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.

Pseudo-Rigid-Body Models of Compliant DNA Origami Mechanisms

2015 ◽  
Author(s):  
Lifeng Zhou ◽  
Alexander E. Marras ◽  
Carlos E. Castro ◽  
Hai-jun Su
Keyword(s):  
Rigid Body ◽  
Strain Energy ◽  
Compliant Mechanisms ◽  
Compliant Mechanism ◽  
Mechanical Energy ◽  
Energy Landscape ◽  
Thermal Fluctuations ◽  
Dna Origami ◽  
Double Stranded Dna ◽  
Flexible Parts

In this paper, we introduce the strategy of designing and analyzing compliant nanomechanisms fabricated with DNA origami which we call compliant DNA origami mechanism (CDOM). The rigid, compliant and flexible parts are constructed by a bunch of double-stranded DNA (dsDNA) helices, fewer dsDNA helices and single-stranded DNA (ssDNA) strands respectively. Just like in macroscopic compliant mechanisms, a CDOM generates its motion via deformation of at least one structural member. During the motion, strain energy is stored and released in the mechanism. These CDOM can suppress thermal fluctuations due to the internal mechanical energy barrier for motion. An example of compliant hinge joint and a bistable four-bar CDOM fabricated with DNA origami are discussed at the end of this paper. The classic pseudo-rigid-body (PRB) model for compliant mechanism is successfully employed to the analysis of these DNA origami nanomechanisms. This PRB model has been used to guide the design of a bistable CDOM for a desired energy landscape.

scholarly journals Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

2021 ◽  
Vol 11 (5) ◽  
pp. 2357
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Hyeongwoon Lee ◽  
Jong Hyun Choi
Keyword(s):  
Self Assembly ◽  
Mechanical Energy ◽  
Single Layer ◽  
Md Simulations ◽  
Dna Origami ◽  
Coarse Grained ◽  
Initial Curvature ◽  
Coarse Grained Model ◽  
Reconfigurable Structures ◽  
Computational Platform

DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.

scholarly journals Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile

2021 ◽  
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Hyeongwoon Lee ◽  
Jong Hyun Choi
Keyword(s):  
Self Assembly ◽  
Mechanical Energy ◽  
Single Layer ◽  
Md Simulations ◽  
Dna Origami ◽  
Coarse Grained ◽  
Initial Curvature ◽  
Coarse Grained Model ◽  
Reconfigurable Structures ◽  
Computational Platform

ABSTRACTDNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn which is slightly different from that of native B-form DNA (10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.

scholarly journals The synergic role of actomyosin architecture and biased detachment in muscle energetics: insights in cross bridge mechanism beyond the lever-arm swing

2021 ◽  
Author(s):  
Lorenzo Marcucci ◽  
Hiroki Fukunaga ◽  
Toshio Yanagida ◽  
Mitsuhiro Iwaki
Keyword(s):  
Muscle Contraction ◽  
Mechanical Energy ◽  
Monte Carlo Model ◽  
Thermal Fluctuations ◽  
Dna Origami ◽  
Conservation Strategy ◽  
Sliding Velocity ◽  
Muscle Energetics ◽  
Lever Arm

AbstractMuscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here we combined experimental measurements of in vitro sliding velocity based on DNA-origami built filaments carrying myosins with different lever arm length and simulations based on a Monte-Carlo model which accounts for three basic components: (i) the geometrical hindrance, (ii) the mechano-sensing mechanism, and (iii) the biased kinetics for stretched or compressed motors. The model simulations showed that the geometrical hindrance due to acto-myosin spatial mismatching and the preferential detachment of compressed motors are synergic in generating the rapid increase in the ATP-ase rate from isometric to moderate velocities of contraction, thus acting as an energy-conservation strategy in muscle contraction. The velocity measurements on a DNA-origami filament that preserves the motors’ distribution showed that geometrical hindrance and biased detachment generate a non-zero sliding velocity even without rotation of the myosin lever-arm, which is widely recognized as the basic event in muscle contraction. Because biased detachment is a mechanism for the rectification of thermal fluctuations, in the Brownian-ratchet framework, we predict that it requires a non-negligible amount of energy to preserve the second law of thermodynamics. Taken together, our theoretical and experimental results elucidate non-conventional components in the chemo-mechanical energy transduction in muscle.

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.

scholarly journals The Synergic Role of Actomyosin Architecture and Biased Detachment in Muscle Energetics: Insights in Cross Bridge Mechanism Beyond the Lever-Arm Swing

2021 ◽  
Vol 22 (13) ◽  
pp. 7037
Author(s):  
Lorenzo Marcucci ◽  
Hiroki Fukunaga ◽  
Toshio Yanagida ◽  
Mitsuhiro Iwaki
Keyword(s):  
Muscle Contraction ◽  
Mechanical Energy ◽  
Second Law Of Thermodynamics ◽  
Thermal Fluctuations ◽  
Dna Origami ◽  
Conservation Strategy ◽  
Sliding Velocity ◽  
Muscle Energetics ◽  
Lever Arm

Muscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here, we combined experimental measurements of in vitro sliding velocity based on DNA-origami built filaments carrying myosins with different lever arm length and Monte Carlo simulations based on a model which accounts for three basic components: (i) the geometrical hindrance, (ii) the mechano-sensing mechanism, and (iii) the biased kinetics for stretched or compressed motors. The model simulations showed that the geometrical hindrance due to acto-myosin spatial mismatching and the preferential detachment of compressed motors are synergic in generating the rapid increase in the ATP-ase rate from isometric to moderate velocities of contraction, thus acting as an energy-conservation strategy in muscle contraction. The velocity measurements on a DNA-origami filament that preserves the motors’ distribution showed that geometrical hindrance and biased detachment generate a non-zero sliding velocity even without rotation of the myosin lever-arm, which is widely recognized as the basic event in muscle contraction. Because biased detachment is a mechanism for the rectification of thermal fluctuations, in the Brownian-ratchet framework, we predict that it requires a non-negligible amount of energy to preserve the second law of thermodynamics. Taken together, our theoretical and experimental results elucidate less considered components in the chemo-mechanical energy transduction in muscle.

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.

Design of a Generic Zero Stiffness Compliant Joint

2010 ◽  
Author(s):  
Femke M. Morsch ◽  
Just L. Herder
Keyword(s):  
Compliant Mechanisms ◽  
Compliant Mechanism ◽  
Great Promise ◽  
Optimized Design ◽  
Analytic Model ◽  
Total Potential ◽  
Fea Model ◽  
Compliant Joint ◽  
Joint Element ◽  
Cross Axis

The objective of this paper is to design a generic zero stiffness compliant joint. This compliant joint could be used as a generic construction element in a compliant mechanism. To avoid the spring-back behavior of conventional compliant joints, the principle of static balancing is applied, implying that for each position of the joint the total potential energy should be constant. To this end, a conventional balanced mechanism, consisting of two pivoted bodies which are balanced with two zero-free-length springs, is taken as an initial concept. The joint is replaced by a compliant cross-axis flexural pivot and each spring is replaced by a pair of compliant leaf springs. For both parts an analytic model was implemented and a configuration with the lowest energy fluctuation was found through optimization. A FEA model was used to verify the analytic model of the optimized design. A prototype was manufactured and tested. Both the FEA model and the experiment confirm the reduction of the needed moment to rotate the compliant joint. The experiment shows the balanced compliant joint is not completely balanced but the moment required to rotate the joint is reduced by 70%. Thus, a statically balanced compliant generic joint element was designed which bears great promise in designing statically balanced compliant mechanisms and making this accessible to any designer.

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