ArticleNucleic acids research2018
DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Bimodal DNA self-origami material with nucleic acid function enhancement.Journal of nanobiotechnology · 2024Article
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.eLife · 2021Review
- Design Approaches and Computational Tools for DNA Nanostructures.IEEE open journal of nanotechnology · 2021Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Understanding DNA interactions in crowded environments with a coarse-grained model.Nucleic acids research · 2020Article
- Free energy landscape of salt-actuated reconfigurable DNA nanodevices.Nucleic acids research · 2020Article
- Bioapplications of DNA nanotechnology at the solid-liquid interface.Chemical Society reviews · 2019Review
- ProgrammingChemical science · 2019Article
- Coarse-grained modelling of the structural properties of DNA origami.Nucleic acids research · 2019Article
- Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants.Chemical science · 2018Article
- Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems.International journal of molecular sciences · 2018Review
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates 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.
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