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T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures

The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly a...

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Autores principales: Schaffter, Samuel W, Green, Leopold N, Schneider, Joanna, Subramanian, Hari K K, Schulman, Rebecca, Franco, Elisa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007251/
https://www.ncbi.nlm.nih.gov/pubmed/29718412
http://dx.doi.org/10.1093/nar/gky283
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author Schaffter, Samuel W
Green, Leopold N
Schneider, Joanna
Subramanian, Hari K K
Schulman, Rebecca
Franco, Elisa
author_facet Schaffter, Samuel W
Green, Leopold N
Schneider, Joanna
Subramanian, Hari K K
Schulman, Rebecca
Franco, Elisa
author_sort Schaffter, Samuel W
collection PubMed
description The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases.
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spelling pubmed-60072512018-06-25 T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures Schaffter, Samuel W Green, Leopold N Schneider, Joanna Subramanian, Hari K K Schulman, Rebecca Franco, Elisa Nucleic Acids Res Synthetic Biology and Bioengineering The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases. Oxford University Press 2018-06-01 2018-04-30 /pmc/articles/PMC6007251/ /pubmed/29718412 http://dx.doi.org/10.1093/nar/gky283 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Synthetic Biology and Bioengineering
Schaffter, Samuel W
Green, Leopold N
Schneider, Joanna
Subramanian, Hari K K
Schulman, Rebecca
Franco, Elisa
T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures
title T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures
title_full T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures
title_fullStr T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures
title_full_unstemmed T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures
title_short T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures
title_sort t7 rna polymerase non-specifically transcribes and induces disassembly of dna nanostructures
topic Synthetic Biology and Bioengineering
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007251/
https://www.ncbi.nlm.nih.gov/pubmed/29718412
http://dx.doi.org/10.1093/nar/gky283
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