Direct observation and rational design of nucleation behavior in addressable self-assembly

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Sajfutdinow, Martin 
Jacobs, William M 
Reinhardt, Aleks 
Schneider, Christoph 
Smith, David M 

To optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on a prototypical “DNA-brick” structure. By combining temperature-dependent dynamic light scattering and atomic force microscopy with coarse-grained simulations, we show how subtle changes in the nucleation pathway profoundly affect the yield of the correctly formed structures. In particular, we can increase the range of conditions over which self-assembly occurs by using stable multisubunit clusters that lower the nucleation barrier for assembling subunits in the interior of the structure. Consequently, modifying only a small portion of a structure is sufficient to optimize its assembly. Due to the generality of our coarse-grained model and the excellent agreement that we find with our experimental results, the design principles reported here are likely to apply generically to addressable, multicomponent self-assembly.

self-assembly, coarse-grained simulation, DNA nanotechnology, nucleation, dynamic light scattering
Journal Title
Proceedings of the National Academy of Sciences of the United States of America
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National Academy of Sciences
Engineering and Physical Sciences Research Council (EP/I001352/1)
This work was supported by the Engineering and Physical Sciences Research Council (Program Grant EP/I001352/1), the European Regional Development Fund (100185665), Fraunhofer Attract Funding (601683), and the National Institutes of Health (Grant F32GM116231).
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