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Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint
In vivo, left-handed DNA duplex (usually refers to Z-DNA) is mainly formed in the region of DNA with alternating purine pyrimidine (APP) sequence and plays significant biological roles. It is well known that d(CG)(n) sequence can form Z-DNA most easily under negative supercoil conditions, but its es...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8789069/ https://www.ncbi.nlm.nih.gov/pubmed/34967416 http://dx.doi.org/10.1093/nar/gkab1283 |
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author | Li, Lin Zhang, Yaping Ma, Wanzhi Chen, Hui Liu, Mengqin An, Ran Cheng, Bingxiao Liang, Xingguo |
author_facet | Li, Lin Zhang, Yaping Ma, Wanzhi Chen, Hui Liu, Mengqin An, Ran Cheng, Bingxiao Liang, Xingguo |
author_sort | Li, Lin |
collection | PubMed |
description | In vivo, left-handed DNA duplex (usually refers to Z-DNA) is mainly formed in the region of DNA with alternating purine pyrimidine (APP) sequence and plays significant biological roles. It is well known that d(CG)(n) sequence can form Z-DNA most easily under negative supercoil conditions, but its essence has not been well clarified. The study on sequence dependence of Z-DNA stability is very difficult without modification or inducers. Here, by the strong topological constraint caused by hybridization of two complementary short circular ssDNAs, left-handed duplex part was generated for various sequences, and their characteristics were investigated by using gel-shift after binding to specific proteins, CD and T(m) analysis, and restriction enzyme cleavage. Under the strong topological constraint, non-APP sequences can also form left-handed DNA duplex as stable as that of APP sequences. As compared with non-APP sequences, the thermal stability difference for APP sequences between Z-form and B-form is smaller, which may be the reason that Z-DNA forms preferentially for APP ones. This result can help us to understand why nature selected APP sequences to regulate gene expression by transient Z-DNA formation, as well as why polymer with chirality can usually form both duplexes with left- or right-handed helix. |
format | Online Article Text |
id | pubmed-8789069 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87890692022-01-26 Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint Li, Lin Zhang, Yaping Ma, Wanzhi Chen, Hui Liu, Mengqin An, Ran Cheng, Bingxiao Liang, Xingguo Nucleic Acids Res Chemical Biology and Nucleic Acid Chemistry In vivo, left-handed DNA duplex (usually refers to Z-DNA) is mainly formed in the region of DNA with alternating purine pyrimidine (APP) sequence and plays significant biological roles. It is well known that d(CG)(n) sequence can form Z-DNA most easily under negative supercoil conditions, but its essence has not been well clarified. The study on sequence dependence of Z-DNA stability is very difficult without modification or inducers. Here, by the strong topological constraint caused by hybridization of two complementary short circular ssDNAs, left-handed duplex part was generated for various sequences, and their characteristics were investigated by using gel-shift after binding to specific proteins, CD and T(m) analysis, and restriction enzyme cleavage. Under the strong topological constraint, non-APP sequences can also form left-handed DNA duplex as stable as that of APP sequences. As compared with non-APP sequences, the thermal stability difference for APP sequences between Z-form and B-form is smaller, which may be the reason that Z-DNA forms preferentially for APP ones. This result can help us to understand why nature selected APP sequences to regulate gene expression by transient Z-DNA formation, as well as why polymer with chirality can usually form both duplexes with left- or right-handed helix. Oxford University Press 2021-12-30 /pmc/articles/PMC8789069/ /pubmed/34967416 http://dx.doi.org/10.1093/nar/gkab1283 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://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 | Chemical Biology and Nucleic Acid Chemistry Li, Lin Zhang, Yaping Ma, Wanzhi Chen, Hui Liu, Mengqin An, Ran Cheng, Bingxiao Liang, Xingguo Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint |
title | Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint |
title_full | Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint |
title_fullStr | Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint |
title_full_unstemmed | Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint |
title_short | Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint |
title_sort | nonalternating purine pyrimidine sequences can form stable left-handed dna duplex by strong topological constraint |
topic | Chemical Biology and Nucleic Acid Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8789069/ https://www.ncbi.nlm.nih.gov/pubmed/34967416 http://dx.doi.org/10.1093/nar/gkab1283 |
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