The Kinematic Principle for Designing Deoxyribose Nucleic Acid Origami Mechanisms: Challenges and Opportunities1

2017 ◽  
Vol 139 (6) ◽  
Author(s):  
Hai-Jun Su ◽  
Carlos E. Castro ◽  
Alexander E. Marras ◽  
Lifeng Zhou
Keyword(s):  
Nucleic Acid ◽  
Self Assembly ◽  
Three Dimensional ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Computational Tools ◽  
Deoxyribose Nucleic Acid ◽  
Double Stranded Dna ◽  
Kinematic Mechanisms ◽  
And Robotics

Deoxyribose nucleic acid (DNA) origami nanotechnology is a recently developed self-assembly process for design and fabrication of complex three-dimensional (3D) nanostructures using DNA as a functional material. This paper reviews our recent progress in applying DNA origami to design kinematic mechanisms at the nanometer scale. These nanomechanisms, which we call DNA origami mechanisms (DOM), are made of relatively stiff bundles of double-stranded DNA (dsDNA), which function as rigid links, connected by highly compliant single-stranded DNA (ssDNA) strands, which function as kinematic joints. The design of kinematic joints including revolute, prismatic, cylindrical, universal, and spherical is presented. The steps as well as necessary software or experimental tools for designing DOM with DNA origami links and joints are detailed. To demonstrate the designs, we presented the designs of Bennett four-bar and crank–slider linkages. Finally, a list of technical challenges such as design automation and computational modeling are presented. These challenges could also be opportunities for mechanism and robotics community to apply well-developed kinematic theories and computational tools to the design of nanorobots and nanomachines.

The Kinematic Principle for Designing DNA Origami Mechanisms: Challenges and Opportunities

2015 ◽  
Author(s):  
Hai-Jun Su ◽  
Carlos E. Castro ◽  
Alexander E. Marras ◽  
Lifeng Zhou
Keyword(s):  
Self Assembly ◽  
Design Automation ◽  
Functional Materials ◽  
Dna Origami ◽  
Nanometer Scale ◽  
Computational Tools ◽  
Double Stranded Dna ◽  
Challenges And Opportunities ◽  
Kinematic Mechanisms ◽  
And Robotics

DNA origami nanotechnology is a recently developed self-assembly process for design and fabrication of complex 3D nanostructures using DNA as functional materials. This paper aims to review our recent progress in applying DNA origami to design of kinematic mechanisms of nanometer scale. These nanomechanisms, which we call DNA Origami Mechanisms (DOM), are made of relatively stiff bundles of double-stranded DNA (dsDNA) which function as rigid links, connected by highly compliant single-stranded DNA (ssDNA) strands which function as kinematic joints. The designs of kinematic joints such as revolute, prismatic, cylindrical, universal and spherical are presented. The steps as well as necessary software or experimental tools for designing DOM with DNA origami links and joints are detailed. To demonstrate the designs, we presented the designs of Bennett 4-bar and crank-slider linkages. At last, a list of technical challenges such as design automation, computational modeling are presented. These challenges could also be opportunities for mechanism and robotics community to apply the well developed kinematic theories and computational tools to design of nanorobots and nanomachines.

DNA-Based Self-Assembly of Gold Nanostructures

2020 ◽  
Author(s):  
Song J
Keyword(s):  
Gold Nanoparticles ◽  
Chemical Stability ◽  
Self Assembly ◽  
Three Dimensional ◽  
Dna Nanotechnology ◽  
Dna Origami ◽  
Gold Nanostructures ◽  
Two Dimensional ◽  
Specific Targeting ◽  
Targeting Ability

Plasmonic assemblies of gold nanoparticles (AuNPs) triggered by DNA exhibited excellent biocompatibility and specific-targeting ability. Moreover, the integration of AuNPs and DNA allows the DNA scaffolds exhibit greater chemical stability and optical plasmonic properties. In this mini review, we summarized the development of DNA nanotechnology, especially DNA framework and DNA origami that were employed to fabricate two-dimensional and three-dimensional (3D) Au nanoassembled nanostructures.

