title: Site-specific replacement of the thymine methyl group by fluorine in thrombin binding aptamer significantly improves structural stability and anticoagulant activity.
abstract: Here we report investigations, based on circular dichroism, nuclear magnetic resonance spectroscopy, molecular modelling, differential scanning calorimetry and prothrombin time assay, on analogues of the thrombin binding aptamer (TBA) in which individual thymidines were replaced by 5-fluoro-2'-deoxyuridine residues. The whole of the data clearly indicate that all derivatives are able to fold in a G-quadruplex structure very similar to the 'chair-like' conformation typical of the TBA. However, only ODNs TBA-F4: and TBA-F13: have shown a remarkable improvement both in the melting temperature (ΔTm ≈ +10) and in the anticoagulant activity in comparison with the original TBA. These findings are unusual, particularly considering previously reported studies in which modifications of T4 and T13 residues in TBA sequence have clearly proven to be always detrimental for the structural stability and biological activity of the aptamer. Our results strongly suggest the possibility to enhance TBA properties through tiny straightforward modifications.
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Virgilio
authors.affiliation: Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II,via Cintia, I-80126 Napoli, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Petraccone
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Vellecco
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors.forename: Mariarosaria
authors.initials: M
authors.lastname: Bucci
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Varra
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Irace
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors.forename: Rita
authors.initials: R
authors.lastname: Santamaria
authors.affiliation: Dipartimento di Scienze, Università degli Studi della Basilicata, Viale dell'Ateneo Lucano 10, I-85100 Potenza, Italy.
authors.forename: Antonietta
authors.initials: A
authors.lastname: Pepe
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Mayol
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy verespos@unina.it.
authors.forename: Veronica
authors.initials: V
authors.lastname: Esposito
authors.affiliation: Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy galeone@unina.it.
authors.forename: Aldo
authors.initials: A
authors.lastname: Galeone
mesh_terms: D000925:Anticoagulants / Q000737:chemistry*; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D002942:Circular Dichroism; D003851:Deoxyribonucleases; D005461:Fluorine / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D011517:Prothrombin Time; D013816:Thermodynamics; D013936:Thymidine / Q000737:chemistry
chemical_list: D000925:Anticoagulants; D052157:Aptamers, Nucleotide; C081676:thrombin aptamer; D005461:Fluorine; D003851:Deoxyribonucleases; D013936:Thymidine