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.
Highlights
Structural DNA nanotechnology, which makes use of DNA as a tractable building block for the construction of arbitrary shapes by molecular self-assembly, has proven an efficient route for building new functional objects with increasing complexity [1,2,3,4,5,6,7]
Good theoretical quantitative understanding of the folding kinetics of large DNA structures is still missing, with very little known about how it is driven from the early assembly events of its basic units
Our starting point was the view of DNA junctions as basic subunits of more complex DNA nanostructures, in contrast to previous reports [22]
Summary
Structural DNA nanotechnology, which makes use of DNA as a tractable building block for the construction of arbitrary shapes by molecular self-assembly, has proven an efficient route for building new functional objects with increasing complexity [1,2,3,4,5,6,7]. The critical temperature has to be empirically found, but once it has, folding can be carried out by maintaining the DNA mixture at that temperature for a relatively short period of time This process was visualized using atomic force microscopy (AFM) [20,21]. Good theoretical quantitative understanding of the folding kinetics of large DNA structures is still missing, with very little known about how it is driven from the early assembly events of its basic units
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