Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

DNA bricks with binding domains of 13 nucleotides instead of the typical 8 make it possible to self-assemble gigadalton-scale, three-dimensional nanostructures consisting of tens of thousands of unique components. Self-made nanostructures DNA self-assembly is widely used to produce nanoscale structu...

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Veröffentlicht in:Nature (London) 2017-12, Vol.552 (7683), p.72-77
Hauptverfasser: Ong, Luvena L., Hanikel, Nikita, Yaghi, Omar K., Grun, Casey, Strauss, Maximilian T., Bron, Patrick, Lai-Kee-Him, Josephine, Schueder, Florian, Wang, Bei, Wang, Pengfei, Kishi, Jocelyn Y., Myhrvold, Cameron, Zhu, Allen, Jungmann, Ralf, Bellot, Gaetan, Ke, Yonggang, Yin, Peng
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container_end_page 77
container_issue 7683
container_start_page 72
container_title Nature (London)
container_volume 552
creator Ong, Luvena L.
Hanikel, Nikita
Yaghi, Omar K.
Grun, Casey
Strauss, Maximilian T.
Bron, Patrick
Lai-Kee-Him, Josephine
Schueder, Florian
Wang, Bei
Wang, Pengfei
Kishi, Jocelyn Y.
Myhrvold, Cameron
Zhu, Allen
Jungmann, Ralf
Bellot, Gaetan
Ke, Yonggang
Yin, Peng
description DNA bricks with binding domains of 13 nucleotides instead of the typical 8 make it possible to self-assemble gigadalton-scale, three-dimensional nanostructures consisting of tens of thousands of unique components. Self-made nanostructures DNA self-assembly is widely used to produce nanoscale structures of ever increasing complexity. The largest structures that can be assembled reliably contain hundreds of individual DNA strands. Peng Yin and colleagues now show that a new generation of DNA bricks—short DNA strands that fold into brick-like shapes and self-assemble according to specific inter-brick interactions—makes it possible to assemble large DNA nanostructures containing a few tens of thousands of individual bricks. One structure, consisting of 10,000 bricks and having 20,000 uniquely addressable 'nano-voxels'—the three-dimensional equivalents of pixels—is used as a molecular analogue of clay to sculpt three-dimensional objects such as letters, a complex helicoid (a shape similar to a spiral staircase) and a teddy bear. With further optimization, the method might produce even larger assemblies that could find use as scaffolds or for positioning functional components. Three related papers is this issue report further advances in DNA origami, and all four are summarized in a News & Views. Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami 4 , which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands 6 , 7 , 10 , 11 , 12 , 13 , 14 . Even larger DNA origami structures are possible 15 , 16 , but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock 8 , 9 . This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation b
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Self-made nanostructures DNA self-assembly is widely used to produce nanoscale structures of ever increasing complexity. The largest structures that can be assembled reliably contain hundreds of individual DNA strands. Peng Yin and colleagues now show that a new generation of DNA bricks—short DNA strands that fold into brick-like shapes and self-assemble according to specific inter-brick interactions—makes it possible to assemble large DNA nanostructures containing a few tens of thousands of individual bricks. One structure, consisting of 10,000 bricks and having 20,000 uniquely addressable 'nano-voxels'—the three-dimensional equivalents of pixels—is used as a molecular analogue of clay to sculpt three-dimensional objects such as letters, a complex helicoid (a shape similar to a spiral staircase) and a teddy bear. With further optimization, the method might produce even larger assemblies that could find use as scaffolds or for positioning functional components. Three related papers is this issue report further advances in DNA origami, and all four are summarized in a News &amp; Views. Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami 4 , which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands 6 , 7 , 10 , 11 , 12 , 13 , 14 . Even larger DNA origami structures are possible 15 , 16 , but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock 8 , 9 . This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success 9 . Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1–1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can be produced within this molecular canvas, enabling the creation of shapes such as letters, a helicoid and a teddy bear. We anticipate that with further optimization of structure design, strand synthesis and assembly procedure even larger structures could be accessible, which could be useful for applications such as positioning functional components.</description><identifier>ISSN: 0028-0836</identifier><identifier>EISSN: 1476-4687</identifier><identifier>DOI: 10.1038/nature24648</identifier><identifier>PMID: 29219968</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>639/301/357/341 ; 639/925/926/1049 ; Annealing ; Binding ; Biology ; Biophysics ; Deoxyribonucleic acid ; Design optimization ; DNA ; DNA sequencing ; Humanities and Social Sciences ; letter ; Life Sciences ; Medical imaging ; Methods ; Microscopy ; multidisciplinary ; Nanostructure ; Nucleic acids ; Nucleotides ; Photonics ; Ribonucleic acid ; RNA ; RNA sequencing ; Science ; Self-assembly ; Strands</subject><ispartof>Nature (London), 2017-12, Vol.552 (7683), p.72-77</ispartof><rights>Macmillan Publishers Limited, part of Springer Nature. All rights reserved. 2017</rights><rights>COPYRIGHT 2017 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Dec 7, 2017</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c694t-2d7b0cd80aa1062656ddbf6a87c976c0c1e6e153779900d8d3fc326055f974453</citedby><cites>FETCH-LOGICAL-c694t-2d7b0cd80aa1062656ddbf6a87c976c0c1e6e153779900d8d3fc326055f974453</cites><orcidid>0000-0002-3354-9513 ; 0000-0002-3551-9377 ; 0000-0002-3292-5070 ; 0000-0002-5611-3325</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nature24648$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nature24648$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29219968$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.umontpellier.fr/hal-02073945$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Ong, Luvena L.</creatorcontrib><creatorcontrib>Hanikel, Nikita</creatorcontrib><creatorcontrib>Yaghi, Omar K.</creatorcontrib><creatorcontrib>Grun, Casey</creatorcontrib><creatorcontrib>Strauss, Maximilian T.</creatorcontrib><creatorcontrib>Bron, Patrick</creatorcontrib><creatorcontrib>Lai-Kee-Him, Josephine</creatorcontrib><creatorcontrib>Schueder, Florian</creatorcontrib><creatorcontrib>Wang, Bei</creatorcontrib><creatorcontrib>Wang, Pengfei</creatorcontrib><creatorcontrib>Kishi, Jocelyn Y.</creatorcontrib><creatorcontrib>Myhrvold, Cameron</creatorcontrib><creatorcontrib>Zhu, Allen</creatorcontrib><creatorcontrib>Jungmann, Ralf</creatorcontrib><creatorcontrib>Bellot, Gaetan</creatorcontrib><creatorcontrib>Ke, Yonggang</creatorcontrib><creatorcontrib>Yin, Peng</creatorcontrib><title>Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components</title><title>Nature (London)</title><addtitle>Nature</addtitle><addtitle>Nature</addtitle><description>DNA bricks with binding domains of 13 nucleotides instead of the typical 8 make it possible to self-assemble gigadalton-scale, three-dimensional nanostructures consisting of tens of thousands of unique components. Self-made nanostructures DNA self-assembly is widely used to produce nanoscale structures of ever increasing complexity. The largest structures that can be assembled reliably contain hundreds of individual DNA strands. Peng Yin and colleagues now show that a new generation of DNA bricks—short DNA strands that fold into brick-like shapes and self-assemble according to specific inter-brick interactions—makes it possible to assemble large DNA nanostructures containing a few tens of thousands of individual bricks. One structure, consisting of 10,000 bricks and having 20,000 uniquely addressable 'nano-voxels'—the three-dimensional equivalents of pixels—is used as a molecular analogue of clay to sculpt three-dimensional objects such as letters, a complex helicoid (a shape similar to a spiral staircase) and a teddy bear. With further optimization, the method might produce even larger assemblies that could find use as scaffolds or for positioning functional components. Three related papers is this issue report further advances in DNA origami, and all four are summarized in a News &amp; Views. Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami 4 , which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands 6 , 7 , 10 , 11 , 12 , 13 , 14 . Even larger DNA origami structures are possible 15 , 16 , but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock 8 , 9 . This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success 9 . Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1–1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can be produced within this molecular canvas, enabling the creation of shapes such as letters, a helicoid and a teddy bear. 