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Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design

DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties o...

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Autores principales: Lee, Jae Young, Kim, Young-Joo, Lee, Chanseok, Lee, Jae Gyung, Yagyu, Hiromasa, Tabata, Osamu, Kim, Do-Nyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326809/
https://www.ncbi.nlm.nih.gov/pubmed/30476210
http://dx.doi.org/10.1093/nar/gky1189
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author Lee, Jae Young
Kim, Young-Joo
Lee, Chanseok
Lee, Jae Gyung
Yagyu, Hiromasa
Tabata, Osamu
Kim, Do-Nyun
author_facet Lee, Jae Young
Kim, Young-Joo
Lee, Chanseok
Lee, Jae Gyung
Yagyu, Hiromasa
Tabata, Osamu
Kim, Do-Nyun
author_sort Lee, Jae Young
collection PubMed
description DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through molecular dynamics simulation for a comprehensive set of distinct DNA oligomers constructed using all possible base-pair steps with and without a nick. We found that torsional rigidity was reduced by 28–82% at the nick depending on its sequence and location although bending and stretching rigidities remained similar to those of regular base-pair steps. No significant effect of a nick on mechanically coupled deformation such as the twist-stretch coupling was observed. These results suggest that the primary structural role of nick is the relaxation of torsional constraint by backbones known to be responsible for relatively high torsional rigidity of DNA. Moreover, we experimentally demonstrated the usefulness of quantified nick properties in self-assembling DNA nanostructure design by constructing twisted DNA origami structures to show that sequence design of nicks successfully controls the twist angle of structures. Our study illustrates the importance as well as the opportunities of considering sequence-dependent properties in structural DNA nanotechnology.
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spelling pubmed-63268092019-01-15 Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design Lee, Jae Young Kim, Young-Joo Lee, Chanseok Lee, Jae Gyung Yagyu, Hiromasa Tabata, Osamu Kim, Do-Nyun Nucleic Acids Res Computational Biology DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through molecular dynamics simulation for a comprehensive set of distinct DNA oligomers constructed using all possible base-pair steps with and without a nick. We found that torsional rigidity was reduced by 28–82% at the nick depending on its sequence and location although bending and stretching rigidities remained similar to those of regular base-pair steps. No significant effect of a nick on mechanically coupled deformation such as the twist-stretch coupling was observed. These results suggest that the primary structural role of nick is the relaxation of torsional constraint by backbones known to be responsible for relatively high torsional rigidity of DNA. Moreover, we experimentally demonstrated the usefulness of quantified nick properties in self-assembling DNA nanostructure design by constructing twisted DNA origami structures to show that sequence design of nicks successfully controls the twist angle of structures. Our study illustrates the importance as well as the opportunities of considering sequence-dependent properties in structural DNA nanotechnology. Oxford University Press 2019-01-10 2018-11-22 /pmc/articles/PMC6326809/ /pubmed/30476210 http://dx.doi.org/10.1093/nar/gky1189 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 Computational Biology
Lee, Jae Young
Kim, Young-Joo
Lee, Chanseok
Lee, Jae Gyung
Yagyu, Hiromasa
Tabata, Osamu
Kim, Do-Nyun
Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design
title Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design
title_full Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design
title_fullStr Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design
title_full_unstemmed Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design
title_short Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design
title_sort investigating the sequence-dependent mechanical properties of dna nicks for applications in twisted dna nanostructure design
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326809/
https://www.ncbi.nlm.nih.gov/pubmed/30476210
http://dx.doi.org/10.1093/nar/gky1189
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