Coarse-graining DNA for simulations of DNA nanotechnology

Abstract

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

20 pages, 9 figures

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Cited by in corpus (28)

• DNA origami
• A nucleotide-level coarse-grained model of RNA
• Coarse-grained modelling of the structural properties of DNA origami
• Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
• Numerical evidence for nucleated self-assembly of DNA brick structures
• Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules
• A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
• Accurate phase diagram of tetravalent DNA nanostars
• DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
• Structure, stability and elasticity of DNA nanotube
• Coarse-grained modelling of strong DNA bending II: Cyclization
• DNA nanotechnology: understanding and optimisation through simulation
• The role of loop stacking in the dynamics of DNA hairpin formation
• SAT-assembly: A new approach for designing self-assembling systems
• Small-angle neutron scattering and Molecular Dynamics structural study of gelling DNA nanostars
• Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal
• A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures
• Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly
• Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach
• Characterizing the bending and flexibility induced by bulges in DNA duplexes
• Incorporating particle flexibility in a density functional description of nematics and cholesterics
• Characterizing the free-energy landscapes of DNA origamis
• Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs
• Substrate-assisted 2D DNA lattices and algorithmic lattices from single-stranded tiles
• pyMBE: the Python-based Molecule Builder for ESPResSo
• Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
• Simulating sticky particles: A Monte Carlo method to sample a stratification
• Towards New Liquid Crystal Phases of DNA mesogens