Cooperativity-based modeling of heterotypic DNA nanostructure assembly

Anastasia Shapiro, Avital Hozeh, Olga Girshevitz, Almogit Abu-Horowitz, Ido Bachelet

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

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.

Original languageEnglish
Pages (from-to)6587-6595
Number of pages9
JournalNucleic Acids Research
Volume43
Issue number13
DOIs
StatePublished - 27 Jul 2015

Bibliographical note

Publisher Copyright:
© The Author(s) 2015.

Funding

FundersFunder number
European Commission
Seventh Framework Programme335332, 321772

    Fingerprint

    Dive into the research topics of 'Cooperativity-based modeling of heterotypic DNA nanostructure assembly'. Together they form a unique fingerprint.

    Cite this