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Modeling DNA Nanodevices Using Graph Rewrite Systems

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Advances in Unconventional Computing

Part of the book series: Emergence, Complexity and Computation ((ECC,volume 23))

Abstract

DNA based nanostructures and devices are becoming ubiquitous in nanotechnology with rapid advancements in theory and experiments in DNA self-assembly which have led to a myriad of DNA nanodevices. However, the modeling methods used by researchers in the field for design and analysis of DNA nanostructures and nanodevices have not progressed at the same rate. Specifically, there does not exist a formal system that can capture the spectrum of the most frequently intended chemical reactions on DNA nanostructures and nanodevices which have branched and pseudo-knotted structures. In this paper we introduce a graph rewriting system for modeling DNA nanodevices. We define pseudo-DNA nanostructures (\(\mathbf {PDN}\)s), which describe the sequence information and secondary structure of DNA nanostructures, but exclude modeling of tertiary structures. We define a class of labeled graphs called DNA graphs, that provide a graph theoretic representation of PDNs. We introduce a set of graph rewrite rules that operate on DNA graphs. Our DNA graphs and graph rewrite rules provide a powerful and expressive way to model DNA nanostructures and their reactions. These rewrite rules model most conventional reactions on DNA nanostructures, which include hybridization, dehybridization, base-stacking, and a large family of enzymatic reactions. A subset of these rewrite rules would likely be used for a basic graph rewrite system modeling most DNA devices, which use just DNA hybridization reactions, whereas other of our rewrite rules could be incorporated as needed for DNA devices for example enzymic reactions. To ensure consistency of our systems, we define a subset of DNA graphs which we call well-formed DNA graphs, whose strands have consistent \(5^\prime \) to \(3^\prime \) polarity. We show that if we start with an input set of well-formed DNA graphs, our rewrite rules produce only well-formed DNA graphs. We give four detailed example applications of our graph rewriting system on (1) Yurke et al. [82] DNA tweezer system, (2) Yurke et al. [77] catalytic hairpin-based triggered branched junctions, (3) Dirks and Pierce [17] HCR, and (4) Qian and Winfree [59] scalable circuit of seesaw gates. Finally, we have a working software prototype (DAGRS) that we have used to generate automatically well-formed DNA graphs using a basic rewriting rule set for some of the examples mentioned.

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Acknowledgments

This work was supported by the National Science Foundation under NSF CCF 1217457 and NSF CCF 1320360.

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Authors and Affiliations

  1. Department of Computer Science, Duke University, Durham, NC, USA

    Reem Mokhtar, Sudhanshu Garg, Hieu Bui, Tianqi Song & John Reif

  2. Google, Mountain View, CA, USA

    Harish Chandran

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  1. Reem Mokhtar
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  2. Sudhanshu Garg
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Correspondence to Reem Mokhtar .

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    Andrew Adamatzky

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Mokhtar, R., Garg, S., Chandran, H., Bui, H., Song, T., Reif, J. (2017). Modeling DNA Nanodevices Using Graph Rewrite Systems. In: Adamatzky, A. (eds) Advances in Unconventional Computing. Emergence, Complexity and Computation, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-319-33921-4_15

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