title: DNA Origami Seesaws as Comparative Binding Assay.
abstract: The application of commonly used force spectroscopy in biological systems is often limited by the need for an invasive tether connecting the molecules of interest to a bead or cantilever tip. Here we present a DNA origami-based prototype in a comparative binding assay. It has the advantage of in situ readout without any physical connection to the macroscopic world. The seesaw-like structure has a lever that is able to move freely relative to its base. Binding partners on each side force the structure into discrete and distinguishable conformations. Model experiments with competing DNA hybridisation reactions yielded a drastic shift towards the conformation with the stronger binding interaction. With reference DNA duplexes of tuneable length on one side, this device can be used to measure ligand interactions in comparative assays.
authors.affiliation: Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
authors.forename: Philipp C
authors.identifier: 0000-0002-7455-3359
authors.initials: PC
authors.lastname: Nickels
authors.affiliation: Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
authors.forename: Hans C
authors.initials: HC
authors.lastname: Høiberg
authors.affiliation: Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
authors.forename: Stephanie S
authors.initials: SS
authors.lastname: Simmel
authors.affiliation: Institut für physikalische und theoretische Chemie, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106, Braunschweig, Germany.
authors.forename: Phil
authors.initials: P
authors.lastname: Holzmeister
authors.affiliation: Institut für physikalische und theoretische Chemie, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106, Braunschweig, Germany.
authors.forename: Philip
authors.initials: P
authors.lastname: Tinnefeld
authors.affiliation: Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany. tim.liedl@physik.lmu.de.
authors.forename: Tim
authors.identifier: 0000-0002-0040-0173
authors.initials: T
authors.lastname: Liedl
mesh_terms: D001667:Binding, Competitive; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism; D046529:Microscopy, Electron, Transmission; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization
chemical_list: D004277:DNA, Single-Stranded; D004247:DNA
keywords: DNA hybridisation; DNA origami; DNA structures; self-assembly; sensors