Erratum: “Moving beyond Watson–Crick models of coarse grained DNA dynamics” [J. Chem. Phys. 135, 205102 (2011)]

Linak, Margaret C.; Tourdot, Richard W.; Dorfman, Kevin D.

doi:10.1063/1.4739534

Cited by 20 publications

(37 citation statements)

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“…Figure 3 shows the melting curves for a ssDNA hairpin: A 10 G 20 T 10 and a dsDNA S1S2: GCGTCATACAGTGC obtained from REMD simulations. The shape of these melting curves is similar to what is expected based on thermodynamic melting behavior of hairpins and dsDNA formation from experiments 50,51 , although the widths of the melting transitions are much broader as found by Linak et al 35,38 as well for a similar model as used here. Such broad transitions (unphysical) are also found in more detailed atomistic models of biomolecular systems such as proteins 52 .…”

Section: Resultssupporting

confidence: 88%

“…To account for electrostatic interactions in a more transparent manner, we are currently developing a DNA model in real units with appropriate size scaling for the backbone and base beads as well as disparate bond lengths for backbone-backbone and basebackbone bonds 37 . No attempt is made here to convert the reduced simulation units to SI units as was done previously by Linak et al 35,38 for the temperature based on the experimental data. Without significant experimental input, such a mapping will likely yield inconsistent results.…”

Section: Model and Simulation Detailsmentioning

confidence: 99%

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Insights into DNA-mediated interparticle interactions from a coarse-grained model

Ding

Mittal

2014

The Journal of Chemical Physics

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DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNAfunctionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

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Section: Resultssupporting

confidence: 88%

Section: Model and Simulation Detailsmentioning

confidence: 99%

Insights into DNA-mediated interparticle interactions from a coarse-grained model

Ding

Mittal

2014

The Journal of Chemical Physics

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“…43 Additionally, reflecting the growth of DNA nanotechnology, 44 many coarse-grained models of DNA assembly have recently been proposed. [45][46][47][48][49][50][51][52][53][54][55][56][57][58][59] In many cases, these simulations report quantitative measures of assembly, such as the fraction of particles involved in clusters of a certain size. Experiments and thermodynamic theories typically involve bulk systems with a large number of particles, capable of forming many target structures.…”

Section: Introductionmentioning

confidence: 99%

Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble

Ouldridge¹

2012

The Journal of Chemical Physics

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In this paper we generalize a methodology [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Phys.: Condens. Matter 22, 104102 (2010)] for dealing with the inference of bulk properties from small simulations of self-assembling systems of characteristic finite size. In particular, schemes for extrapolating the results of simulations of a single self-assembling object to the bulk limit are established in three cases: for assembly involving multiple particle species, for systems with one species localized in space and for simulations in the grand canonical ensemble. Furthermore, methodologies are introduced for evaluating the accuracy of these extrapolations. Example systems demonstrate that differences in cluster concentrations between simulations of a single self-assembling structure and bulk studies of the same model under identical conditions can be large, and that convergence on bulk results as system size is increased can be slow and non-trivial.

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“…To date, this has been most successfully done with 'top-down' approaches 118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,13 Here, physically-motivated interactions such as hydrogen-bonding and stacking are included and parameterised to reproduce overall thermodynamic, mechanical and structural properties of DNA. In this article I focus on oxDNA 137,138,139 , an attempt to incorporate thermodynamics as parameterised by the nearest-neighbour model into a description with continuous degrees of freedom that captures structural and mechanical properties of DNA.…”

Section: Coarse-grained Modelling Of Dna Nanotechnologymentioning

confidence: 99%

“…Due to the emphasis placed on capturing the duplex formation transition in the development of oxDNA, it has been used to study nanotechnological systems more extensively than other models. However, duplex and hairpin formation transitions have been systematically investigated by a number of groups 119,120,121,123,124,127,130,132,140,141,142,143,144 , nanostructure conformation has been studied by Bombelli et oxDNA treats each nucleotide as a 3-dimensional rigid body. The potential energy of a configuration is given by…”

Section: Coarse-grained Modelling Of Dna Nanotechnologymentioning

confidence: 99%

DNA nanotechnology: understanding and optimisation through simulation

Ouldridge

2014

Molecular Physics

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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.

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Erratum: “Moving beyond Watson–Crick models of coarse grained DNA dynamics” [J. Chem. Phys. 135, 205102 (2011)]

Cited by 20 publications

References 1 publication

Insights into DNA-mediated interparticle interactions from a coarse-grained model

Insights into DNA-mediated interparticle interactions from a coarse-grained model

Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble

DNA nanotechnology: understanding and optimisation through simulation

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