Design of DNA Origami Machines and Mechanisms

2012 ◽  
Author(s):  
Alex E. Marras ◽  
Haijun J. Su ◽  
Carlos E. Castro
Keyword(s):  
Self Assembly ◽  
Degrees Of Freedom ◽  
Higher Order ◽  
Dna Origami ◽  
Motion Path ◽  
3D Structures ◽  
Detail Design ◽  
Macro Scale ◽  
Viable Approach ◽  
Kinematic Mechanisms

This research introduces DNA origami as a viable approach to design and fabricate nanoscale mechanisms and machines. DNA origami is a recently developed nanotechnology that has enabled the construction of objects with unprecedented nanoscale geometric complexity via self-assembly. These objects are made up of thousands of DNA base-pairs packed into 3D structures with typical dimensions of 10–100nm. The majority of DNA origami research to date focuses on assembly of static 2D or 3D structures. In this work, we aim to extend the scope of DNA origami to include design of objects with kinematically constrained moving parts. Borrowing concepts from macro-scale kinematic mechanisms, we propose the concept of DNA Origami Mechanisms and Machines (DOMM) comprised of multiple links connected by joints. The links are designed by bundling double stranded DNA (dsDNA) helices to achieve the desired geometry and stiffness. The joints are designed by combining links with strategic placement flexible single stranded DNA (ssDNA) to enable motion in specific degrees of freedom. We detail design approaches for links and common joints including revolute, prismatic, and spherical, and discuss their integration into higher order mechanisms. As a proof of concept, we built a nanoscale hinge (revolute joint) and integrated four of these hinges into a prototype DOMM, namely a Bennett 4-bar linkage, which can be completely folded into a closed bundle geometry and unfolded into an open square geometry with a specified kinematic motion path. A kinematic analysis shows that the DNA Bennett linkage closely follows the 3D motion path of the rigid body counterpart. Our results demonstrate that DNA origami has high potential for the design and assembly of nanoscale machines. The ultimate goal of this work is to develop a library of nanoscale DNA-based links and joints that can be widely used in the design and assembly of higher order mechanisms and machines. We anticipate that, in the future, these components can be used to build nanorobots for useful applications including drug delivery, nanomanufacturing, and biosensing.

Pseudorigid-Body Models of Compliant DNA Origami Mechanisms

2016 ◽  
Vol 8 (5) ◽  
Author(s):  
Lifeng Zhou ◽  
Alexander E. Marras ◽  
Carlos E. Castro ◽  
Hai-Jun Su
Keyword(s):  
Self Assembly ◽  
Strain Energy ◽  
Compliant Mechanism ◽  
Mechanical Energy ◽  
Thermal Fluctuations ◽  
Dna Origami ◽  
Analysis Method ◽  
Double Stranded Dna ◽  
Compliant Joint ◽  
Flexible Parts

In this paper, we introduce a strategy for the design and computational analysis of compliant DNA origami mechanisms (CDOMs), which are compliant nanomechanisms fabricated via DNA origami self-assembly. The rigid, compliant, and flexible parts are constructed by bundles of many double-stranded DNA (dsDNA) helices, bundles of a few dsDNA helices or a single dsDNA helix, and single-stranded DNA (ssDNA) strands, respectively. Similar to its macroscopic counterparts, a CDOM generates its motion via deformation of at least one structural member. During the motion, strain energy is stored and released in the compliant components. Therefore, these CDOMs have the advantage of suppressing thermal fluctuations due to the internal mechanical energy barrier for motion. Here, we show that classic pseudorigid-body (PRB) models for compliant mechanism are successfully employed to the analysis of these DNA origami nanomechanisms and can serve to guide the design and analysis method. An example of compliant joint and a bistable four-bar CDOM fabricated with DNA origami are presented.

In vitro and in vivo polysaccharides assembly: ultrastructural and cytochemical study of growing plant cell wall components.

1978 ◽  
Vol 36 (2) ◽  
pp. 434-435
Author(s):  
D. Reis ◽  
B. Vian ◽  
J. C. Roland
Keyword(s):  
Cell Wall ◽  
Self Assembly ◽  
Plant Cell Wall ◽  
Higher Plants ◽  
Three Dimensional ◽  
Cytochemical Study ◽  
Wall Components

Wall morphogenesis in higher plants is a problem still open to controversy. Until now the possibility of a transmembrane control and the involvement of microtubules were mostly envisaged. Self-assembly processes have been observed in the case of walls of Chlamydomonas and bacteria. Spontaneous gelling interactions between xanthan and galactomannan from Ceratonia have been analyzed very recently. The present work provides indications that some processes of spontaneous aggregation could occur in higher plants during the formation and expansion of cell wall.Observations were performed on hypocotyl of mung bean (Phaseolus aureus) for which growth characteristics and wall composition have been previously defined.In situ, the walls of actively growing cells (primary walls) show an ordered three-dimensional organization (fig. 1). The wall is typically polylamellate with multifibrillar layers alternately transverse and longitudinal. Between these layers intermediate strata exist in which the orientation of microfibrils progressively rotates. Thus a progressive change in the morphogenetic activity occurs.

