title: A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin.
abstract: Structural properties determine binding affinities of DNA aptamers specific to thrombin. Our paper is the first to focus on a family of eight G-quadruplex-based aptamers with varied duplex region length (from two to eight base pairs). We have shown that the duplex, which is not the main binding domain, greatly influences the interaction with thrombin and prothrombin. Furthermore, the affinity of an aptamer to thrombin and prothrombin increases (respectively from 2.7×10⁻⁸ M to 5.6×10⁻¹⁰ M and from 1.8×10⁻⁵ M to 7.1×10⁻⁹ M) with an increase in the number of nucleotide pairs in the duplex region.
authors.affiliation: A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia.
authors.forename: V A
authors.initials: VA
authors.lastname: Spiridonova
authors.affiliation: A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia.
authors.forename: K V
authors.initials: KV
authors.lastname: Barinova
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia.
authors.forename: K A
authors.initials: KA
authors.lastname: Glinkina
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia.
authors.forename: A V
authors.initials: AV
authors.lastname: Melnichuk
authors.affiliation: Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia.
authors.forename: A A
authors.initials: AA
authors.lastname: Gainutdynov
authors.affiliation: A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia.
authors.forename: I V
authors.initials: IV
authors.lastname: Safenkova
authors.affiliation: A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia. Electronic address: dzantiev@inbi.ras.ru.
authors.forename: B B
authors.initials: BB
authors.lastname: Dzantiev
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D020029:Base Pairing; D002942:Circular Dichroism; D006801:Humans; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D008970:Molecular Weight; D009691:Nucleic Acid Denaturation; D059372:Nucleotide Motifs; D011516:Prothrombin / Q000737:chemistry / Q000378:metabolism*; D020349:Surface Plasmon Resonance; D013917:Thrombin / Q000737:chemistry / Q000378:metabolism*; D044366:Transition Temperature
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D011516:Prothrombin; D013917:Thrombin
keywords: Aptamer; Equilibrium constant; Kinetic constant; Prothrombin; Surface plasmon resonance; Thrombin