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Triple-Stranded DNA As a Structural Element in DNA Origami

[Image: see text] Molecular self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly linked with covalent phosphodiester strand crossovers to build up three-dimensional ob...

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Autores principales: Sachenbacher, Ken, Khoshouei, Ali, Honemann, Maximilian Nicolas, Engelen, Wouter, Feigl, Elija, Dietz, Hendrik
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210531/
https://www.ncbi.nlm.nih.gov/pubmed/37159224
http://dx.doi.org/10.1021/acsnano.2c11402
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author Sachenbacher, Ken
Khoshouei, Ali
Honemann, Maximilian Nicolas
Engelen, Wouter
Feigl, Elija
Dietz, Hendrik
author_facet Sachenbacher, Ken
Khoshouei, Ali
Honemann, Maximilian Nicolas
Engelen, Wouter
Feigl, Elija
Dietz, Hendrik
author_sort Sachenbacher, Ken
collection PubMed
description [Image: see text] Molecular self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly linked with covalent phosphodiester strand crossovers to build up three-dimensional objects. To expand the palette of structural motifs in DNA origami, here we describe hybrid duplex–triplex DNA motifs as pH-dependent building blocks in DNA origami. We investigate design rules for incorporating triplex forming oligonucleotides and noncanonical duplex–triplex crossovers in multilayer DNA origami objects. We use single-particle cryoelectron microscopy to elucidate the structural basis of triplex domains and of duplex–triplex crossovers. We find that duplex–triplex crossovers can complement and fully replace the canonical duplex–duplex crossovers within DNA origami objects, for example, to increase the crossover density for potentially greater rigidity and reduced interhelical spacing, and to create connections at sites where conventional crossovers may be undesirable. We also show the pH-induced formation of a DNA origami object stabilized entirely by triplex-mediated strand crossovers.
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spelling pubmed-102105312023-05-26 Triple-Stranded DNA As a Structural Element in DNA Origami Sachenbacher, Ken Khoshouei, Ali Honemann, Maximilian Nicolas Engelen, Wouter Feigl, Elija Dietz, Hendrik ACS Nano [Image: see text] Molecular self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly linked with covalent phosphodiester strand crossovers to build up three-dimensional objects. To expand the palette of structural motifs in DNA origami, here we describe hybrid duplex–triplex DNA motifs as pH-dependent building blocks in DNA origami. We investigate design rules for incorporating triplex forming oligonucleotides and noncanonical duplex–triplex crossovers in multilayer DNA origami objects. We use single-particle cryoelectron microscopy to elucidate the structural basis of triplex domains and of duplex–triplex crossovers. We find that duplex–triplex crossovers can complement and fully replace the canonical duplex–duplex crossovers within DNA origami objects, for example, to increase the crossover density for potentially greater rigidity and reduced interhelical spacing, and to create connections at sites where conventional crossovers may be undesirable. We also show the pH-induced formation of a DNA origami object stabilized entirely by triplex-mediated strand crossovers. American Chemical Society 2023-05-09 /pmc/articles/PMC10210531/ /pubmed/37159224 http://dx.doi.org/10.1021/acsnano.2c11402 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Sachenbacher, Ken
Khoshouei, Ali
Honemann, Maximilian Nicolas
Engelen, Wouter
Feigl, Elija
Dietz, Hendrik
Triple-Stranded DNA As a Structural Element in DNA Origami
title Triple-Stranded DNA As a Structural Element in DNA Origami
title_full Triple-Stranded DNA As a Structural Element in DNA Origami
title_fullStr Triple-Stranded DNA As a Structural Element in DNA Origami
title_full_unstemmed Triple-Stranded DNA As a Structural Element in DNA Origami
title_short Triple-Stranded DNA As a Structural Element in DNA Origami
title_sort triple-stranded dna as a structural element in dna origami
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210531/
https://www.ncbi.nlm.nih.gov/pubmed/37159224
http://dx.doi.org/10.1021/acsnano.2c11402
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