DNA Ring Motif with Flexible Joints

DNA and peptides are two of the most commonly used biomolecules for building self-assembling materials, but few examples exist of hybrid nanostructures that contain both components. Here we report the modification of two peptides that comprise a coiled-coil heterodimer pair with orthogonal DNA handles in order to link DNA origami nanostructures bearing complementary strands into micrometer long one-dimensional arrays. We probed the effect of number of coils on self-assembly and demonstrated the formation of self-assembled structures through multiple routes, to form dimers and trimers, an alternating copolymer of two different origami bundles, and stepwise assembly of purified structures with coiled-coil conjugates. Our results demonstrate the successful merging of two distinct self-assembly modes to create hybrid bionanomaterials expected to have a range of potential applications in the future.

Download Full-text

Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures

Beilstein Journal of Nanotechnology ◽

10.3762/bjnano.7.87 ◽

2016 ◽

Vol 7 ◽

pp. 948-956 ◽

Cited By ~ 1

Author(s):

Anja Henning-Knechtel ◽

Matthew Wiens ◽

Mathias Lakatos ◽

Andreas Heerwig ◽

Frieder Ostermaier ◽

...

Keyword(s):

Gold Nanoparticle ◽

Self Assembly ◽

Metallic Nanoparticles ◽

Linear Chain ◽

Construction Materials ◽

Dna Origami ◽

Hybrid Structures ◽

Dna Nanostructures ◽

Electrode Structure ◽

Electrical Field Strength

DNA nanostructures are promising construction materials to bridge the gap between self-assembly of functional molecules and conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac dielectrophoresis. The dielectrophoretic behavior was investigated employing fluorescence microscopy. For the pristine origami, a significant dielectrophoretic response was found to take place in the megahertz range, whereas, due to the higher polarizability of the metallic nanoparticles, the nanoparticle/DNA hybrid structures required a lower electrical field strength and frequency for a comparable trapping at the edges of the electrode structure. The nanoparticle conjugation additionally resulted in a remarkable alteration of the DNA structure arrangement. The growth of linear, chain-like structures in between electrodes at applied frequencies in the megahertz range was observed. The long-range chain formation is caused by a local, gold nanoparticle-induced field concentration along the DNA nanostructures, which in turn, creates dielectrophoretic forces that enable the observed self-alignment of the hybrid structures.

Download Full-text

Control of the stepwise assembly–disassembly of DNA origami nanoclusters by pH stimuli-responsive DNA triplexes

Nanoscale ◽

10.1039/c9nr05047g ◽

2019 ◽

Vol 11 (39) ◽

pp. 18026-18030 ◽

Cited By ~ 1

Author(s):

Shuo Yang ◽

Wenyan Liu ◽

Risheng Wang

Keyword(s):

Self Assembly ◽

Dna Origami ◽

Dna Nanostructures ◽

Stimuli Responsive ◽

Dna Triplexes ◽

Stepwise Assembly

We demonstrate the pH-regulated, multistep self-assembly of DNA nanostructures by employing DNA triplexes as dynamic linkers in a stepwise, selective, and reversible fashion.

Download Full-text

Directed Self-Assembly of Polystyrene Nanospheres by Direct Laser-Writing Lithography

Nanomaterials ◽

10.3390/nano10020280 ◽

2020 ◽

Vol 10 (2) ◽

pp. 280

Author(s):

Eleonora Cara ◽

Federico Ferrarese Lupi ◽

Matteo Fretto ◽

Natascia De Leo ◽

Mauro Tortello ◽

...

Keyword(s):

Self Assembly ◽

Large Scale ◽

The Self ◽

Assembly Process ◽

Systematic Assessment ◽

Self Assembling ◽

Polystyrene Nanospheres ◽

Direct Laser ◽

Novel Method ◽

Spinning Speed

In this work, we performed a systematic study on the effect of the geometry of pre-patterned templates and spin-coating conditions on the self-assembling process of colloidal nanospheres. To achieve this goal, large-scale templates, with different size and shape, were generated by direct laser-writer lithography over square millimetre areas. When deposited over patterned templates, the ordering dynamics of the self-assembled nanospheres exhibits an inverse trend with respect to that observed for the maximisation of the correlation length ξ on a flat surface. Furthermore, the self-assembly process was found to be strongly dependent on the height (H) of the template sidewalls. In particular, we observed that, when H is 0.6 times the nanospheres diameter and spinning speed 2500 rpm, the formation of a confined and well ordered monolayer is promoted. To unveil the defects generation inside the templates, a systematic assessment of the directed self-assembly quality was performed by a novel method based on Delaunay triangulation. As a result of this study, we found that, in the best deposition conditions, the self-assembly process leads to well-ordered monolayer that extended for tens of micrometres within the linear templates, where 96.2% of them is aligned with the template sidewalls.

Download Full-text

DNA Origami “Quick” Refolding inside of a Micron-Sized Compartment

Molecules ◽

10.3390/molecules25010008 ◽

2019 ◽

Vol 25 (1) ◽

pp. 8 ◽

Cited By ~ 2

Author(s):

Taiki Watanabe ◽

Yusuke Sato ◽

Hayato Otaka ◽

Ibuki Kawamata ◽

Satoshi Murata ◽

...

Keyword(s):

Self Assembly ◽

Average Diameter ◽

Test Tube ◽

Dna Origami ◽

Bulk Solution ◽

Dna Nanostructures ◽

Force Microscopy ◽

Annealing Conditions ◽

Atomic Force ◽

Life Phenomena

Investigations into the refolding of DNA origami leads to the creation of reconstructable nanostructures and deepens our understanding of the sustainability of life. Here, we report the refolding of the DNA origami structure inside a micron-sized compartment. In our experiments, conventional DNA origami and truss-type DNA origami were annealed and purified to remove the excess staples in a test tube. The DNA origami was then encapsulated inside of a micron-sized compartment of water-in-oil droplets, composed of neutral surfactants. The re-annealing process was then performed to initiate refolding in the compartment. The resulting 100-nm-sized DNA nanostructures were observed using atomic force microscopy (AFM), and the qualities of their structures were evaluated based on their shape. We found that the refolding of the DNA origami structure was favored inside the droplets compared with refolding in bulk solution. The refolded structures were able to fold even under “quick” one-minute annealing conditions. In addition, the smaller droplets (average diameter: 1.2 µm) appeared to be more advantageous for the refolding of the origamis than larger droplets. These results are expected to contribute to understanding the principles of life phenomena based on multimolecular polymer self-assembly in a micron-sized compartment, and for the production and maintenance of artificially designed molecules.

Download Full-text

Hierarchical Assembly of DNA Origami Nanostructures Using Coiled-coil Peptides

10.26434/chemrxiv.9789248 ◽

2019 ◽

Author(s):

Alex Buchberger ◽

Chad Simmons ◽

Nour Fahmi ◽

Ronit Freeman ◽

Nicholas Stephanopoulos

Keyword(s):

Self Assembly ◽

Coiled Coil ◽

Dna Origami ◽

Hybrid Nanostructures ◽

Hierarchical Assembly ◽

Alternating Copolymer ◽

Self Assembling ◽

Potential Applications ◽

Multiple Routes ◽

Stepwise Assembly

DNA and peptides are two of the most commonly used biomolecules for building self-assembling materials, but few examples exist of hybrid nanostructures that contain both components. Here we report the modification of two peptides that comprise a coiled-coil heterodimer pair with orthogonal DNA handles in order to link DNA origami nanostructures bearing complementary strands into micrometer long one-dimensional arrays. We probed the effect of number of coils on self-assembly and demonstrated the formation of self-assembled structures through multiple routes, to form dimers and trimers, an alternating copolymer of two different origami bundles, and stepwise assembly of purified structures with coiled-coil conjugates. Our results demonstrate the successful merging of two distinct self-assembly modes to create hybrid bionanomaterials expected to have a range of potential applications in the future.

Download Full-text

Auxetic Two-Dimensional Nanostructures from DNA

10.1101/2020.08.21.262139 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ruixin Li ◽

Haorong Chen ◽

Jong Hyun Choi

Keyword(s):

Self Assembly ◽

Md Simulations ◽

Dna Origami ◽

Coarse Grained ◽

Two Dimensional ◽

Materials Chemistry ◽

Dna Nanostructures ◽

Unit Cells ◽

Materials Used ◽

Architectured Materials

ABSTRACTArchitectured materials exhibit negative Poisson’s ratios and enhanced mechanical properties compared with regular materials. Their auxetic behaviors should emerge from periodic cellular structures regardless of the materials used. The majority of such metamaterials are constructed by top-down approaches and macroscopic with unit cells of microns or larger. On the other extreme, there are molecular-scale auxetics including naturally-occurring crystals which are not designable. There is a gap from few nanometers to microns, which may be filled by bottom-up biomolecular self-assembly. Here we demonstrate two-dimensional auxetic nanostructures using DNA origami. Structural reconfiguration experiments are performed by strand displacement and complemented by mechanical deformation studies using coarse-grained molecular dynamics (MD) simulations. We find that the auxetic properties of DNA nanostructures are mostly defined by geometrical designs, yet materials’ chemistry also plays an important role. From elasticity theory, we introduce a set of design principles for auxetic DNA metamaterials, which should find diverse applications.

