title: "DNA Origami Traffic Lights" with a Split Aptamer Sensor for a Bicolor Fluorescence Readout.
abstract: A split aptamer for adenosine triphosphate (ATP) was embedded as a recognition unit into two levers of a nanomechanical DNA origami construct by extension and modification of selected staple strands. An additional optical module in the stem of the split aptamer comprised two different cyanine-styryl dyes that underwent an energy transfer from green (donor) to red (acceptor) emission if two ATP molecules were bound as target molecule to the recognition module and thereby brought the dyes in close proximity. As a result, the ATP as a target triggered the DNA origami shape transition and yielded a fluorescence color change from green to red as readout. Conventional atomic force microscopy (AFM) images confirmed the topology change from the open form of the DNA origami in the absence of ATP into the closed form in the presence of the target molecule. The obtained closed/open ratios in the absence and presence of target molecules tracked well with the fluorescence color ratios and thereby validated the bicolor fluorescence readout. The correct positioning of the split aptamer as the functional unit farthest away from the fulcrum of the DNA origami was crucial for the aptasensing by fluorescence readout. The fluorescence color change allowed additionally to follow the topology change of the DNA origami aptasensor in real time in solution. The concepts of fluorescence energy transfer for bicolor readout in a split aptamer in solution, and AFM on surfaces, were successfully combined in a single DNA origami construct to obtain a bimodal readout. These results are important for future custom DNA devices for chemical-biological and bioanalytical purposes because they are not only working as simple aptamers but are also visible by AFM on the single-molecule level.
authors.affiliation: Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
authors.forename: Heidi-Kristin
authors.initials: HK
authors.lastname: Walter
authors.affiliation: Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Bauer
authors.affiliation: Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
authors.forename: Jeannine
authors.initials: J
authors.lastname: Steinmeyer
authors.affiliation: Department of Chemistry and Materials Engineering, Kansai University , 3-3-35 Yamate, Suita, Osaka 564-8680, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Kuzuya
authors.affiliation: Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
authors.forename: Christof M
authors.initials: CM
authors.lastname: Niemeyer
authors.affiliation: Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
authors.forename: Hans-Achim
authors.identifier: 0000-0003-4849-2887
authors.initials: HA
authors.lastname: Wagenknecht
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D015374:Biosensing Techniques / Q000379:methods*; D003116:Color; D004247:DNA / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D005456:Fluorescent Dyes / Q000737:chemistry; D018625:Microscopy, Atomic Force / Q000379:methods; D049329:Nanostructures / Q000737:chemistry; D009690:Nucleic Acid Conformation
chemical_list: D052157:Aptamers, Nucleotide; D005456:Fluorescent Dyes; D000255:Adenosine Triphosphate; D004247:DNA
keywords: ATP; Energy transfer; atomic force microscopy; click chemistry; dye; nucleic acid