Nanoscale Self-Assembly Using Ion and Electron Beam Techniques: A Rapid Review

MRS Advances ◽  
2020 ◽  
Vol 5 (64) ◽  
pp. 3507-3520
Author(s):  
Chunhui Dai ◽  
Kriti Agarwal ◽  
Jeong-Hyun Cho
Keyword(s):  
Electron Beam ◽  
Self Assembly ◽  
Ion Beam ◽  
Three Dimensional ◽  
The Self ◽  
Stress Generation ◽  
Rapid Review ◽  
High Yield ◽  
3D Nanostructures ◽  
Self Assembled

AbstractNanoscale self-assembly, as a technique to transform two-dimensional (2D) planar patterns into three-dimensional (3D) nanoscale architectures, has achieved tremendous success in the past decade. However, an assembly process at nanoscale is easily affected by small unavoidable variations in sample conditions and reaction environment, resulting in a low yield. Recently, in-situ monitored self-assembly based on ion and electron irradiation has stood out as a promising candidate to overcome this limitation. The usage of ion and electron beam allows stress generation and real-time observation simultaneously, which significantly enhances the controllability of self-assembly. This enables the realization of various complex 3D nanostructures with a high yield. The additional dimension of the self-assembled 3D nanostructures opens the possibility to explore novel properties that cannot be demonstrated in 2D planar patterns. Here, we present a rapid review on the recent achievements and challenges in nanoscale self-assembly using electron and ion beam techniques, followed by a discussion of the novel optical properties achieved in the self-assembled 3D nanostructures.

scholarly journals Picosecond time-resolved photon antibunching measures nanoscale exciton motion and the true number of chromophores

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gordon J. Hedley ◽  
Tim Schröder ◽  
Florian Steiner ◽  
Theresa Eder ◽  
Felix J. Hofmann ◽  
...  
Keyword(s):  
Rational Design ◽  
Three Dimensional ◽  
Dna Origami ◽  
Fluorescent Nanoparticles ◽  
Time Resolved ◽  
Exciton Diffusion ◽  
Polymer Aggregates ◽  
True Number ◽  
Particle Level ◽  
Photon Antibunching

AbstractThe particle-like nature of light becomes evident in the photon statistics of fluorescence from single quantum systems as photon antibunching. In multichromophoric systems, exciton diffusion and subsequent annihilation occurs. These processes also yield photon antibunching but cannot be interpreted reliably. Here we develop picosecond time-resolved antibunching to identify and decode such processes. We use this method to measure the true number of chromophores on well-defined multichromophoric DNA-origami structures, and precisely determine the distance-dependent rates of annihilation between excitons. Further, this allows us to measure exciton diffusion in mesoscopic H- and J-type conjugated-polymer aggregates. We distinguish between one-dimensional intra-chain and three-dimensional inter-chain exciton diffusion at different times after excitation and determine the disorder-dependent diffusion lengths. Our method provides a powerful lens through which excitons can be studied at the single-particle level, enabling the rational design of improved excitonic probes such as ultra-bright fluorescent nanoparticles and materials for optoelectronic devices.

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 Polymer cyclization for the emergence of hierarchical nanostructures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chaojian Chen ◽  
Manjesh Kumar Singh ◽  
Katrin Wunderlich ◽  
Sean Harvey ◽  
Colette J. Whitfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Hierarchical Structures ◽  
Structural Similarity ◽  
Vital Role ◽  
Nanomaterial Synthesis ◽  
Wide Range ◽  
Linear Poly ◽  
Polymer Folding ◽  
Dynamics Simulations

AbstractThe creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here we demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike and higher-ordered structures. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.

scholarly journals A mini DNA-RNA hybrid origami nanobrick

2021 ◽  
Author(s):  
Lifeng Zhou ◽  
Arun Richard Chandrasekaran ◽  
Mengwen Yan ◽  
Vibhav A. Valsangkar ◽  
Jeremy I. Feldblyum ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Origami ◽  
Complex Geometries ◽  
Single Stranded Dna ◽  
Dna Scaffold

DNA origami is typically used to fold a long single-stranded DNA scaffold into nanostructures with complex geometries using many short DNA staple strands. Integration of RNA into nucleic acid nanostructures...

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