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A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures
Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7328391/ https://www.ncbi.nlm.nih.gov/pubmed/32486951 http://dx.doi.org/10.1098/rsif.2019.0866 |
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author | Badelt, Stefan Grun, Casey Sarma, Karthik V. Wolfe, Brian Shin, Seung Woo Winfree, Erik |
author_facet | Badelt, Stefan Grun, Casey Sarma, Karthik V. Wolfe, Brian Shin, Seung Woo Winfree, Erik |
author_sort | Badelt, Stefan |
collection | PubMed |
description | Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species. |
format | Online Article Text |
id | pubmed-7328391 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | The Royal Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-73283912020-07-02 A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures Badelt, Stefan Grun, Casey Sarma, Karthik V. Wolfe, Brian Shin, Seung Woo Winfree, Erik J R Soc Interface Life Sciences–Engineering interface Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species. The Royal Society 2020-06 2020-06-03 /pmc/articles/PMC7328391/ /pubmed/32486951 http://dx.doi.org/10.1098/rsif.2019.0866 Text en © 2020 The Authors. http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/http://creativecommons.org/licenses/by/4.0/Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. |
spellingShingle | Life Sciences–Engineering interface Badelt, Stefan Grun, Casey Sarma, Karthik V. Wolfe, Brian Shin, Seung Woo Winfree, Erik A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures |
title | A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures |
title_full | A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures |
title_fullStr | A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures |
title_full_unstemmed | A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures |
title_short | A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures |
title_sort | domain-level dna strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures |
topic | Life Sciences–Engineering interface |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7328391/ https://www.ncbi.nlm.nih.gov/pubmed/32486951 http://dx.doi.org/10.1098/rsif.2019.0866 |
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