title: Barcode extension for analysis and reconstruction of structures.
abstract: Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.|Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Cameron
authors.initials: C
authors.lastname: Myhrvold
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Michael
authors.identifier: 0000-0003-1303-5598
authors.initials: M
authors.lastname: Baym
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.
authors.forename: Nikita
authors.initials: N
authors.lastname: Hanikel
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.
authors.forename: Luvena L
authors.initials: LL
authors.lastname: Ong
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Gootenberg
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.|Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Peng
authors.initials: P
authors.lastname: Yin
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000648:ultrastructure*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D004587:Electrophoresis, Agar Gel; D018625:Microscopy, Atomic Force; D046529:Microscopy, Electron, Transmission; D049329:Nanostructures / Q000737:chemistry / Q000648:ultrastructure*; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA