DNA nanotechnology: understanding and optimisation through simulation

Abstract

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 provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended `overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.

To appear in Mol. Phys

References in corpus (29)

• DNA-based Self-Assembly of Chiral Plasmonic Nanostructures with Tailored Optical Response
• Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
• Sampling rare switching events in biochemical networks
• Langevin Thermostat for Rigid Body Dynamics
• Forward Flux Sampling for rare event simulations
• Sequence-dependent thermodynamics of a coarse-grained DNA model
• Representability problems for coarse-grained water potentials
• DNA hybridization kinetics: zippering, internal displacement and sequence dependence
• Mechanical unfolding of RNA hairpins
• Coarse-graining DNA for simulations of DNA nanotechnology
• A nucleotide-level coarse-grained model of RNA
• A Coarse-Grained Model for Predicting RNA Folding Thermodynamics
• The role of collective motion in examples of coarsening and self-assembly
• A systematically coarse-grained model for DNA, and its predictions for persistence length, stacking, twist, and chirality
• Numerical evidence for nucleated self-assembly of DNA brick structures
• Model for Assembly and Gelation of Four-Armed DNA Dendrimers
• DNA: From rigid base-pairs to semiflexible polymers
• Accurate phase diagram of tetravalent DNA nanostars
• DNA flexibility on short length scales probed by atomic force microscopy
• Mesoscopic modeling for nucleic acid chain dynamics
• Heat conductivity of DNA double helix
• Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model
• The self-assembly of DNA Holliday junctions studied with a minimal model
• Coarse Graining RNA Nanostructures for Molecular Dynamics Simulations
• Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble
• Slow closure of denaturation bubbles in DNA: twist matters
• Stretching and twisting of the DNA duplexes in coarse grained dynamical models
• DNA nano-mechanics: how proteins deform the double helix
• LAMMPS Framework for Dynamic Bonding and an Application Modeling DNA

Cited by in corpus (5)

• The interstellar chemistry of H2C3O isomers
• Microphase separation in two dimensional suspensions of self-propelled spheres and dumbbells
• Nanoscale Structure and Elasticity of Pillared DNA Nanotubes
• On a common carrier hypothesis for the 6613.6 and 6196.0 Å diffuse interstellar bands
• Robust control of biochemical reaction networks via stochastic morphing