ArticleNucleic acids research2019
Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.
Article in Nucleic acids research, 2019. 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.
- DNA Mechanical Strain Steers Transcription Factor Recognition.Research square · 2026Article
- Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates.Nature communications · 2025Article
- Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies.Nature communications · 2024Article
- Prediction of DNA origami shape using graph neural network.Nature materials · 2024Article
- A computational model for structural dynamics and reconfiguration of DNA assemblies.Nature communications · 2023Article
- Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations.Nature communications · 2023Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
- Design Approaches and Computational Tools for DNA Nanostructures.IEEE open journal of nanotechnology · 2021Article
- Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.Nature communications · 2020Article
- Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness.Nucleic acids research · 2020Article
- Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.Chemical science · 2020Article
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7 authors.
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Abstract
DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through molecular dynamics simulation for a comprehensive set of distinct DNA oligomers constructed using all possible base-pair steps with and without a nick. We found that torsional rigidity was reduced by 28-82% at the nick depending on its sequence and location although bending and stretching rigidities remained similar to those of regular base-pair steps. No significant effect of a nick on mechanically coupled deformation such as the twist-stretch coupling was observed. These results suggest that the primary structural role of nick is the relaxation of torsional constraint by backbones known to be responsible for relatively high torsional rigidity of DNA. Moreover, we experimentally demonstrated the usefulness of quantified nick properties in self-assembling DNA nanostructure design by constructing twisted DNA origami structures to show that sequence design of nicks successfully controls the twist angle of structures. Our study illustrates the importance as well as the opportunities of considering sequence-dependent properties in structural DNA nanotechnology.
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