title: Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages.
abstract: A series of DNA aptamers bearing triazole internucleotide linkages that bind to thrombin was synthesized. The novel aptamers are structurally analogous to the well-known thrombin-inhibiting G-quadruplexes TBA15 and TBA31. The secondary structure stability, binding affinity for thrombin and anticoagulant effects of the triazole-modified aptamers were measured. A modification in the central loop of the aptamer quadruplex resulted in increased nuclease resistance and an inhibition efficiency similar to that of TBA15. The likely aptamer-thrombin binding mode was determined by molecular dynamics simulations. Due to their relatively high activity and the increased resistance to nuclease digestion imparted by the triazole internucleotide linkages, the novel aptamers are a promising alternative to known DNA-based anticoagulant agents.
authors.affiliation: Institute for Physical-Chemical medicine, Malaya Pirogovskaya Str., 1a, Moscow 119435, Russia; Engelhardt Institute of Molecular Biology, Vavilov Str., 32 Moscow 119991, Russia. Electronic address: annavarizhuk@gmail.com.
authors.forename: Anna M
authors.initials: AM
authors.lastname: Varizhuk
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Tsvetkov
authors.forename: Olga N
authors.initials: ON
authors.lastname: Tatarinova
authors.forename: Dmitry N
authors.initials: DN
authors.lastname: Kaluzhny
authors.forename: Vladimir L
authors.initials: VL
authors.lastname: Florentiev
authors.forename: Edward N
authors.initials: EN
authors.lastname: Timofeev
authors.forename: Anna K
authors.initials: AK
authors.lastname: Shchyolkina
authors.forename: Olga F
authors.initials: OF
authors.lastname: Borisova
authors.forename: Igor P
authors.initials: IP
authors.lastname: Smirnov
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Grokhovsky
authors.forename: Anton V
authors.initials: AV
authors.lastname: Aseychev
authors.forename: Galina E
authors.initials: GE
authors.lastname: Pozmogova
mesh_terms: D052157:Aptamers, Nucleotide / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D001665:Binding Sites; D004305:Dose-Response Relationship, Drug; D054856:G-Quadruplexes; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009711:Nucleotides / Q000737:chemistry*; D015842:Serine Proteinase Inhibitors / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D013329:Structure-Activity Relationship; D013917:Thrombin / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism*; D014230:Triazoles / Q000737:chemistry* / Q000494:pharmacology
chemical_list: D052157:Aptamers, Nucleotide; D009711:Nucleotides; D015842:Serine Proteinase Inhibitors; D014230:Triazoles; C081676:thrombin aptamer; D013917:Thrombin
keywords: Anticoagulants; CD; DNA aptamers; EDTA; EMSA; G-Quadruplexes; HPLC; HR ES MS; MALDI TOF MS; MD; MST; TBA; TLC; TT; Thr; Thrombin inhibition; Triazole internucleotide linkages; X-ray diffraction analysis; XDA; circular dichroism; electrophoretic mobility shift assay; ethylendiamine tetraacetic acid; high performance liquid chromatography; high-resolution electrospray ionization mass spectrometry; matrix-assisted laser desorption/ionization-time of flight mass spectrometry; microscale thermophoresis; molecular dynamics; thin layer liquid chromatography; thrombin; thrombin binding aptamer; thrombin time