title: Cooperativity-based modeling of heterotypic DNA nanostructure assembly.
abstract: DNA origami is a robust method for the fabrication of nanoscale 2D and 3D objects with complex features and geometries. The process of DNA origami folding has been recently studied, however quantitative understanding of it is still elusive. Here, we describe a systematic quantification of the assembly process of DNA nanostructures, focusing on the heterotypic DNA junction-in which arms are unequal-as their basic building block. Using bulk fluorescence studies we tracked this process and identified multiple levels of cooperativity from the arms in a single junction to neighboring junctions in a large DNA origami object, demonstrating that cooperativity is a central underlying mechanism in the process of DNA nanostructure assembly. We show that the assembly of junctions in which the arms are consecutively ordered is more efficient than junctions with randomly-ordered components, with the latter showing assembly through several alternative trajectories as a potential mechanism explaining the lower efficiency. This highlights consecutiveness as a new design consideration that could be implemented in DNA nanotechnology CAD tools to produce more efficient and high-yield designs. Altogether, our experimental findings allowed us to devise a quantitative, cooperativity-based heuristic model for the assembly of DNA nanostructures, which is highly consistent with experimental observations.
authors.affiliation: Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Shapiro
authors.affiliation: Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Avital
authors.initials: A
authors.lastname: Hozeh
authors.affiliation: Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Olga
authors.initials: O
authors.lastname: Girshevitz
authors.affiliation: Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Almogit
authors.initials: A
authors.lastname: Abu-Horowitz
authors.affiliation: Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel dogbach@gmail.com.
authors.forename: Ido
authors.initials: I
authors.lastname: Bachelet
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D019277:Entropy; D007700:Kinetics; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA