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Information-based autonomous reconfiguration in systems of interacting DNA nanostructures

Petersen, Philip and Tikhomirov, Grigory and Qian, Lulu (2018) Information-based autonomous reconfiguration in systems of interacting DNA nanostructures. Nature Communications, 9 . Art. No. 5362. ISSN 2041-1723. PMCID PMC6299139; PMC6342961. http://resolver.caltech.edu/CaltechAUTHORS:20181218-111943825

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Abstract

The dynamic interactions between complex molecular structures underlie a wide range of sophisticated behaviors in biological systems. In building artificial molecular machines out of DNA, an outstanding challenge is to develop mechanisms that can control the kinetics of interacting DNA nanostructures and that can compose the interactions together to carry out system-level functions. Here we show a mechanism of DNA tile displacement that follows the principles of toehold binding and branch migration similar to DNA strand displacement, but occurs at a larger scale between interacting DNA origami structures. Utilizing this mechanism, we show controlled reaction kinetics over five orders of magnitude and programmed cascades of reactions in multi-structure systems. Furthermore, we demonstrate the generality of tile displacement for occurring at any location in an array in any order, illustrated as a tic-tac-toe game. Our results suggest that tile displacement is a simple-yet-powerful mechanism that opens up the possibility for complex structural components in artificial molecular machines to undergo information-based reconfiguration in response to their environments.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41467-018-07805-7DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299139PubMed CentralArticle
https://doi.org/10.1038/s41467-019-08439-zDOIAuthor Correction
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342961PubMed CentralAuthor Correction
ORCID:
AuthorORCID
Tikhomirov, Grigory0000-0001-6061-3843
Qian, Lulu0000-0003-4115-2409
Additional Information:© 2018 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Received 12 September 2018; Accepted 28 November 2018; Published 18 December 2018. We thank R.M. Murray for sharing an acoustic liquid-handling robot. We thank P.W.K. Rothemund and E. Winfree for critiques on the manuscript. G.T. and L.Q. were supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund (1010684) and the Shurl and Kay Curci Foundation. P.P. was supported by a NIH/NRSA training grant (5 T32 GM07616). L.Q. was also supported by a Faculty Early Career Development Award from NSF (1351081) and an NSF expedition in computing (1317694). Data availability: All data supporting the findings of this study are included in the manuscript and its Supplementary Information. Author Contributions: P.P., G.T., and L.Q. initiated the project; P.P. and G.T. designed and performed the experiments, and analyzed the data; P.P. developed the software tool; P.P., G.T., and L.Q. wrote the manuscript; and L.Q. guided the project. The authors declare no competing interests.
Errata:The original version of this Article omitted a reference to previous work in ‘Stojanovic, M. N. & Stefanovic, D. A deoxyribozyme-based molecular automaton. Nat. Biotechnol. 21, 1069–1074 (2003)’. This has been added as reference 42. The following has been added after the third sentence of the fifth paragraph of the Discussion: ‘Integration could also allow more sophisticated information processing, for example as shown by the classic deoxyribozyme-based automaton that plays tic-tac-toe^(42), to direct structural reconfiguration (Supplementary Discussion)’. This has been corrected in the PDF and HTML versions of the Article.
Funders:
Funding AgencyGrant Number
Burroughs Wellcome Fund1010684
Shurl and Kay Curci FoundationUNSPECIFIED
NIH Predoctoral Fellowship5 T32 GM07616
NSFCCF-1351081
NSFCCF-1317694
PubMed Central ID:PMC6299139; PMC6342961
Record Number:CaltechAUTHORS:20181218-111943825
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20181218-111943825
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91895
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:18 Dec 2018 19:32
Last Modified:28 Jan 2019 15:20

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