Talk abstracts

Talk on Wednesday 04:15-04:30pm submitted by Joshua Johnson

Orthogonal self-assembly of multiple DNA nanostructures in a single reaction

Joshua Johnson (Biophysics Program), Vasiliki Kolliopoulos (Department of Chemical and Biomolecular Engineering, OSU), Alexander Marras (Institute for Molecular Engineering, University of Chicago), Carlos Castro (Department of Mechanical and Aerospace Engineering)

Abstract:
The field of DNA origami continually strives towards the development of more complex nanostructures while maintaining simple and high yield fabrication protocols[1, 2]. However, the intricacies of the DNA origami folding process and therefore the mechanisms to control, improve, and optimize the self-assembly process are not completely understood. Previous studies have gained insight in the self-assembly process by studying competitive folding with dimeric M13mp18 scaffolds[3] or with a mixture of staple sets from two distinct structures[4]. In these studies, it was found that well defined regions of structures could still fold which appear to be determined by favorable folding pathways. The folding pathways can then be directed by tuning staple affinity through varying staple routing, length or relative concentration[5], such that one particular structure folded completely or a combination of parts from multiple structures formed out of the same scaffold to create a collection of distinct chimeric origami structures. Here we present a novel outcome of competitive folding reactions which help shed light on fundamental principles of kinetics and thermodynamics of DNA origami self-assembly. Specifically, we show that appropriate tuning of isothermal annealing protocols and concentrations from two different staple sets, we can effectively bifurcate the folding pathways to enable the orthogonal self-assembly of two different structures simultaneously in one pot. Our approach does not rely on any optimization of staple routing, but rather uses standard routing of previously studied structures. Furthermore, it appears that multiple staple sets can facilitate folding in low concentration limits where the individual structures would otherwise exhibit poor folding yields. This is likely due to the competition effectively reducing the concentration of scaffold in solution.

References:
[1] Hong, F., et al., DNA origami: scaffolds for creating higher order structures. Chemical reviews, 2017. 117(20): p. 12584-12640.
[2] Wagenbauer, K.F., C. Sigl, and H. Dietz, Gigadalton-scale shape-programmable DNA assemblies. Nature, 2017. 552(7683): p. 78.
[3]Dunn, K.E., et al., Guiding the folding pathway of DNA origami. Nature, 2015. 525(7567): p. 82.
[4] Majikes, J.M., J.A. Nash, and T.H. LaBean, Competitive annealing of multiple DNA origami: formation of chimeric origami. New Journal of Physics, 2016. 18(11): p. 115001.
[5] Marras, A., et al., Directing folding pathways for multi-component DNA origami nanostructures with complex topology. New Journal of Physics, 2016. 18(5): p. 055005.

Keywords: Self-assembly, nanotechnology, DNA