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Accelerating Self-Assembly of Crisscross Slat Systems

Authors David Doty , Hunter Fleming, Daniel Hader, Matthew J. Patitz , Lukas A. Vaughan

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Author Details

David Doty
  • University of California-Davis, CA, USA
Hunter Fleming
  • University of Arkansas, Fayetteville, AR, USA
Daniel Hader
  • University of Arkansas, Fayetteville, AR, USA
Matthew J. Patitz
  • University of Arkansas, Fayetteville, AR, USA
Lukas A. Vaughan
  • University of Arkansas, Fayetteville, AR, USA

Funding

  • Doty, David: This author’s work was supported by NSF grants 2211793, 1900931, and CAREER-1844976.
  • Fleming, Hunter: This author’s work was supported in part by NSF grant CAREER-1553166.
  • Hader, Daniel: This author’s work was supported in part by NSF grant CAREER-1553166.
  • Patitz, Matthew J.: This author’s work was supported in part by NSF grant CAREER-1553166.
  • Vaughan, Lukas A.: This author’s work was supported in part by NSF grant CAREER-1553166.

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David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, and Lukas A. Vaughan. Accelerating Self-Assembly of Crisscross Slat Systems. In 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), Volume 276, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023) https://doi.org/10.4230/LIPIcs.DNA.29.7

Abstract

We present an abstract model of self-assembly of systems composed of "crisscross slats", which have been experimentally implemented as a single-stranded piece of DNA [Minev et al., 2021] or as a complete DNA origami structure [Wintersinger et al., 2022]. We then introduce a more physically realistic "kinetic" model and show how important constants in the model were derived and tuned, and compare simulation-based results to experimental results [Minev et al., 2021; Wintersinger et al., 2022]. Using these models, we show how we can apply optimizations to designs of slat systems in order to lower the numbers of unique slat types required to build target structures. In general, we apply two types of techniques to achieve greatly reduced numbers of slat types. Similar to the experimental work implementing DNA origami-based slats, in our designs the slats oriented in horizontal and vertical directions are each restricted to their own plane and sets of them overlap each other in square regions which we refer to as macrotiles. Our first technique extends their previous work of reusing slat types within macrotiles and requires analyses of binding domain patterns to determine the potential for errors consisting of incorrect slat types attaching at undesired translations and reflections. The second technique leverages the power of algorithmic self-assembly to efficiently reuse entire macrotiles which self-assemble in patterns following designed algorithms that dictate the dimensions and patterns of growth.
Using these designs, we demonstrate that in kinetic simulations the systems with reduced numbers of slat types self-assemble more quickly than those with greater numbers. This provides evidence that such optimizations will also result in greater assembly speeds in experimental systems. Furthermore, the reduced numbers of slat types required have the potential to vastly reduce the cost and number of lab steps for crisscross assembly experiments.

Subject Classification

ACM Subject Classification
  • Theory of computation → Models of computation
Keywords
  • DNA origami
  • self-assembly
  • kinetic modeling
  • computational modeling

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