Multi-micron crisscross structures from combinatorially assembled DNA-origami slats

Wintersinger, Christopher M.; Minev, Dionis; Ershova, Anastasia; Sasaki, Hiroshi; Gowri, Gokul; Berengut, Jonathan F.; Corea-Dilbert, Flanklin E.; Yin, Peng; Shih, William M.

doi:10.1101/2022.01.06.475243

Cited by 9 publications

(11 citation statements)

References 51 publications

(54 reference statements)

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“…Therefore, precision NP placement within large ribosome-sized macromolecules can be achieved using DNA frameworks. Currently, it is possible to produce addressable DNA structures comprising millions of nucleotides and macroscopic DNA lattices containing ∼10 12 DNA origami components . The ever-expanding dimensions of the DNA-based platforms and the foreseen integrated dynamicity of the assemblies , open opportunities for optically transparent metamaterials, substrates, and devices, for example, with stimuli-triggered responses …”

Section: Dna-guided Assemblymentioning

confidence: 99%

“… 24 They are commonly megadalton-sized (dimensions <100 nm) yet are extendable to the gigadalton scale (dimensions >1 μm). 25 Importantly, DNA origami enables accurate positioning of DNA-conjugated molecular components, even at sub-nanometer resolution. 26 …”

Section: Introductionmentioning

confidence: 99%

“…This is promoted by the robust DNA origami technique, where single-stranded DNA (ssDNA) molecules, called “staples”, fold into predefined 2D or 3D nanostructures through Watson–Crick base pairing . They are commonly megadalton-sized (dimensions <100 nm) yet are extendable to the gigadalton scale (dimensions >1 μm) . Importantly, DNA origami enables accurate positioning of DNA-conjugated molecular components, even at sub-nanometer resolution …”

Section: Introductionmentioning

confidence: 99%

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From Precision Colloidal Hybrid Materials to Advanced Functional Assemblies

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Conspectus The concept of colloids encompasses a wide range of isotropic and anisotropic particles with diverse sizes, shapes, and functions from synthetic nanoparticles, nanorods, and nanosheets to functional biological units. They are addressed in materials science for various functions, while they are ubiquitous in the biological world for multiple functions. A large variety of synthetic colloids have been researched due to their scientific and technological importance; still they characteristically suffer from finite size distributions, imperfect shapes and interactions, and not fully engineered functions. This contrasts with biological colloids that offer precision in their size, shape, and functionality. Materials science has searched for inspiration from the biological world to allow structural control by self-assembly and hierarchy and to identify novel routes for combinations of functions in bio-inspiration. Herein, we first discuss different approaches for highly defined structural control of technically relevant synthetic colloids based on guided assemblies of biological motifs. First, we describe how polydisperse nanoparticles can be assembled within hollow protein cages to allow well-defined assemblies and hierarchical packings. Another approach relies on DNA nanotechnology-based assemblies, where engineered DNA structures allow programmed assembly. Then we will discuss synthetic colloids that have either particularly narrow size dispersity or even atomically precise structures for new assemblies and potential functions. Such colloids can have well-defined packings for membranes allowing high modulus. They can be switchable using light-responsive moieties, and they can initiate packing of larger assemblies of different geometrical shapes. The emphasis is on atomically defined nanoclusters that allow well-defined assemblies by supramolecular interactions, such as directional hydrogen bonding. Finally, we will discuss stimulus-responsive colloids for new functions, even toward complex responsive functions inspired by life. Therein, stimulus-responsive materials inspired by biological learning could allow the next generation of such materials. Classical conditioning is among the simplest biological learning concepts, requiring two stimuli and triggerable memory. Therein we use thermoresponsive hydrogels with plasmonic gold nanoparticles and a spiropyran photoacid as a model. Heating is the unconditioned stimulus leading to melting of the thermoresponsive gel, whereas light (at a specified wavelength) originally leads to reduced pH without plasmonic or structural changes because of steric gel stabilization. Under heat-induced gel melting, light results in pH-decrease and chain-like aggregation of the gold nanoparticles, allowing a new plasmonic response. Thus, simultaneous heating and light irradiation allow conditioning for a newly derived stimulus, where the logic diagram is analogous to Pavlovian conditioning. The shown assemblies demonstrate the different functionalitie...

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Section: Dna-guided Assemblymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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From Precision Colloidal Hybrid Materials to Advanced Functional Assemblies

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“…It has become a major technique in the ever-expanding toolbox for sub-nanometer accurate DNA nanostructure design. Currently, automated design paradigms ( Linko and Kostiainen, 2016 ; Huang et al., 2021a ), meshed wireframe structures ( Piskunen et al., 2020 ), ∼10 7 -nt-size discrete/finite structures ( Wintersinger et al, 2022 ), and macroscopic lattices assembled from ∼10 12 individual DNA origami components ( Xin et al., 2021 ) are available. Moreover, inorganic nanostructure engineering ( Heuer-Jungemann and Linko, 2021 ) and versatile chemical modifications for DNA ( Madsen and Gothelf, 2019 ) are accessible for a variety of bioimplementations.…”

Section: Introductionmentioning

confidence: 99%

Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond

et al. 2022

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“…We believe that by circumventing the complexity of the design process and removing the hefty cost and infrastructure associated with DNA origami fabrication, valuable educational milestones can be achieved by young students in fields such as engineering, chemistry, physics, biology, materials science, medicine, and computer science. For example, specific learning opportunities that lie in DNA nanostructure fabrication include topics such as charge screening, mechanical deformations, conformational dynamics and free energy landscapes, nanoscale stimulus response, polymerization, and algorithmic design and assembly [13][14][15][16][17][18] . However, current DNA origami methods are not suitable for translation to classrooms, even for well-equipped instructional laboratories.…”

Section: Introductionmentioning

confidence: 99%

Translating DNA origami Nanotechnology to Middle School, High School, and Undergraduate Laboratories

Beshay

Kucinic

Wile

et al. 2022

Preprint

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DNA origami is a rapidly emerging nanotechnology that enables researchers to create nanostructures with unprecedented geometric precision that have tremendous potential to advance a variety of fields including molecular sensing, robotics, and nanomedicine. Hence, many students could benefit from exposure to basic knowledge of DNA origami nanotechnology. However, due to the complexity of design, cost of materials, and cost of equipment, experiments with DNA origami have been limited mainly to research institutions in graduate level laboratories with significant prior expertise and well-equipped laboratories. This work focuses on overcoming critical barriers to translating DNA origami methods to educational laboratory settings. In particular, we present a streamlined protocol for fabrication and analysis of DNA origami nanostructures that can be carried out within a 2-hour laboratory course using low-cost equipment, much of which is readily available in educational laboratories and science classrooms. We focus this educational experiment module on a DNA origami nanorod structure that was previously developed for drug delivery applications. In addition to fabricating nanostructures, we demonstrate a protocol for students to analyze structures via gel electrophoresis using classroom-ready gel equipment. These results establish a basis to expose students to DNA origami nanotechnology and can enable or reinforce valuable learning milestones in fields such as biomaterials, biological engineering, and nanomedicine. Furthermore, introducing students to DNA nanotechnology and related fields can also have the potential to increase interest and future involvement by young students.

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Multi-micron crisscross structures from combinatorially assembled DNA-origami slats

Cited by 9 publications

References 51 publications

From Precision Colloidal Hybrid Materials to Advanced Functional Assemblies

From Precision Colloidal Hybrid Materials to Advanced Functional Assemblies

Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond

Translating DNA origami Nanotechnology to Middle School, High School, and Undergraduate Laboratories

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