Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

@article{ulc2013SimulatingAB,
  title={Simulating a burnt-bridges DNA motor with a coarse-grained DNA model},
  author={Petr {\vS}ulc and Thomas E. Ouldridge and Flavio Romano and Jonathan P. K. Doye and Ard A. Louis},
  journal={Natural Computing},
  year={2013},
  volume={13},
  pages={535-547}
}
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a ‘burnt-bridges’ DNA motor consisting of a single-stranded cargo that steps processively along a track of single-stranded stators. We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the stepping process to the spatial separation of stators, finding that an increased distance can suppress successful… 
Coarse-graining DNA for simulations of DNA nanotechnology.
TLDR
An overview of different approaches to coarse-graining DNA, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied, is provided.
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly.
TLDR
A two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures.
Coarse-grained modelling of nucleic acids and DNA hybridization
TLDR
It is argued that duplex association rates can be tuned by the choice of sequence, with possible applications in DNA nanotechnology.
DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size
TLDR
The ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions are demonstrated.
Direct Simulation of the Self-Assembly of a Small DNA Origami.
By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in
How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures
TLDR
Computational simulations are used to study how well the rigidity of a driving DNA duplex can rupture a double-stranded DNA target into single-Stranded segments and how well this stress can discriminate between unzipping or shearing geometries.
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
TLDR
An extended version of oxDNA is introduced, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA, which improves the ability of the model to treat large structures, such as DNA origami, which are sensitive to these geometric features.
Coarse-grained simulations of DNA overstretching.
TLDR
That S-DNA (overstretched duplex DNA), even though there is clear experimental evidence for this mode of overstretching under certain conditions, suggests that it is not simply an unstacked but hydrogen-bonded duplex, but instead probably has a more exotic structure.
Coarse-grained modelling of the structural properties of DNA origami
TLDR
The oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA Origami.
...
1
2
3
...

References

SHOWING 1-10 OF 129 REFERENCES
DNA nanotweezers studied with a coarse-grained model of DNA.
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands, duplex hybridization, single-stranded stacking, and hairpin formation, and also
Coarse-graining DNA for simulations of DNA nanotechnology.
TLDR
An overview of different approaches to coarse-graining DNA, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied, is provided.
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.
Moving beyond Watson-Crick models of coarse grained DNA dynamics.
TLDR
An experimentally parameterized, coarse-grained model that incorporates Hoogsteen bonds is developed that reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures.
The self-assembly of DNA Holliday junctions studied with a minimal model.
TLDR
A simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the sugar-phosphate backbone and the base is introduced, which is able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA.
Direct observation of stepwise movement of a synthetic molecular transporter.
TLDR
This work assembles a 100-nm-long DNA track on a two-dimensional scaffold, and shows that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of theTrack, a journey comprising 16 consecutive steps for the motor.
Studying the structural dynamics of bipedal DNA motors with single-molecule fluorescence spectroscopy.
TLDR
This work demonstrates that single-molecule fluorescence, based on its ability to provide detailed in situ structural dynamics information, inaccessible for traditional methods, constitutes an excellent tool for chaperoning the development of DNA-based technology.
Sequence-dependent thermodynamics of a coarse-grained DNA model.
TLDR
A sequence-dependent parametrization for a coarse-grained DNA model originally designed to reproduce the properties of DNA molecules with average sequences is introduced, able to fit parameters to the melting temperatures of thousands of sequences.
A DNAzyme that walks processively and autonomously along a one-dimensional track.
TLDR
A DNA nanodevice that autonomously and processively moves along a DNA track that is in sharp contrast with cellular protein motors and manmade machines at the macroscale, both of which can continuously work without human interference.
On the biophysics and kinetics of toehold-mediated DNA strand displacement
TLDR
This work study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects to provide a biophysical explanation of strand displacement kinetics.
...
1
2
3
4
5
...