Download Full-text

Generating DNA Origami Nanostructures through Shape Annealing

Applied Sciences ◽

10.3390/app11072950 ◽

2021 ◽

Vol 11 (7) ◽

pp. 2950

Author(s):

Bolutito Babatunde ◽

D. Sebastian Arias ◽

Jonathan Cagan ◽

Rebecca E. Taylor

Keyword(s):

Self Assembly ◽

Design Space ◽

Simulated Annealing Algorithm ◽

Dna Nanotechnology ◽

Dna Origami ◽

Design Tools ◽

Dna Nanostructures ◽

Formal Approach ◽

Annealing Algorithm ◽

Structural Dna Nanotechnology

Structural DNA nanotechnology involves the design and self-assembly of DNA-based nanostructures. As a field, it has progressed at an exponential rate over recent years. The demand for unique DNA origami nanostructures has driven the development of design tools, but current CAD tools for structural DNA nanotechnology are limited by requiring users to fully conceptualize a design for implementation. This article introduces a novel formal approach for routing the single-stranded scaffold DNA that defines the shape of DNA origami nanostructures. This approach for automated scaffold routing broadens the design space and generates complex multilayer DNA origami designs in an optimally driven way, based on a set of constraints and desired features. This technique computes unique designs of DNA origami assemblies by utilizing shape annealing, which is an integration of shape grammars and the simulated annealing algorithm. The results presented in this article illustrate the potential of the technique to code desired features into DNA nanostructures.

Download Full-text

Factors Affecting Molecular Self-Assembly and Its Mechanism

Scientific Research Journal ◽

10.24191/srj.v9i1.5385 ◽

2012 ◽

Vol 9 (1) ◽

pp. 43 ◽

Cited By ~ 1

Author(s):

Hueyling Tan

Keyword(s):

Self Assembly ◽

Building Blocks ◽

Molecular Engineering ◽

Molecular Structures ◽

Polymer Science ◽

New Approach ◽

Factors Affecting ◽

Dna Structures ◽

Self Assembling ◽

Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

Download Full-text

Flow Chemistry Controls Both Self-Assembly and the Entrapped Oscillatory Cargo in Belousov-Zhabotinsky Driven Polymerization-Induced Self-Assembly

10.26434/chemrxiv.7895891 ◽

2019 ◽

Author(s):

Liman Hou ◽

Marta Dueñas-Diez ◽

Rohit Srivastava ◽

Juan Perez-Mercader

Keyword(s):

Self Assembly ◽

Flow Chemistry ◽

Batch Reactors ◽

Equilibrium Conditions ◽

One Pot ◽

Bz Reaction ◽

Polymer Vesicles ◽

Simultaneous Control ◽

Novel Method ◽

Continuously Stirred Tank Reactor

Belousov-Zhabotinsky (B-Z) reaction driven polymerization-induced self-assembly (PISA), or B-Z PISA, is a novel method for the autonomous one-pot synthesis of polymer vesicles from a macroCTA (macro chain transfer agent) and monomer solution (“soup”) containing the above and the BZ reaction components. In it, the polymerization is driven (and controlled) by periodically generated radicals generated in the oscillations of the B-Z reaction. These are inhibitor/activator radicals for the polymerization. Until now B-Z PISA has only been carried out in batch reactors. In this manuscript we present the results of running the system using a continuously stirred tank reactor (CSTR) configuration which offers some interesting advantages.Indeed, by controlling the CSTR parameters we achieve reproducible and simultaneous control of the PISA process and of the properties of the oscillatory cargo encapsulated in the resulting vesicles. Furthermore, the use of flow chemistry enables a more precise morphology control and chemical cargo tuning. Finally, in the context of biomimetic applications a CSTR operation mimics more closely the open non-equilibrium conditions of living systems and their surrounding environments.

Download Full-text