Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis

Nanoscale ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 1647-1660 ◽  
Author(s):  
Chao-Min Huang ◽  
Anjelica Kucinic ◽  
Jenny V. Le ◽  
Carlos E. Castro ◽  
Hai-Jun Su
Keyword(s):  
Uncertainty Quantification ◽  
Dna Origami ◽  
Variance Analysis ◽  
Coarse Grained ◽  
Computational Framework ◽  
Coarse Grained Model

We report a hybrid computational framework combining coarse-grained modeling with kinematic variance analysis for predicting uncertainties in the motion pathway of a multi-component DNA origami mechanism.

scholarly journals A coarse-grained model for DNA origami

2017 ◽  
Vol 46 (3) ◽  
pp. 1102-1112 ◽  
Author(s):  
Roman V Reshetnikov ◽  
Anastasia V Stolyarova ◽  
Arthur O Zalevsky ◽  
Dmitry Y Panteleev ◽  
Galina V Pavlova ◽  
...  
Keyword(s):  
Dna Origami ◽  
Coarse Grained ◽  
Coarse Grained Model

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.

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

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