Multilayer DNA Origami Packed on a Square Lattice

Ke, Yonggang; Douglas, Shawn M.; Liu, Minghui; Sharma, Jaswinder; Cheng, Anchi; Leung, Albert; Liu, Yan; Shih, William M.; Yan, Hao

doi:10.1021/ja906381y

Cited by 386 publications

(352 citation statements)

References 30 publications

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“…The global shape of the reconstructed density is in agreement with the designed topology of the object. The overall dimensions of the object and the extent of global twist that results from a mismatch of B-form DNA helicity and the imposed squarelattice packing also agree with a prediction (21,22) when using 2.6-nm effective helix diameter and 10.44 bp/turn reciprocal twist density (17) (Fig. S5).…”

supporting

confidence: 72%

“…Molecular self-assembly with DNA is considered a candidate route to achieve this goal (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). Densely packed 3D DNA-origami objects (14)(15)(16)(17)(18) seem particularly suited for use as rigid scaffolds to position reactive groups at target locations in space, and to implement features known from natural macromolecular complexes, such as shape complementarity and controlled domain movement. Designing such objects to meet precise structural specifications will benefit strongly from detailed 3D structural feedback.…”

mentioning

confidence: 99%

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Cryo-EM structure of a 3D DNA-origami object

Bai

Martin

Scheres

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

239

266

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A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNAtemplated design steered by structural feedback.N atural macromolecular machines have complex 3D shapes with subnanometer-precise structural features that enable executing tasks such as signal transduction, molecular transport, and enzymatic catalysis (1). A key goal for nanotechnology is to fabricate synthetic objects with similarly precise features to ultimately control tasks known today only from natural "nanomachines." Molecular self-assembly with DNA is considered a candidate route to achieve this goal (2-13). Densely packed 3D DNA-origami objects (14-18) seem particularly suited for use as rigid scaffolds to position reactive groups at target locations in space, and to implement features known from natural macromolecular complexes, such as shape complementarity and controlled domain movement. Designing such objects to meet precise structural specifications will benefit strongly from detailed 3D structural feedback. Here we present a cryo-EM map of an asymmetric, densely packed DNA object that comprises 15,238 nt in 164 chains. Combined with prior knowledge about the topology of chain connectivity, this map provided sufficient detail to construct a full pseudoatomic model for this particle. Thereby, our results provide structural feedback on DNA-templated design that will prove valuable for the design of complex functionalities.Results and Discussion DNA-Templated Design and Synthesis. Our DNA object was designed to be suitable for structure determination by cryo-EM singleparticle analysis, because the choice of a distinctly asymmetric shape facilitated the recognition of different particle orientations in electron micrographs (Fig. 1A). The object was designed to assemble as 82 parallel dsDNA helices of varying length in a square lattice (17) of 10 columns and 12 rows and comprising a total of 15,238 nt with a molecular mass of 4.8 MDa (Fig. S1). A total of 740 nt were distributed among flexible loops at the ends of the helices to prevent aggregation by blunt-end stacking (19). Synthesis of the object was based on templated molecular selfassembly (3) with a 7,249-nt-long "scaffold" DNA strand derived from M13 bacteriophage an...

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supporting

confidence: 72%

mentioning

confidence: 99%

Cryo-EM structure of a 3D DNA-origami object

Bai

Martin

Scheres

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

239

266

View full text Add to dashboard Cite

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“…Examples of structures designed include the square nut, railed bridge, genie bottle, stacked cross, slotted cross, and monolith shapes (Figure 3) [7]. Multi-layer, highly compact lattice patterns have also been developed based on the square lattice [8]. Additionally, multi-layer lattice patterns curved into barrels of controlled diameter have been developed, with the potential to create electronic or optic wires at the molecular level [9].…”

Section: D Dna Origamimentioning

confidence: 99%

Beyond the smiley face: applications of structural DNA nanotechnology

Arora

Silva

2018

Nano Reviews & Experiments

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Since the development of DNA origami by Paul Rothemund in 2006, the field of structural DNA nanotechnology has undergone tremendous growth. Through DNA origami and related approaches, self-assembly of specified DNA sequences allows for the ‘bottom-up’ construction of diverse nanostructures. By utilizing different sets of small ‘staple’ DNA strands to direct the folding of a long scaffold strand in diverse ways, DNA origami has particularly been incorporated into a variety of prototypical applications beyond the two-dimensional (2D) smiley face. In this review, the basis of DNA nanotechnology, methods of self-assembly, and Rothemund’s DNA origami breakthrough are discussed first. Next, some of the most promising applications of structural DNA nanotechnology since 2006 are summarized. These include utilizing DNA origami as a tool for creating 3D nanostructures (including DNA bricks), as well as structural (ligand capsid binding, viral capsid binding, DNA NanoOctahedron, DNA mold, photonic devices, energy transfer units), and dynamic (DNA box-with-lid, DNA nano-robot, DNA barges, amphipathic DNA structures, DNA nanocircuits) applications of DNA origami.

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“…(c) Arrangement of double helices on a hexagonal lattice (view along the helix axis) is commensurable with DNA's natural helix rise (10.5 bp/turn = 3 × 7 bp for two turns) and thus allows for unstrained three-dimensional assemblies. (d) Multilayered arrangement on a rectangular lattice is also possible (but potentially requires strain correction) and results in a higher packing density of helices (Ke et al 2009). The origami structure depicted in (a) and (b) is the special case of a single-layer DNA origami.…”

Section: A Brief Overview Of Structural Dna Nanotechnologymentioning

confidence: 99%

DNA origami – art, science, and engineering

Simmel¹

2012

Frontiers in Life Science

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The DNA origami method is an extraordinarily powerful and robust method for the assembly of almost arbitrarily shaped nanoscale objects made from DNA. Technological advances such as DNA origami and the availability of a range of computational tools have transformed DNA self-assembly from an art into a genuine engineering discipline. Investigators with diverse backgrounds are now beginning to use the origami method in their field of research. Potential applications range from single molecule bio-and nanophysics over structural biology to synthetic biology and nanomedicine. This article discusses the transition of DNA nanotechnology to molecular scale engineering and describes, citing several examples, the power and utility of DNA origami for scientific research.Keywords: DNA nanotechnology; bioengineering; synthetic biology IntroductionThe past few years have seen tremendous progress in the field of DNA nanotechnology. This progress is a result of a variety of technical advances in the production of DNAbased nanoscale structures, which have opened up the field to a much larger group of researchers than maybe 10 years ago. Most notably, the "DNA origami" technique provides a conceptually simple and robust method for the assembly of molecular nanostructures at high yield. The method can in principle be automatized and therefore may be regarded as one of the first successful examples for genuine nanoscale engineering utilizing nanoscale self-assembly.In this article, the transformation of DNA nanotechnology from an "art" to a "technology" will be briefly discussed. A few emerging applications of this technology will be described, notably applications as tools for single-molecule studies as well as applications in nanoscale physics and nanomedicine. The article also briefly addresses the question whether DNA nanotechnology has to be seen as an engineering discipline that simply provides nanoscale researchers with an enabling technology or whether it itself leads to novel and fundamental scientific questions.

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Multilayer DNA Origami Packed on a Square Lattice

Cited by 386 publications

References 30 publications

Cryo-EM structure of a 3D DNA-origami object

Cryo-EM structure of a 3D DNA-origami object

Beyond the smiley face: applications of structural DNA nanotechnology

DNA origami – art, science, and engineering

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