Sequence-dependent cost for Z-form shapes the torsion-driven B-Z transition via close interplay of Z-DNA and DNA bubble
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Kim, Sook Ho | - |
dc.contributor.author | Jung, Hae Jun | - |
dc.contributor.author | Lee, Il-Buem | - |
dc.contributor.author | Lee, Nam-Kyung | - |
dc.contributor.author | Hong, Seok-Cheol | - |
dc.date.accessioned | 2022-03-02T03:42:28Z | - |
dc.date.available | 2022-03-02T03:42:28Z | - |
dc.date.created | 2022-02-09 | - |
dc.date.issued | 2021-04-19 | - |
dc.identifier.issn | 0305-1048 | - |
dc.identifier.uri | https://scholar.korea.ac.kr/handle/2021.sw.korea/137451 | - |
dc.description.abstract | Despite recent genome-wide investigations of functional DNA elements, the mechanistic details about their actions remain elusive. One intriguing possibility is that DNA sequences with special patterns play biological roles, adopting non-B-DNA conformations. Here we investigated dynamics of thymine-guanine (TG) repeats, microsatellite sequences and recurrently found in promoters, as well as cytosine-guanine (CG) repeats, best-known Z-DNA forming sequence, in the aspect of Z-DNA formation. We measured the energy barriers of the B-Z transition with those repeats and discovered the sequence-dependent penalty for Z-DNA generates distinctive thermodynamic and kinetic features in the torque-induced transition. Due to the higher torsional stress required for Z-form in TG repeats, a bubble could be induced more easily, suppressing Z-DNA induction, but facilitate the B-Z interconversion kinetically at the transition midpoint. Thus, the Z-form by TG repeats has advantages as a torsion buffer and bubble selector while the Z-form by CG repeats likely behaves as torsion absorber. Our statistical physics model supports quantitatively the populations of Z-DNA and reveals the pivotal roles of bubbles in state dynamics. All taken together, a quantitative picture for the transition was deduced within the close interplay among bubbles, plectonemes and Z-DNA. | - |
dc.language | English | - |
dc.language.iso | en | - |
dc.publisher | OXFORD UNIV PRESS | - |
dc.subject | HANDED Z-DNA | - |
dc.subject | TO-Z TRANSITION | - |
dc.subject | TORQUE MEASUREMENTS | - |
dc.subject | TRANSCRIPTION | - |
dc.subject | ELASTICITY | - |
dc.subject | REVEALS | - |
dc.subject | ANTIBODIES | - |
dc.subject | DYNAMICS | - |
dc.subject | GENE | - |
dc.title | Sequence-dependent cost for Z-form shapes the torsion-driven B-Z transition via close interplay of Z-DNA and DNA bubble | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Hong, Seok-Cheol | - |
dc.identifier.doi | 10.1093/nar/gkab153 | - |
dc.identifier.scopusid | 2-s2.0-85105689758 | - |
dc.identifier.wosid | 000649006000010 | - |
dc.identifier.bibliographicCitation | NUCLEIC ACIDS RESEARCH, v.49, no.7, pp.3651 - 3660 | - |
dc.relation.isPartOf | NUCLEIC ACIDS RESEARCH | - |
dc.citation.title | NUCLEIC ACIDS RESEARCH | - |
dc.citation.volume | 49 | - |
dc.citation.number | 7 | - |
dc.citation.startPage | 3651 | - |
dc.citation.endPage | 3660 | - |
dc.type.rims | ART | - |
dc.type.docType | Article | - |
dc.description.journalClass | 1 | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Biochemistry & Molecular Biology | - |
dc.relation.journalWebOfScienceCategory | Biochemistry & Molecular Biology | - |
dc.subject.keywordPlus | HANDED Z-DNA | - |
dc.subject.keywordPlus | TO-Z TRANSITION | - |
dc.subject.keywordPlus | TORQUE MEASUREMENTS | - |
dc.subject.keywordPlus | TRANSCRIPTION | - |
dc.subject.keywordPlus | ELASTICITY | - |
dc.subject.keywordPlus | REVEALS | - |
dc.subject.keywordPlus | ANTIBODIES | - |
dc.subject.keywordPlus | DYNAMICS | - |
dc.subject.keywordPlus | GENE | - |
Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.
(02841) 서울특별시 성북구 안암로 14502-3290-1114
COPYRIGHT © 2021 Korea 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.