title: DNA origami design of dolphin-shaped structures with flexible tails.
abstract: The DNA origami method allows the folding of long, single-stranded DNA sequences into arbitrary two-dimensional structures by a set of designed oligonucleotides. The method has revealed an unexpected strength and efficiency for programmed self-assembly of molecular nanostructures and makes it possible to produce fully addressable nanostructures with wide-reaching application potential within the emerging area of nanoscience. Here we present a user-friendly software package for designing DNA origami structures ( http://www.cdna.dk/origami ) and demonstrate its use by the design of a dolphin-like DNA origami structure that was imaged by high-resolution AFM in liquid. The software package provides automatic generation of DNA origami structures, manual editing, interactive overviews, atomic models, tracks the design history, and has a fully extendable toolbox. From the AFM images, it was demonstrated that different designs of the dolphin tail region provided various levels of flexibility in a predictable fashion. Finally, we show that the addition of specific attachment sites promotes dimerization between two independently self-assembled dolphin structures, and that these interactions stabilize the flexible tail.
authors.affiliation: Danish National Research Foundation, Centre for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, DK-8000 Aarhus, Denmark.
authors.forename: Ebbe S
authors.initials: ES
authors.lastname: Andersen
authors.forename: Mingdong
authors.initials: M
authors.lastname: Dong
authors.forename: Morten M
authors.initials: MM
authors.lastname: Nielsen
authors.forename: Kasper
authors.initials: K
authors.lastname: Jahn
authors.forename: Allan
authors.initials: A
authors.lastname: Lind-Thomsen
authors.forename: Wael
authors.initials: W
authors.lastname: Mamdouh
authors.forename: Kurt V
authors.initials: KV
authors.lastname: Gothelf
authors.forename: Flemming
authors.initials: F
authors.lastname: Besenbacher
authors.forename: Jørgen
authors.initials: J
authors.lastname: Kjems
mesh_terms: D003198:Computer Simulation; D017076:Computer-Aided Design; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D046911:Macromolecular Substances / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D049329:Nanostructures / Q000737:chemistry / Q000648:ultrastructure; D036103:Nanotechnology / Q000379:methods; D010316:Particle Size; D012984:Software; D013499:Surface Properties
chemical_list: D046911:Macromolecular Substances; D004247:DNA