scholarly journals Modelling DNA origami self-assembly at the domain level

2015 ◽  
Vol 143 (16) ◽  
pp. 165102 ◽  
Author(s):  
Frits Dannenberg ◽  
Katherine E. Dunn ◽  
Jonathan Bath ◽  
Marta Kwiatkowska ◽  
Andrew J. Turberfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Domain Level

scholarly journals Automated exploration of DNA-based structure self-assembly networks

2021 ◽  
Vol 8 (10) ◽  
Author(s):  
L. Cazenille ◽  
A. Baccouche ◽  
N. Aubert-Kato
Keyword(s):  
Dna Sequences ◽  
Self Assembly ◽  
Search Space ◽  
Dna Origami ◽  
Reaction Pathways ◽  
Reaction Networks ◽  
Dna Structures ◽  
Search Spaces ◽  
Dna Strands ◽  
Domain Level

Finding DNA sequences capable of folding into specific nanostructures is a hard problem, as it involves very large search spaces and complex nonlinear dynamics. Typical methods to solve it aim to reduce the search space by minimizing unwanted interactions through restrictions on the design (e.g. staples in DNA origami or voxel-based designs in DNA Bricks). Here, we present a novel methodology that aims to reduce this search space by identifying the relevant properties of a given assembly system to the emergence of various families of structures (e.g. simple structures, polymers, branched structures). For a given set of DNA strands, our approach automatically finds chemical reaction networks (CRNs) that generate sets of structures exhibiting ranges of specific user-specified properties, such as length and type of structures or their frequency of occurrence. For each set, we enumerate the possible DNA structures that can be generated through domain-level interactions, identify the most prevalent structures, find the best-performing sequence sets to the emergence of target structures, and assess CRNs' robustness to the removal of reaction pathways. Our results suggest a connection between the characteristics of DNA strands and the distribution of generated structure families.

scholarly journals Co-self-assembly of multiple DNA origami nanostructures in a single pot

2021 ◽  
Author(s):  
Joshua A. Johnson ◽  
Vasiliki Kolliopoulos ◽  
Carlos E. Castro
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Folding Pathways

We demonstrate co-self-assembly of two distinct DNA origami structures with a common scaffold strand through programmable bifurcation of folding pathways.

scholarly journals A Structurally Variable Hinged Tetrahedron Framework from DNA Origami

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
David M. Smith ◽  
Verena Schüller ◽  
Carsten Forthmann ◽  
Robert Schreiber ◽  
Philip Tinnefeld ◽  
...  
Keyword(s):  
Self Assembly ◽  
Gel Electrophoresis ◽  
Imaging Techniques ◽  
Building Blocks ◽  
Dna Origami ◽  
Microscopy Technique ◽  
Wire Frame ◽  
Wide Range ◽  
Potential Applications ◽  
Linker Molecules

Nanometer-sized polyhedral wire-frame objects hold a wide range of potential applications both as structural scaffolds as well as a basis for synthetic nanocontainers. The utilization of DNA as basic building blocks for such structures allows the exploitation of bottom-up self-assembly in order to achieve molecular programmability through the pairing of complementary bases. In this work, we report on a hollow but rigid tetrahedron framework of 75 nm strut length constructed with the DNA origami method. Flexible hinges at each of their four joints provide a means for structural variability of the object. Through the opening of gaps along the struts, four variants can be created as confirmed by both gel electrophoresis and direct imaging techniques. The intrinsic site addressability provided by this technique allows the unique targeted attachment of dye and/or linker molecules at any point on the structure's surface, which we prove through the superresolution fluorescence microscopy technique DNA PAINT.

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates

2009 ◽  
Vol 5 (1) ◽  
pp. 61-66 ◽  
Author(s):  
Hareem T. Maune ◽  
Si-ping Han ◽  
Robert D. Barish ◽  
Marc Bockrath ◽  
William A. Goddard III ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Self Assembly ◽  
Dna Origami ◽  
Two Dimensional

scholarly journals Self-assembly of highly ordered DNA origami lattices at solid-liquid interfaces by controlling cation binding and exchange

Nano Research ◽  
2020 ◽  
Vol 13 (11) ◽  
pp. 3142-3150 ◽  
Author(s):  
Yang Xin ◽  
Salvador Martinez Rivadeneira ◽  
Guido Grundmeier ◽  
Mario Castro ◽  
Adrian Keller
Keyword(s):  
Correlation Length ◽  
Self Assembly ◽  
High Speed ◽  
Time Course ◽  
Divalent Cations ◽  
Topological Analysis ◽  
Monovalent Cation ◽  
Cation Binding ◽  
Dna Origami ◽  
Lattice Order

Abstract The surface-assisted hierarchical self-assembly of DNA origami lattices represents a versatile and straightforward method for the organization of functional nanoscale objects such as proteins and nanoparticles. Here, we demonstrate that controlling the binding and exchange of different monovalent and divalent cation species at the DNA-mica interface enables the self-assembly of highly ordered DNA origami lattices on mica surfaces. The development of lattice quality and order is quantified by a detailed topological analysis of high-speed atomic force microscopy (HS-AFM) images. We find that lattice formation and quality strongly depend on the monovalent cation species. Na+ is more effective than Li+ and K+ in facilitating the assembly of high-quality DNA origami lattices, because it is replacing the divalent cations at their binding sites in the DNA backbone more efficiently. With regard to divalent cations, Ca2+ can be displaced more easily from the backbone phosphates than Mg2+ and is thus superior in guiding lattice assembly. By independently adjusting incubation time, DNA origami concentration, and cation species, we thus obtain a highly ordered DNA origami lattice with an unprecedented normalized correlation length of 8.2. Beyond the correlation length, we use computer vision algorithms to compute the time course of different topological observables that, overall, demonstrate that replacing MgCl2 by CaCl2 enables the synthesis of DNA origami lattices with drastically increased lattice order.

Use DNA origami as a scaffold for self-assembly of optical metamolecules

2015 ◽  
Author(s):  
Yoon Jo Hwang ◽  
Shelley F. J. Wickham ◽  
Steven D. Perrault ◽  
Sanghyun Yoo ◽  
Sung Ha Park ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Origami

DNA Origami Guided Self-Assembly of Plasmonic Polymers with Robust Long-Range Plasmonic Resonance

Nano Letters ◽  
2020 ◽  
Vol 20 (12) ◽  
pp. 8926-8932
Author(s):  
Pengfei Wang ◽  
Ji-Hyeok Huh ◽  
Haedong Park ◽  
Donglei Yang ◽  
Yingwei Zhang ◽  
...  
Keyword(s):  
Long Range ◽  
Self Assembly ◽  
Dna Origami ◽  
Plasmonic Resonance

Complexing DNA Origami Frameworks through Sequential Self-Assembly Based on Directed Docking

2018 ◽  
Vol 130 (24) ◽  
pp. 7179-7183 ◽  
Author(s):  
Yuki Suzuki ◽  
Hiroshi Sugiyama ◽  
Masayuki Endo
Keyword(s):  
Self Assembly ◽  
Dna Origami

Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials

2016 ◽  
Vol 138 (24) ◽  
pp. 7733-7740 ◽  
Author(s):  
Pengfei Wang ◽  
Stavros Gaitanaros ◽  
Seungwoo Lee ◽  
Mark Bathe ◽  
William M. Shih ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Two Dimensional ◽  
Plasmonic Metamaterials

scholarly journals Programmed self-assembly of DNA origami nanoblocks into anisotropic higher-order nanopatterns

2013 ◽  
Vol 58 (21) ◽  
pp. 2646-2650 ◽  
Author(s):  
YanMing Fu ◽  
Jie Chao ◽  
HuaJie Liu ◽  
ChunHai Fan
Keyword(s):  
Self Assembly ◽  
Higher Order ◽  
Dna Origami
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