title: In vitro selection of DNA-based aptamers that exhibit RNA-like conformations using a chimeric oligonucleotide library that contains two different xeno-nucleic acids.
abstract: We successfully generated chimeric DNA aptamers that contained six nucleoside analogs of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) in the primer region and multiple guanosine analogs of 2'-deoxy-2'-fluoro-ribonucleic acid (FNA) in the non-primer region using capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX). Active species enrichment became saturated only after five selection rounds, and we obtained DNA-based xeno-nucleic acid (XNA) aptamers that had high binding affinities for the target human thrombin, with dissociation constant (Kd) values of ≥10 nanomolar. Based on sequence and circular dichroism (CD) analyses, these XNA aptamers exhibited RNA-like conformations, which could cause DNA-based strands to adopt structurally diverse conformations.
authors.affiliation: Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan. mkuwa@gunma-u.ac.jp.
authors.forename: Kenta
authors.initials: K
authors.lastname: Hagiwara
authors.forename: Hiroto
authors.initials: H
authors.lastname: Fujita
authors.forename: Yuuya
authors.initials: Y
authors.lastname: Kasahara
authors.forename: Yuuta
authors.initials: Y
authors.lastname: Irisawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Obika
authors.forename: Masayasu
authors.initials: M
authors.lastname: Kuwahara
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000235:genetics / Q000493:pharmacokinetics; D001665:Binding Sites; D015723:Gene Library; D006801:Humans; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry* / Q000235:genetics; D009841:Oligonucleotides / Q000737:chemistry* / Q000235:genetics; D011485:Protein Binding; D012313:RNA / Q000737:chemistry*; D052156:SELEX Aptamer Technique; D013329:Structure-Activity Relationship; D013917:Thrombin / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D009696:Nucleic Acids; D009841:Oligonucleotides; D012313:RNA; D013917:Thrombin