title: Designer nanoscale DNA assemblies programmed from the top down.
abstract: Scaffolded DNA origami is a versatile means of synthesizing complex molecular architectures. However, the approach is limited by the need to forward-design specific Watson-Crick base pairing manually for any given target structure. Here, we report a general, top-down strategy to design nearly arbitrary DNA architectures autonomously based only on target shape. Objects are represented as closed surfaces rendered as polyhedral networks of parallel DNA duplexes, which enables complete DNA scaffold routing with a spanning tree algorithm. The asymmetric polymerase chain reaction is applied to produce stable, monodisperse assemblies with custom scaffold length and sequence that are verified structurally in three dimensions to be high fidelity by single-particle cryo-electron microscopy. Their long-term stability in serum and low-salt buffer confirms their utility for biological as well as nonbiological applications.
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Rémi
authors.initials: R
authors.lastname: Veneziano
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Sakul
authors.initials: S
authors.lastname: Ratanalert
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Kaiming
authors.initials: K
authors.lastname: Zhang
authors.affiliation: School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ 85287, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: Zhang
authors.affiliation: School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ 85287, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Yan
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Wah
authors.initials: W
authors.lastname: Chiu
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. mark.bathe@mit.edu.
authors.forename: Mark
authors.initials: M
authors.lastname: Bathe
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D020285:Cryoelectron Microscopy; D004277:DNA, Single-Stranded / Q000737:chemistry*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation
chemical_list: D004277:DNA, Single-Stranded