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Characterizing the length-dependence of DNA nanotube end-to-end joining rates

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Abstract

DNA nanotechnology offers a route towards the synthesis of custom nano-structured materials and circuits through hierarchical assembly processes. While predictive kinetic models are being developed for the assembly of DNA nanostructures from small monomeric components, a general model for the hierarchical assembly of DNA nanostructures remains elusive. DNA tile nanotubes provide an ideal model system for the study of hierarchical assembly via end-to-end joining. In this study, we experimentally characterize the length-dependence of the end-to-end joining rate of DNA tile nanotubes. We then test the ability of three different models of polymer end-to-end joining to reproduce experimentally measured changes in nanotube lengths during a joining reaction using an ODE model for nanotube joining. All three models predict physically realistic joining rates that are consistent with prior measurements, with a length-independent end-to-end joining rate model providing the best fit to the experimental data. A length-independent constant joining rate is consistent with other DNA self-assembly processes across a broad range of length scales and also suggests how tractable models for hierarchical DNA nanostructure could be developed.

Graphical abstract: Characterizing the length-dependence of DNA nanotube end-to-end joining rates

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Article information


Submitted
07 Jun 2019
Accepted
09 Dec 2019
First published
11 Dec 2019

Mol. Syst. Des. Eng., 2020, Advance Article
Article type
Paper

Characterizing the length-dependence of DNA nanotube end-to-end joining rates

M. S. Pacella, V. Mardanlou, S. Agarwal, A. Patel, E. Jelezniakov, A. M. Mohammed, E. Franco and R. Schulman, Mol. Syst. Des. Eng., 2020, Advance Article , DOI: 10.1039/C9ME00068B

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