Strategies for Constructing and Operating DNA Origami Linear Actuators

Benson, Erik; Carrascosa Marzo, Rafael; Bath, Jonathan; Turberfield, Andrew J.

doi:10.1002/smll.202007704

Title: Strategies for Constructing and Operating DNA Origami Linear Actuators

Journal Article · 03 May 2021 · Small

DOI: https://doi.org/10.1002/smll.202007704 · OSTI ID:1781435

Benson, Erik ^[1];

^[1];

^[1]

Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK

Abstract Linear actuators are ubiquitous components at all scales of engineering. DNA nanotechnology offers a unique opportunity for bottom‐up assembly at the molecular scale, providing nanoscale precision with multiple methods for constructing and operating devices. In this paper, DNA origami linear actuators with up to 200 nm travel, based on a rail threading a topologically locked slider, are demonstrated. Two strategies, one‐ and two‐pot assembly, are demonstrated whereby the two components are folded from one or two DNA scaffold strands, respectively. In order to control the position of the slider on the rail, the rail and the inside of the slider are decorated with single‐stranded oligonucleotides with distinct sequences. Two positioning strategies, based on diffusion and capture of signaling strands, are used to link the slider reversibly to determined positions on the rail with high yield and precision. These machine components provide a basis for applications in molecular machinery and nanoscale manufacture including programmed chemical synthesis.

View Journal Article

Cite

Export

Save

Research Organization:: Univ. of Oxford (United Kingdom)

Sponsoring Organization:: European Research Council (ERC); USDOE; USDOE Office of Energy Efficiency and Renewable Energy (EERE), Energy Efficiency Office. Advanced Manufacturing Office

Grant/Contract Number:: EE0008310

OSTI ID:: 1781435

Journal Information:: Small, Journal Name: Small Journal Issue: 20 Vol. 17; ISSN 1613-6810

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: Germany

Language:: English

References (50)

DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching Powell, John T.; Akhuetie-Oni, Benjamin O.; Zhang, Zhao Angewandte Chemie International Edition, Vol. 55, Issue 38 https://doi.org/10.1002/anie.201604621	journal	August 2016
DNA Origami Post‐Processing by CRISPR‐Cas12a Xiong, Qiancheng; Xie, Chun; Zhang, Zhao Angewandte Chemie International Edition, Vol. 59, Issue 10 https://doi.org/10.1002/anie.201915555	journal	January 2020
TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami Suma, Antonio; Poppleton, Erik; Matthies, Michael Journal of Computational Chemistry, Vol. 40, Issue 29 https://doi.org/10.1002/jcc.26029	journal	July 2019
Nucleic acid junctions and lattices Seeman, Nadrian C. Journal of Theoretical Biology, Vol. 99, Issue 2 https://doi.org/10.1016/0022-5193(82)90002-9	journal	November 1982
[1] Production of single-stranded plasmid DNA Vieira, Jeffrey; Messing, Joachim Methods in Enzymology, Vol. 153, p. 3-11 https://doi.org/10.1016/0076-6879(87)53044-0	book	December 1986
Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds Engelhardt, Floris A. S.; Praetorius, Florian; Wachauf, Christian H. ACS Nano, Vol. 13, Issue 5 https://doi.org/10.1021/acsnano.9b01025	journal	April 2019
A Synthetic DNA Walker for Molecular Transport Shin, Jong-Shik; Pierce, Niles A. Journal of the American Chemical Society, Vol. 126, Issue 35 https://doi.org/10.1021/ja047543j	journal	September 2004
Reversible Light Switch for Macrocycle Mobility in a DNA Rotaxane Lohmann, Finn; Ackermann, Damian; Famulok, Michael Journal of the American Chemical Society, Vol. 134, Issue 29 https://doi.org/10.1021/ja3042096	journal	July 2012
DNA Origami as a Carrier for Circumvention of Drug Resistance Jiang, Qiao; Song, Chen; Nangreave, Jeanette Journal of the American Chemical Society, Vol. 134, Issue 32 https://doi.org/10.1021/ja304263n	journal	August 2012
DNA Scissors Device Used to Measure MutS Binding to DNA Mis-pairs Gu, Hongzhou; Yang, Wei; Seeman, Nadrian C. Journal of the American Chemical Society, Vol. 132, Issue 12 https://doi.org/10.1021/ja910188p	journal	March 2010
Allosteric Control of Oxidative Catalysis by a DNA Rotaxane Nanostructure Centola, Mathias; Valero, Julián; Famulok, Michael Journal of the American Chemical Society, Vol. 139, Issue 45 https://doi.org/10.1021/jacs.7b08839	journal	November 2017
A Precisely Controlled DNA Biped Walking Device Sherman, William B.; Seeman, Nadrian C. Nano Letters, Vol. 4, Issue 7 https://doi.org/10.1021/nl049527q	journal	July 2004
Direct Mechanical Measurements Reveal the Material Properties of Three-Dimensional DNA Origami Kauert, Dominik J.; Kurth, Thomas; Liedl, Tim Nano Letters, Vol. 11, Issue 12 https://doi.org/10.1021/nl203503s	journal	December 2011
Shape-Controlled Synthesis of Gold Nanostructures Using DNA Origami Molds Helmi, Seham; Ziegler, Christoph; Kauert, Dominik J. Nano Letters, Vol. 14, Issue 11 https://doi.org/10.1021/nl503441v	journal	October 2014
DNA Origami Delivery System for Cancer Therapy with Tunable Release Properties Zhao, Yong-Xing; Shaw, Alan; Zeng, Xianghui ACS Nano, Vol. 6, Issue 10 https://doi.org/10.1021/nn3022662	journal	September 2012
Purification of Functionalized DNA Origami Nanostructures Shaw, Alan; Benson, Erik; Högberg, Björn ACS Nano, Vol. 9, Issue 5 https://doi.org/10.1021/nn507035g	journal	May 2015
DNA nanotechnology Seeman, Nadrian C.; Sleiman, Hanadi F. Nature Reviews Materials, Vol. 3, Issue 1 https://doi.org/10.1038/natrevmats.2017.68	journal	November 2017
Folding DNA to create nanoscale shapes and patterns Rothemund, Paul W. K. Nature, Vol. 440, Issue 7082, p. 297-302 https://doi.org/10.1038/nature04586	journal	March 2006
Self-assembly of a nanoscale DNA box with a controllable lid Andersen, Ebbe S.; Dong, Mingdong; Nielsen, Morten M. Nature, Vol. 459, Issue 7243 https://doi.org/10.1038/nature07971	journal	May 2009
Self-assembly of DNA into nanoscale three-dimensional shapes Douglas, Shawn M.; Dietz, Hendrik; Liedl, Tim Nature, Vol. 459, Issue 7245 https://doi.org/10.1038/nature08016	journal	May 2009
A proximity-based programmable DNA nanoscale assembly line Gu, Hongzhou; Chao, Jie; Xiao, Shou-Jun Nature, Vol. 465, Issue 7295 https://doi.org/10.1038/nature09026	journal	May 2010
DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response Kuzyk, Anton; Schreiber, Robert; Fan, Zhiyuan Nature, Vol. 483, Issue 7389 https://doi.org/10.1038/nature10889	journal	March 2012
An autonomous molecular assembler for programmable chemical synthesis Meng, Wenjing; Muscat, Richard A.; McKee, Mireya L. Nature Chemistry, Vol. 8, Issue 6 https://doi.org/10.1038/nchem.2495	journal	April 2016
Long-range movement of large mechanically interlocked DNA nanostructures List, Jonathan; Falgenhauer, Elisabeth; Kopperger, Enzo Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12414	journal	August 2016
Interlocked DNA nanostructures controlled by a reversible logic circuit Li, Tao; Lohmann, Finn; Famulok, Michael Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5940	journal	September 2014
Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT Jungmann, Ralf; Avendaño, Maier S.; Woehrstein, Johannes B. Nature Methods, Vol. 11, Issue 3 https://doi.org/10.1038/nmeth.2835	journal	February 2014
Reconfigurable, braced, three-dimensional DNA nanostructures Goodman, Russell P.; Heilemann, Mike; Doose, Sören Nature Nanotechnology, Vol. 3, Issue 2 https://doi.org/10.1038/nnano.2008.3	journal	February 2008
Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates Maune, Hareem T.; Han, Si-ping; Barish, Robert D. Nature Nanotechnology, Vol. 5, Issue 1 https://doi.org/10.1038/nnano.2009.311	journal	November 2009
Self-assembly of three-dimensional prestressed tensegrity structures from DNA Liedl, Tim; Högberg, Björn; Tytell, Jessica Nature Nanotechnology, Vol. 5, Issue 7 https://doi.org/10.1038/nnano.2010.107	journal	June 2010
Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker He, Yu; Liu, David R. Nature Nanotechnology, Vol. 5, Issue 11 https://doi.org/10.1038/nnano.2010.190	journal	October 2010
A double-stranded DNA rotaxane Ackermann, Damian; Schmidt, Thorsten L.; Hannam, Jeffrey S. Nature Nanotechnology, Vol. 5, Issue 6 https://doi.org/10.1038/nnano.2010.65	journal	April 2010
Super-resolution microscopy with DNA-PAINT Schnitzbauer, Joerg; Strauss, Maximilian T.; Schlichthaerle, Thomas Nature Protocols, Vol. 12, Issue 6 https://doi.org/10.1038/nprot.2017.024	journal	May 2017
Control of enzyme reactions by a reconfigurable DNA nanovault Grossi, Guido; Dalgaard Ebbesen Jepsen, Mette; Kjems, Jørgen Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01072-8	journal	October 2017
Real-time magnetic actuation of DNA nanodevices via modular integration with stiff micro-levers Lauback, Stephanie; Mattioli, Kara R.; Marras, Alexander E. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03601-5	journal	April 2018
Mechanical design of DNA nanostructures Castro, Carlos E.; Su, Hai-Jun; Marras, Alexander E. Nanoscale, Vol. 7, Issue 14 https://doi.org/10.1039/C4NR07153K	journal	January 2015
An easy-to-prepare mini-scaffold for DNA origami Brown, S.; Majikes, J.; Martínez, A. Nanoscale, Vol. 7, Issue 40 https://doi.org/10.1039/C5NR04921K	journal	January 2015
From The Cover: Triggered amplification by hybridization chain reaction Dirks, R. M.; Pierce, N. A. Proceedings of the National Academy of Sciences, Vol. 101, Issue 43 https://doi.org/10.1073/pnas.0407024101	journal	October 2004
Programmable motion of DNA origami mechanisms Marras, Alexander E.; Zhou, Lifeng; Su, Hai-Jun Proceedings of the National Academy of Sciences, Vol. 112, Issue 3 https://doi.org/10.1073/pnas.1408869112	journal	January 2015
Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation Poppleton, Erik; Bohlin, Joakim; Matthies, Michael Nucleic Acids Research, Vol. 48, Issue 12 https://doi.org/10.1093/nar/gkaa417	journal	May 2020
Rapid prototyping of 3D DNA-origami shapes with caDNAno Douglas, Shawn M.; Marblestone, Adam H.; Teerapittayanon, Surat Nucleic Acids Research, Vol. 37, Issue 15 https://doi.org/10.1093/nar/gkp436	journal	June 2009
Coarse-grained modelling of the structural properties of DNA origami Snodin, Benedict E. K.; Schreck, John S.; Romano, Flavio Nucleic Acids Research, Vol. 47, Issue 3 https://doi.org/10.1093/nar/gky1304	journal	January 2019
Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion Green, S. J.; Bath, J.; Turberfield, A. J. Physical Review Letters, Vol. 101, Issue 23 https://doi.org/10.1103/PhysRevLett.101.238101	journal	December 2008
Nanoscale rotary apparatus formed from tight-fitting 3D DNA components Ketterer, Philip; Willner, Elena M.; Dietz, Hendrik Science Advances, Vol. 2, Issue 2 https://doi.org/10.1126/sciadv.1501209	journal	February 2016
Uncovering the forces between nucleosomes using DNA origami Funke, Jonas J.; Ketterer, Philip; Lieleg, Corinna Science Advances, Vol. 2, Issue 11 https://doi.org/10.1126/sciadv.1600974	journal	November 2016
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades Qian, L.; Winfree, E. Science, Vol. 332, Issue 6034 https://doi.org/10.1126/science.1200520	journal	June 2011
A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads Douglas, S. M.; Bachelet, I.; Church, G. M. Science, Vol. 335, Issue 6070 https://doi.org/10.1126/science.1214081	journal	February 2012
Tug-of-War in Motor Protein Ensembles Revealed with a Programmable DNA Origami Scaffold Derr, N. D.; Goodman, B. S.; Jungmann, R. Science, Vol. 338, Issue 6107 https://doi.org/10.1126/science.1226734	journal	October 2012
Casting inorganic structures with DNA molds Sun, W.; Boulais, E.; Hakobyan, Y. Science, Vol. 346, Issue 6210 https://doi.org/10.1126/science.1258361	journal	October 2014
Molecular force spectroscopy with a DNA origami–based nanoscopic force clamp Nickels, Philipp C.; Wünsch, Bettina; Holzmeister, Phil Science, Vol. 354, Issue 6310 https://doi.org/10.1126/science.aah5974	journal	October 2016
A self-assembled nanoscale robotic arm controlled by electric fields Kopperger, Enzo; List, Jonathan; Madhira, Sushi Science, Vol. 359, Issue 6373 https://doi.org/10.1126/science.aao4284	journal	January 2018

Similar Records

A DNA molecular printer capable of programmable positioning and patterning in two dimensions

Journal Article · 2022 · Science Robotics · OSTI ID:1863930

Benson, Erik; Marzo, Rafael Carrascosa; Bath, Jonathan; +1 more

Multilayer DNA Origami with Terminal Interfaces That Are Flat and Wide-Area

Journal Article · 2023 · ACS Nano · OSTI ID:2367585

Kilwing, Luzia; Lill, Pascal; Nathwani, Bhavik; +4 more

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Journal Article · 2023 · Angewandte Chemie · OSTI ID:2203578

Yang, Yunqi; Lu, Qinyi; Chen, Yu; +4 more

Related Subjects

77 NANOSCIENCE AND NANOTECHNOLOGY
DNA mechanisms
DNA nanotechnology
DNA origami
linear actuators
self‐assembly

Title: Strategies for Constructing and Operating DNA Origami Linear Actuators

Citation Formats

References (50)

Similar Records

Related Subjects