title: Structure and target interaction of a G-quadruplex RNA-aptamer.
abstract: G-quadruplexes have recently moved into focus of research in nucleic acids, thereby evolving in scientific significance from exceptional secondary structure motifs to complex modulators of gene regulation. Aptamers (nucleic acid based ligands with recognition properties for a specific target) that form Gquadruplexes may have particular potential for therapeutic applications as they combine the characteristics of specific targeting and Gquadruplex mediated stability and regulation. We have investigated the structure and target interaction properties of one such aptamer: AIR-3 and its truncated form AIR-3A. These RNA aptamers are specific for human interleukin-6 receptor (hIL-6R), a key player in inflammatory diseases and cancer, and have recently been exploited for in vitro drug delivery studies. With the aim to resolve the RNA structure, global shape, RNA:protein interaction site and binding stoichiometry, we now investigated AIR-3 and AIR-3A by different methods including RNA structure probing, Small Angle X-ray scattering and microscale thermophoresis. Our findings suggest a broader spectrum of folding species than assumed so far and remarkable tolerance toward different modifications. Mass spectrometry based binding site analysis, supported by molecular modeling and docking studies propose a general Gquadruplex affinity for the target molecule hIL-6R.
authors.affiliation: a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany.
authors.forename: Kristina
authors.initials: K
authors.lastname: Szameit
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: a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Kruspe
authors.affiliation: b European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany.
authors.forename: Erica
authors.initials: E
authors.lastname: Valentini
authors.affiliation: a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany.
authors.forename: Eileen
authors.initials: E
authors.lastname: Magbanua
authors.affiliation: c University Medical Center Hamburg-Eppendorf , Department of Clinical Chemistry , Hamburg , Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Kwiatkowski
authors.affiliation: d Physics Department , Technical University Munich , Garching , Germany.
authors.forename: Isaure
authors.initials: I
authors.lastname: Chauvot de Beauchêne
authors.affiliation: e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany.
authors.forename: Boris
authors.initials: B
authors.lastname: Krichel
authors.affiliation: e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany.
authors.forename: Kira
authors.initials: K
authors.lastname: Schamoni
authors.affiliation: e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany.|f European XFEL GmbH , Hamburg , Germany.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Uetrecht
authors.affiliation: b European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany.
authors.forename: Dmitri I
authors.initials: DI
authors.lastname: Svergun
authors.affiliation: c University Medical Center Hamburg-Eppendorf , Department of Clinical Chemistry , Hamburg , Germany.
authors.forename: Hartmut
authors.initials: H
authors.lastname: Schlüter
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.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Hahn
keywords: Aptamers; G-quadruplexes; SAXS; interleukin-6 receptor; molecular modeling; protein-RNA interaction