title: DNA rendering of polyhedral meshes at the nanoscale.
abstract: It was suggested more than thirty years ago that Watson-Crick base pairing might be used for the rational design of nanometre-scale structures from nucleic acids. Since then, and especially since the introduction of the origami technique, DNA nanotechnology has enabled increasingly more complex structures. But although general approaches for creating DNA origami polygonal meshes and design software are available, there are still important constraints arising from DNA geometry and sense/antisense pairing, necessitating some manual adjustment during the design process. Here we present a general method of folding arbitrary polygonal digital meshes in DNA that readily produces structures that would be very difficult to realize using previous approaches. The design process is highly automated, using a routeing algorithm based on graph theory and a relaxation simulation that traces scaffold strands through the target structures. Moreover, unlike conventional origami designs built from close-packed helices, our structures have a more open conformation with one helix per edge and are therefore stable under the ionic conditions usually used in biological assays.
authors.affiliation: 1] Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden [2] Department of Neuroscience, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Benson
authors.affiliation: Department of Computer Science, Aalto University, FI-00076 Aalto, Finland.
authors.forename: Abdulmelik
authors.initials: A
authors.lastname: Mohammed
authors.affiliation: 1] Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden [2] Department of Neuroscience, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Gardell
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
authors.forename: Sergej
authors.initials: S
authors.lastname: Masich
authors.affiliation: Department of Computer Science, Aalto University, FI-00076 Aalto, Finland.
authors.forename: Eugen
authors.initials: E
authors.lastname: Czeizler
authors.affiliation: Department of Computer Science, Aalto University, FI-00076 Aalto, Finland.
authors.forename: Pekka
authors.initials: P
authors.lastname: Orponen
authors.affiliation: 1] Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden [2] Department of Neuroscience, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
authors.forename: Björn
authors.initials: B
authors.lastname: Högberg
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D002021:Buffers; D020285:Cryoelectron Microscopy; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry* / Q000648:ultrastructure; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure; D036103:Nanotechnology / Q000379:methods*
chemical_list: D002021:Buffers; D004247:DNA