region is folded towards the surface of the protein. This structural feature, which has never been observed in other anti-exosite I aptamers with a shorter duplex motif, hinders the approach of a protein substrate to the active site region and may well explain the significant increase in the anticoagulant activity of M08s-1 compared to the other anti-exosite I aptamers.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Thrombin-binding Aptamer; G-quadruplex Dna; Anticoagulant Activity; Nmr-spectroscopy; Base-pairs; Recognition; Complexes; Sequence; Site; Rna
ISSN (print) / ISBN 0305-1048
e-ISSN 1362-4962
Journal Nucleic Acids Research
Quellenangaben Volume: 51, Issue: 16, Pages: 8880-8890 Article Number: , Supplement: ,
Publisher Oxford University Press
Publishing Place Great Clarendon St, Oxford Ox2 6dp, England
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Structural Biology (STB)