title: RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity.
abstract: Aptamers are an emerging class of highly specific targeting ligands. They can be selected in vitro for a large variety of targets, ranging from small molecules to whole cells. Most aptamers selected are nucleic acid-based, allowing chemical synthesis and easy modification. Although their properties make them interesting drug candidates for a broad spectrum of applications and an interesting alternative to antibodies or fusion proteins, they are not yet broadly used. One major drawback of aptamers is their susceptibility to abundant serum nucleases, resulting in their fast degradation in biological fluids. Using modified nucleic acids has become a common strategy to overcome these disadvantages, greatly increasing their half-life under cell culture conditions or even in vivo. Whereas pre-selective modifications of the initial library for aptamer selection are relatively easy to obtain, post-selective modifications of already selected aptamers are still generally very labor-intensive and often compromise the aptamers ability to bind its target molecule. Here we report the selection, characterization and post-selective modification of a 34 nucleotide (nt) RNA aptamer for a non-dominant, novel target site (domain 3) of the interleukin-6 receptor (IL-6R). We performed structural analyses and investigated the affinity of the aptamer to the membrane-bound and soluble forms (sIL-6R) of the IL-6R. Further, we performed structural analyses of the aptamer in solution using small-angle X-ray scattering and determined its overall shape and oligomeric state. Post-selective exchange of all pyrimidines against their 2'-fluoro analogs increased the aptamers stability significantly without compromising its affinity for the target protein. The resulting modified aptamer could be shortened to its minimal binding motif without loss of affinity.
authors.affiliation: a Institute for Biochemistry and Molecular Biology ; Department of Chemistry ; University of Hamburg ; Hamburg , Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Mittelberger
authors.affiliation: b Howard Hughes Medical Institute; Laboratory of RNA Molecular Biology; Rockefeller University ; New York , NY USA.
authors.forename: Cindy
authors.initials: C
authors.lastname: Meyer
authors.affiliation: c CONARIS Research Institute AG ; Kiel , Germany.
authors.forename: Georg H
authors.initials: GH
authors.lastname: Waetzig
authors.affiliation: d Physics Department ; Technical University Munich ; Garching , Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias
authors.affiliation: a Institute for Biochemistry and Molecular Biology ; Department of Chemistry ; University of Hamburg ; Hamburg , Germany.|e European Molecular Biology Laboratory; Hamburg Unit ; Hamburg , Germany.
authors.forename: Erica
authors.initials: E
authors.lastname: Valentini
authors.affiliation: e European Molecular Biology Laboratory; Hamburg Unit ; Hamburg , Germany.
authors.forename: Dmitri I
authors.initials: DI
authors.lastname: Svergun
authors.affiliation: a Institute for Biochemistry and Molecular Biology ; Department of Chemistry ; University of Hamburg ; Hamburg , Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Berg
authors.affiliation: f Institute of Biochemistry; University of Kiel ; Kiel , Germany.
authors.forename: Inken
authors.initials: I
authors.lastname: Lorenzen
authors.affiliation: f Institute of Biochemistry; University of Kiel ; Kiel , Germany.
authors.forename: Joachim
authors.initials: J
authors.lastname: Grötzinger
authors.affiliation: f Institute of Biochemistry; University of Kiel ; Kiel , Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Rose-John
authors.affiliation: a Institute for Biochemistry and Molecular Biology ; Department of Chemistry ; University of Hamburg ; Hamburg , Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Hahn
mesh_terms: D000818:Animals; D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D002460:Cell Line; D006801:Humans; D015850:Interleukin-6 / Q000378:metabolism; D051379:Mice; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D019947:Receptors, Interleukin-6 / Q000737:chemistry / Q000378:metabolism*; D052156:SELEX Aptamer Technique
chemical_list: D052157:Aptamers, Nucleotide; D015850:Interleukin-6; D019947:Receptors, Interleukin-6
keywords: Aptamers; Interleukin-6 receptor; SAXS; cell biology; cytokine signaling; internalization; molecular modelling; post-selective modification; protein-RNA interactions