title: Thrombin-aptamer recognition: a revealed ambiguity.
abstract: Aptamers are structured oligonucleotides that recognize molecular targets and can function as direct protein inhibitors. The best-known example is the thrombin-binding aptamer, TBA, a single-stranded 15-mer DNA that inhibits the activity of thrombin, the key enzyme of coagulation cascade. TBA folds as a G-quadruplex structure, as proved by its NMR structure. The X-ray structure of the complex between TBA and human α-thrombin was solved at 2.9-Å resolution, but did not provide details of the aptamer conformation and the interactions with the protein molecule. TBA is rapidly processed by nucleases. To improve the properties of TBA, a number of modified analogs have been produced. In particular, a modified TBA containing a 5'-5' polarity inversion site, mTBA, has higher stability and higher affinity toward thrombin with respect to TBA, although it has a lower inhibitory activity. We present the crystal structure of the thrombin-mTBA complex at 2.15-Å resolution; the resulting model eventually provides a clear picture of thrombin-aptamers interaction, and also highlights the structural bases of the different properties of TBA and mTBA. Our findings open the way for a rational design of modified aptamers with improved potency as anticoagulant drugs.
authors.affiliation: Università di Napoli Federico II, Via Cintia, Napoli, Italia.
authors.forename: Irene
authors.initials: I
authors.lastname: Russo Krauss
authors.forename: Antonello
authors.initials: A
authors.lastname: Merlino
authors.forename: Concetta
authors.initials: C
authors.lastname: Giancola
authors.forename: Antonio
authors.initials: A
authors.lastname: Randazzo
authors.forename: Lelio
authors.initials: L
authors.lastname: Mazzarella
authors.forename: Filomena
authors.initials: F
authors.lastname: Sica
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D013917:Thrombin / Q000737:chemistry*
chemical_list: D052157:Aptamers, Nucleotide; D004268:DNA-Binding Proteins; C081676:thrombin aptamer; D013917:Thrombin