Investigating the sequence-dependent mechanical properties of DNA nick for applications in twisted DNA nanostructure design
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Lee, Jae Young | - |
dc.contributor.author | Kim, Young-Joo | - |
dc.contributor.author | Lee, Chanseok | - |
dc.contributor.author | Lee, Jae Gyung | - |
dc.contributor.author | Yagyu, Hiromasa | - |
dc.contributor.author | Tabata, Osamu | - |
dc.contributor.author | Kim, Do-Nyun | - |
dc.date.accessioned | 2024-03-27T02:30:25Z | - |
dc.date.available | 2024-03-27T02:30:25Z | - |
dc.date.issued | 2019-01 | - |
dc.identifier.issn | 0305-1048 | - |
dc.identifier.issn | 1362-4962 | - |
dc.identifier.uri | https://scholarworks.bwise.kr/erica/handle/2021.sw.erica/118185 | - |
dc.description.abstract | 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. © The Author(s) 2018. | - |
dc.format.extent | 10 | - |
dc.language | 영어 | - |
dc.language.iso | ENG | - |
dc.publisher | Oxford University Press | - |
dc.title | Investigating the sequence-dependent mechanical properties of DNA nick for applications in twisted DNA nanostructure design | - |
dc.type | Article | - |
dc.publisher.location | 영국 | - |
dc.identifier.doi | 10.1093/nar/gky1189 | - |
dc.identifier.scopusid | 2-s2.0-85059797490 | - |
dc.identifier.wosid | 000462586700015 | - |
dc.identifier.bibliographicCitation | Nucleic Acids Research, v.47, no.1, pp 93 - 102 | - |
dc.citation.title | Nucleic Acids Research | - |
dc.citation.volume | 47 | - |
dc.citation.number | 1 | - |
dc.citation.startPage | 93 | - |
dc.citation.endPage | 102 | - |
dc.type.docType | 정기학술지(Article(Perspective Article포함)) | - |
dc.description.isOpenAccess | Y | - |
dc.description.journalRegisteredClass | sci | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Biochemistry & Molecular Biology | - |
dc.relation.journalWebOfScienceCategory | Biochemistry & Molecular Biology | - |
dc.subject.keywordPlus | MOLECULAR-DYNAMICS | - |
dc.subject.keywordPlus | B-DNA | - |
dc.subject.keywordPlus | STRUCTURAL TRANSITIONS | - |
dc.subject.keywordPlus | SINGLE-MOLECULE | - |
dc.subject.keywordPlus | BASE-STACKING | - |
dc.subject.keywordPlus | STRANDED-DNA | - |
dc.subject.keywordPlus | FOLDING DNA | - |
dc.subject.keywordPlus | ELASTICITY | - |
dc.subject.keywordPlus | RNA | - |
dc.subject.keywordPlus | FLEXIBILITY | - |
dc.identifier.url | https://academic.oup.com/nar/article/47/1/93/5198482?login=true | - |
Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.
55 Hanyangdeahak-ro, Sangnok-gu, Ansan, Gyeonggi-do, 15588, Korea+82-31-400-4269 sweetbrain@hanyang.ac.kr
COPYRIGHT © 2021 HANYANG UNIVERSITY. ALL RIGHTS RESERVED.
Certain data included herein are derived from the © Web of Science of Clarivate Analytics. All rights reserved.
You may not copy or re-distribute this material in whole or in part without the prior written consent of Clarivate Analytics.