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Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Earth, Atmospheric &amp; Aquatic Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest One Psychology</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>University of Michigan</collection><collection>Genetics Abstracts</collection><collection>SIRS Editorial</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Nature (London)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ong, Luvena L.</au><au>Hanikel, Nikita</au><au>Yaghi, Omar K.</au><au>Grun, Casey</au><au>Strauss, Maximilian T.</au><au>Bron, Patrick</au><au>Lai-Kee-Him, Josephine</au><au>Schueder, Florian</au><au>Wang, Bei</au><au>Wang, Pengfei</au><au>Kishi, Jocelyn Y.</au><au>Myhrvold, Cameron</au><au>Zhu, Allen</au><au>Jungmann, Ralf</au><au>Bellot, Gaetan</au><au>Ke, Yonggang</au><au>Yin, Peng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components</atitle><jtitle>Nature (London)</jtitle><stitle>Nature</stitle><addtitle>Nature</addtitle><date>2017-12-07</date><risdate>2017</risdate><volume>552</volume><issue>7683</issue><spage>72</spage><epage>77</epage><pages>72-77</pages><issn>0028-0836</issn><eissn>1476-4687</eissn><abstract>DNA bricks with binding domains of 13 nucleotides instead of the typical 8 make it possible to self-assemble gigadalton-scale, three-dimensional nanostructures consisting of tens of thousands of unique components. Self-made nanostructures DNA self-assembly is widely used to produce nanoscale structures of ever increasing complexity. The largest structures that can be assembled reliably contain hundreds of individual DNA strands. Peng Yin and colleagues now show that a new generation of DNA bricks—short DNA strands that fold into brick-like shapes and self-assemble according to specific inter-brick interactions—makes it possible to assemble large DNA nanostructures containing a few tens of thousands of individual bricks. One structure, consisting of 10,000 bricks and having 20,000 uniquely addressable 'nano-voxels'—the three-dimensional equivalents of pixels—is used as a molecular analogue of clay to sculpt three-dimensional objects such as letters, a complex helicoid (a shape similar to a spiral staircase) and a teddy bear. With further optimization, the method might produce even larger assemblies that could find use as scaffolds or for positioning functional components. Three related papers is this issue report further advances in DNA origami, and all four are summarized in a News &amp; Views. Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami 4 , which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands 6 , 7 , 10 , 11 , 12 , 13 , 14 . Even larger DNA origami structures are possible 15 , 16 , but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock 8 , 9 . This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success 9 . Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1–1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can be produced within this molecular canvas, enabling the creation of shapes such as letters, a helicoid and a teddy bear. We anticipate that with further optimization of structure design, strand synthesis and assembly procedure even larger structures could be accessible, which could be useful for applications such as positioning functional components.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>29219968</pmid><doi>10.1038/nature24648</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0002-3354-9513</orcidid><orcidid>https://orcid.org/0000-0002-3551-9377</orcidid><orcidid>https://orcid.org/0000-0002-3292-5070</orcidid><orcidid>https://orcid.org/0000-0002-5611-3325</orcidid><oa>free_for_read</oa></addata></record>
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identifier ISSN: 0028-0836
ispartof Nature (London), 2017-12, Vol.552 (7683), p.72-77
issn 0028-0836
1476-4687
language eng
recordid cdi_hal_primary_oai_HAL_hal_02073945v1
source SpringerLink Journals; Nature Journals Online
subjects 639/301/357/341
639/925/926/1049
Annealing
Binding
Biology
Biophysics
Deoxyribonucleic acid
Design optimization
DNA
DNA sequencing
Humanities and Social Sciences
letter
Life Sciences
Medical imaging
Methods
Microscopy
multidisciplinary
Nanostructure
Nucleic acids
Nucleotides
Photonics
Ribonucleic acid
RNA
RNA sequencing
Science
Self-assembly
Strands
title Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components
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