DNA nanotechnology: understanding and optimisation through simulation

@article{Ouldridge2014DNANU,
  title={DNA nanotechnology: understanding and optimisation through simulation},
  author={Thomas E. Ouldridge},
  journal={Molecular Physics},
  year={2014},
  volume={113},
  pages={1 - 15}
}
  • T. Ouldridge
  • Published 7 November 2014
  • Biology
  • Molecular Physics
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article, I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to… 
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22 Citations
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22 Citations

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Citation Type

Exploring Cation Mediated DNA Interactions Using Computer Simulations
TLDR
Computer simulations offer unprecedented detail into the dynamics and thermodynamics of DNA interactions that can potentially help to understand the biological DNA and also develop novel DNA based nanotechnologies.
A coarse-grained simulation study of the structures, energetics, and dynamics of linear and circular DNA with its ions.
TLDR
The treatment of electrostatics is examined and it is determined that a large cutoff is necessary to properly reproduce the DNA flexibility, and detailed molecular structures from the various superhelical conformations generated by the CG MD of the DNA minicircles are generated.
Nanoscale Structure and Elasticity of Pillared DNA Nanotubes.
TLDR
An atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties are presented and a gradual increase of persistence length with an increasing number of pillars is found, in quantitative agreement with previous experimental findings.
Molecular Dynamics Simulations of DNA-Functionalized Nanoparticle Building Blocks on GPUs
TLDR
This thesis implements the nBLOCK computational model as an extension to the coarse grain molecular simulator oxDNA to explore greater simulation time scales and provides descriptions of the scripting utilities which support nBLock assembly generation, simulation, and analysis.
Multiscale simulation of DNA.
Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations.
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable…
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement
TLDR
This work proposes using mismatches in a DNA duplex to drive catalytic reactions forward whilst maintaining tight catalytic control, and demonstrates that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design.
Self-Assembly of Structures with Addressable Complexity.
TLDR
This Perspective focuses on the prediction of kinetic pathways for self-assembly and implications for the design of robust experimental protocols, which will enable the engineering of complex materials using a much wider range of building blocks than is currently possible.
Rational design of hidden thermodynamic driving through DNA mismatch repair
TLDR
This work proposes a new mechanism for enhancing thermodynamic drive of DNA strand displacement reactions whilst barely perturbing forward reaction rates - introducing mismatches in an internal location within the initial duplex.
DNA and DNA computation based on toehold-mediated strand displacement reactions
TLDR
The progress of DNA structure and mechanical properties in recent years are reviewed, the microcosmic mechanism of DNA strand replacement reaction is discussed, and the latest achievements in DNA molecular computing and its application in DNA constant temperature self-assembly are introduced.
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References

SHOWING 1-10 OF 484 REFERENCES
Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
TLDR
It is demonstrated that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA walker that is designed to step along a reusable track, thereby offering the possibility of optimizing the design of such systems.
DNA closed nanostructures: a structural and Monte Carlo simulation study.
TLDR
The structural features obtained by Monte Carlo simulations and atomic force microscopy are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.
Modelling the folding of DNA origami
TLDR
A model for the folding and melting processes of DNA origamis is developed that is able to reproduce accurately several thermodynamic quantities measurable from UV absorption experiments and shows that cooperativity is key to quantitatively understand the folding process.
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
TLDR
The structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers are explored, resulting in an "average base" description of DNA.
Assembly and structural analysis of a covalently closed nano-scale DNA cage
TLDR
The design, construction and structural analysis of a covalently closed and stable 3D DNA structure with the connectivity of an octahedron that assembles from eight oligonucleotides with a yield of ∼30%.
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
TLDR
The first atomically precise portrait of DNA origami in solution is obtained using a large supercomputer system to create trajectories of millions of atoms to characterize the structural and mechanical properties of DNA Origami objects in unprecedented microscopic detail.
Understanding the mechanical properties of DNA origami tiles and controlling the kinetics of their folding and unfolding reconfiguration.
TLDR
It is shown that a two-dimensional origami rectangle can be effectively folded into a short, cylindrical tube by connecting the two opposite edges through the hybridization of linker strands and that this process can be efficiently reversed via toehold-mediated strand displacement.
Self-assembly of a nanoscale DNA box with a controllable lid
TLDR
The DNA origami method is extended into three dimensions by creating an addressable DNA box that can be opened in the presence of externally supplied DNA ‘keys’, and controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications.
Reconfigurable, braced, three-dimensional DNA nanostructures.
TLDR
This work demonstrates the operation of reconfigurable DNA tetrahedra whose shapes change precisely and reversibly in response to specific molecular signals.
Numerical evidence for nucleated self-assembly of DNA brick structures.
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, predesigned DNA strands can assemble into three-dimensional target structures came as a great surprise, as no…
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