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Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane

DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibilit...

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Autores principales: Li, Qi, Li, Jing, Cui, Yixiao, Liu, Sheng, An, Ran, Liang, Xingguo, Komiyama, Makoto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225352/
https://www.ncbi.nlm.nih.gov/pubmed/30189687
http://dx.doi.org/10.3390/molecules23092270
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author Li, Qi
Li, Jing
Cui, Yixiao
Liu, Sheng
An, Ran
Liang, Xingguo
Komiyama, Makoto
author_facet Li, Qi
Li, Jing
Cui, Yixiao
Liu, Sheng
An, Ran
Liang, Xingguo
Komiyama, Makoto
author_sort Li, Qi
collection PubMed
description DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibility of dynamic motions. However, there has been no established way to synthesize catenanes in which Lk is controlled to a predetermined value. This paper reports a new methodology to selectively synthesize Lk 1 catenanes composed of single-stranded DNA rings, in which these rings can most freely rotate each other due to minimal inter-ring interactions. To the mixture for the synthesis, two holder strands (oligonucleotides of 18–46 nt) were added, and the structure of the quasi-catenane intermediate was interlocked through Watson–Crick base pairings into a favorable conformation for Lk 1 catenation. The length of the complementary part between the two quasi-rings was kept at 10 bp or shorter. Under these steric constraints, two quasi-rings were cyclized with the use of T4 DNA ligase. By this simple procedure, the formation of undesired topoisomers (Lk ≥ 2) was almost completely inhibited, and Lk 1 catenane was selectively prepared in high yield up to 70 mole%. These Lk 1 catenanes have high potentials as dynamic parts for versatile DNA architectures.
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spelling pubmed-62253522018-11-13 Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane Li, Qi Li, Jing Cui, Yixiao Liu, Sheng An, Ran Liang, Xingguo Komiyama, Makoto Molecules Article DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibility of dynamic motions. However, there has been no established way to synthesize catenanes in which Lk is controlled to a predetermined value. This paper reports a new methodology to selectively synthesize Lk 1 catenanes composed of single-stranded DNA rings, in which these rings can most freely rotate each other due to minimal inter-ring interactions. To the mixture for the synthesis, two holder strands (oligonucleotides of 18–46 nt) were added, and the structure of the quasi-catenane intermediate was interlocked through Watson–Crick base pairings into a favorable conformation for Lk 1 catenation. The length of the complementary part between the two quasi-rings was kept at 10 bp or shorter. Under these steric constraints, two quasi-rings were cyclized with the use of T4 DNA ligase. By this simple procedure, the formation of undesired topoisomers (Lk ≥ 2) was almost completely inhibited, and Lk 1 catenane was selectively prepared in high yield up to 70 mole%. These Lk 1 catenanes have high potentials as dynamic parts for versatile DNA architectures. MDPI 2018-09-05 /pmc/articles/PMC6225352/ /pubmed/30189687 http://dx.doi.org/10.3390/molecules23092270 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Li, Qi
Li, Jing
Cui, Yixiao
Liu, Sheng
An, Ran
Liang, Xingguo
Komiyama, Makoto
Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane
title Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane
title_full Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane
title_fullStr Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane
title_full_unstemmed Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane
title_short Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane
title_sort two-holder strategy for efficient and selective synthesis of lk 1 ssdna catenane
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225352/
https://www.ncbi.nlm.nih.gov/pubmed/30189687
http://dx.doi.org/10.3390/molecules23092270
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