title: Anomeric DNA quadruplexes.
abstract: Thrombin-binding aptamer (TBA) is a 15-nt DNA oligomer that efficiently inhibits thrombin. It has been shown that TBA folds into an anti-parallel unimolecular G-quadruplex. Its three-dimensional chair-like structure consists of two G-tetrads connected by TT and TGT loops. TBA undergoes fast degradation by nucleases in vivo. To improve the nuclease resistance of TBA, a number of modified analogs have been proposed. Here, we describe anomeric modifications of TBA. Non-natural α anomers were used to replace selected nucleotides in the loops and core. Significant stabilization of the quadruplex was observed for the anomeric modification of TT loops at T4 and T13. Replacement of the core guanines either prevents quadruplex assembly or induces rearrangement in G-tetrads. It was found that the anticoagulant properties of chimeric aptamers could be retained only with intact TT loops. On the contrary, modification of the TGT loop was shown to substantially increase nuclease resistance of the chimeric aptamer without a notable disturbance of its anticoagulant activity.
authors.affiliation: a Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; Moscow, Russia.
authors.forename: Natalia A
authors.initials: NA
authors.lastname: Kolganova
authors.forename: Anna M
authors.initials: AM
authors.lastname: Varizhuk
authors.forename: Roman A
authors.initials: RA
authors.lastname: Novikov
authors.forename: Vladimir L
authors.initials: VL
authors.lastname: Florentiev
authors.forename: Galina E
authors.initials: GE
authors.lastname: Pozmogova
authors.forename: Olga F
authors.initials: OF
authors.lastname: Borisova
authors.forename: Anna K
authors.initials: AK
authors.lastname: Shchyolkina
authors.forename: Igor P
authors.initials: IP
authors.lastname: Smirnov
authors.forename: Dmitry N
authors.initials: DN
authors.lastname: Kaluzhny
authors.forename: Edward N
authors.initials: EN
authors.lastname: Timofeev
mesh_terms: D000925:Anticoagulants / Q000737:chemistry / Q000494:pharmacology; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000494:pharmacology; D001483:Base Sequence; D002942:Circular Dichroism; D054856:G-Quadruplexes; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D013918:Thrombin Time
chemical_list: D000925:Anticoagulants; D052157:Aptamers, Nucleotide; C081676:thrombin aptamer
keywords: anomer; anticoagulant properties; nuclease resistance; quadruplex; thombin binding aptamer