title: Comparison of the 'chemical' and 'structural' approaches to the optimization of the thrombin-binding aptamer.
abstract: Noncanonically structured DNA aptamers to thrombin were examined. Two different approaches were used to improve stability, binding affinity and biological activity of a known thrombin-binding aptamer. These approaches are chemical modification and the addition of a duplex module to the aptamer core structure. Several chemically modified aptamers and the duplex-bearing ones were all studied under the same conditions by a set of widely known and some relatively new methods. A number of the thrombin-binding aptamer analogs have demonstrated improved characteristics. Most importantly, the study allowed us to compare directly the two approaches to aptamer optimization and to analyze their relative advantages and disadvantages as well as their potential in drug design and fundamental studies.
authors.affiliation: Institute for Physical-Chemical Medicine, Moscow, Russia.
authors.forename: Olga
authors.initials: O
authors.lastname: Tatarinova
authors.affiliation: Institute for Physical-Chemical Medicine, Moscow, Russia ; Orekhovich Institute of Biomedical Chemistry, Moscow, Russia ; Topchiev Institute of Petrochemical Synthesis, Moscow, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Tsvetkov
authors.affiliation: Institute for Physical-Chemical Medicine, Moscow, Russia.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Basmanov
authors.affiliation: Institute for Physical-Chemical Medicine, Moscow, Russia.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Barinov
authors.affiliation: Institute for Physical-Chemical Medicine, Moscow, Russia.
authors.forename: Igor
authors.initials: I
authors.lastname: Smirnov
authors.affiliation: Engelhardt Institute of Molecular Biology, Moscow, Russia.
authors.forename: Edward
authors.initials: E
authors.lastname: Timofeev
authors.affiliation: Engelhardt Institute of Molecular Biology, Moscow, Russia.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Kaluzhny
authors.affiliation: Engelhardt Institute of Molecular Biology, Moscow, Russia.
authors.forename: Andrey
authors.initials: A
authors.lastname: Chuvilin
authors.affiliation: Institute for Physical-Chemical Medicine, Moscow, Russia ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Klinov
authors.affiliation: Institute for Physical-Chemical Medicine, Moscow, Russia ; Engelhardt Institute of Molecular Biology, Moscow, Russia.
authors.forename: Anna
authors.initials: A
authors.lastname: Varizhuk
authors.affiliation: Institute for Physical-Chemical Medicine, Moscow, Russia.
authors.forename: Galina
authors.initials: G
authors.lastname: Pozmogova
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D054856:G-Quadruplexes; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D013329:Structure-Activity Relationship; D013917:Thrombin / Q000037:antagonists & inhibitors / Q000378:metabolism*; D014230:Triazoles / Q000737:chemistry*
chemical_list: D052157:Aptamers, Nucleotide; D014230:Triazoles; C081676:thrombin aptamer; D013917:Thrombin