title: Design principles for rapid folding of knotted DNA nanostructures.
abstract: Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the 'free-end' rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins.
authors.affiliation: Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia.|Graduate school of Biomedicine, University of Ljubljana, Ljubljana 1000, Slovenia.
authors.forename: Vid
authors.initials: V
authors.lastname: Kočar
authors.affiliation: Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
authors.forename: John S
authors.initials: JS
authors.lastname: Schreck
authors.affiliation: Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia.
authors.forename: Slavko
authors.initials: S
authors.lastname: Čeru
authors.affiliation: Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia.|EN-FIST, Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana 1000, Slovenia.
authors.forename: Helena
authors.initials: H
authors.lastname: Gradišar
authors.affiliation: Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana 1000, Slovenia.
authors.forename: Nino
authors.initials: N
authors.lastname: Bašić
authors.affiliation: Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, Ljubljana 1000, Slovenia.|FAMNIT, University of Primorska, Glagoljaška 8, Koper 6000, Slovenia.
authors.forename: Tomaž
authors.initials: T
authors.lastname: Pisanski
authors.affiliation: Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
authors.forename: Jonathan P K
authors.initials: JPK
authors.lastname: Doye
authors.affiliation: Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia.|EN-FIST, Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana 1000, Slovenia.
authors.forename: Roman
authors.identifier: http://orcid.org/0000-0002-6337-5251
authors.initials: R
authors.lastname: Jerala
mesh_terms: D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D008958:Models, Molecular; D049329:Nanostructures; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000737:chemistry
chemical_list: D011506:Proteins; D004247:DNA