Leak-Resistant Design of DNA Strand Displacement Systems

Vinay Gautam

doi:10.1007/978-3-030-57115-3_7

Leak-Resistant Design of DNA Strand Displacement Systems

Vinay Gautam^*

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

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Abstract

Although a number of dynamically-controlled nanostructures and programmable DNA Strand Displacement (DSD) systems have been designed using DNA strand displacement, predictability and scalability of these DNA-based systems remain limited due to leakages introduced by spuriously triggered displacement events. We present a systematic design method for implementing leak-resistant DNA strand displacement systems in which each legitimate displacement event requires signal species to bind cooperatively at the two designated toehold binding sites in the protected fuel complexes, and thus inhibits spurious displacement events. To demonstrate the potential of the leak-resistant design approach for the construction of arbitrary complex digital circuits and systems with analog behaviors, we present domain-level designs and displacement pathways of the basic building blocks of the DNA strand displacement cascades, e.g. OR, AND gates, and an elementary bimolecular reaction.

Original language	English
Title of host publication	Bio-inspired Information and Communication Technologies - 12th EAI International Conference, BICT 2020, Proceedings
Editors	Yifan Chen, Tadashi Nakano, Lin Lin, Mohammad Upal Mahfuz, Weisi Guo
Pages	80-96
Number of pages	17
DOIs	https://doi.org/10.1007/978-3-030-57115-3_7
Publication status	Published - 2020
MoE publication type	A4 Article in a conference publication
Event	International Conference on Bio-inspired Information and Communications Technologies - Shanghai, China Duration: 7 Jul 2020 → 8 Jul 2020 Conference number: 12

Publication series

Name	Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST
Publisher	Springer
Volume	329 LNICST
ISSN (Print)	1867-8211

Conference

Conference	International Conference on Bio-inspired Information and Communications Technologies
Abbreviated title	BICT
Country/Territory	China
City	Shanghai
Period	07/07/2020 → 08/07/2020

Keywords

DNA Strand Displacement
Dynamic DNA Nanotechnology
Leak-resistant
Leakages
Leakless

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10.1007/978-3-030-57115-3_7

SCI_Gautam_2020_BICT_manuscript_peer_reviewed_preprintAccepted author manuscript, 659 KB

Cite this

Gautam, V. (2020). Leak-Resistant Design of DNA Strand Displacement Systems. In Y. Chen, T. Nakano, L. Lin, M. U. Mahfuz, & W. Guo (Eds.), Bio-inspired Information and Communication Technologies - 12th EAI International Conference, BICT 2020, Proceedings (pp. 80-96). (Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST; Vol. 329 LNICST). https://doi.org/10.1007/978-3-030-57115-3_7

Gautam, Vinay. / Leak-Resistant Design of DNA Strand Displacement Systems. Bio-inspired Information and Communication Technologies - 12th EAI International Conference, BICT 2020, Proceedings. editor / Yifan Chen ; Tadashi Nakano ; Lin Lin ; Mohammad Upal Mahfuz ; Weisi Guo. 2020. pp. 80-96 (Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST).

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abstract = "Although a number of dynamically-controlled nanostructures and programmable DNA Strand Displacement (DSD) systems have been designed using DNA strand displacement, predictability and scalability of these DNA-based systems remain limited due to leakages introduced by spuriously triggered displacement events. We present a systematic design method for implementing leak-resistant DNA strand displacement systems in which each legitimate displacement event requires signal species to bind cooperatively at the two designated toehold binding sites in the protected fuel complexes, and thus inhibits spurious displacement events. To demonstrate the potential of the leak-resistant design approach for the construction of arbitrary complex digital circuits and systems with analog behaviors, we present domain-level designs and displacement pathways of the basic building blocks of the DNA strand displacement cascades, e.g. OR, AND gates, and an elementary bimolecular reaction.",

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Gautam, V 2020, Leak-Resistant Design of DNA Strand Displacement Systems. in Y Chen, T Nakano, L Lin, MU Mahfuz & W Guo (eds), Bio-inspired Information and Communication Technologies - 12th EAI International Conference, BICT 2020, Proceedings. Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST, vol. 329 LNICST, pp. 80-96, International Conference on Bio-inspired Information and Communications Technologies, Shanghai, China, 07/07/2020. https://doi.org/10.1007/978-3-030-57115-3_7

Leak-Resistant Design of DNA Strand Displacement Systems. / Gautam, Vinay.

Bio-inspired Information and Communication Technologies - 12th EAI International Conference, BICT 2020, Proceedings. ed. / Yifan Chen; Tadashi Nakano; Lin Lin; Mohammad Upal Mahfuz; Weisi Guo. 2020. p. 80-96 (Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST; Vol. 329 LNICST).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

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AU - Gautam, Vinay

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PY - 2020

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N2 - Although a number of dynamically-controlled nanostructures and programmable DNA Strand Displacement (DSD) systems have been designed using DNA strand displacement, predictability and scalability of these DNA-based systems remain limited due to leakages introduced by spuriously triggered displacement events. We present a systematic design method for implementing leak-resistant DNA strand displacement systems in which each legitimate displacement event requires signal species to bind cooperatively at the two designated toehold binding sites in the protected fuel complexes, and thus inhibits spurious displacement events. To demonstrate the potential of the leak-resistant design approach for the construction of arbitrary complex digital circuits and systems with analog behaviors, we present domain-level designs and displacement pathways of the basic building blocks of the DNA strand displacement cascades, e.g. OR, AND gates, and an elementary bimolecular reaction.

AB - Although a number of dynamically-controlled nanostructures and programmable DNA Strand Displacement (DSD) systems have been designed using DNA strand displacement, predictability and scalability of these DNA-based systems remain limited due to leakages introduced by spuriously triggered displacement events. We present a systematic design method for implementing leak-resistant DNA strand displacement systems in which each legitimate displacement event requires signal species to bind cooperatively at the two designated toehold binding sites in the protected fuel complexes, and thus inhibits spurious displacement events. To demonstrate the potential of the leak-resistant design approach for the construction of arbitrary complex digital circuits and systems with analog behaviors, we present domain-level designs and displacement pathways of the basic building blocks of the DNA strand displacement cascades, e.g. OR, AND gates, and an elementary bimolecular reaction.

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T3 - Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST

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A2 - Chen, Yifan

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Gautam V. Leak-Resistant Design of DNA Strand Displacement Systems. In Chen Y, Nakano T, Lin L, Mahfuz MU, Guo W, editors, Bio-inspired Information and Communication Technologies - 12th EAI International Conference, BICT 2020, Proceedings. 2020. p. 80-96. (Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering, LNICST). https://doi.org/10.1007/978-3-030-57115-3_7

Leak-Resistant Design of DNA Strand Displacement Systems

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