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Design and Simulation of a DNA Origami Nanopore for Large Cargoes

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Abstract

Since less than a decade ago, the DNA origami technique has become an important tool in nanopore fabrication. DNA origami nanopores are highly efficient because of their compatibility with biomolecules and the possibility to precisely engineer their dimensions and designs. However, accurate comprehension of their molecular behavior under various conditions is still unsatisfactory. In this study, a thin plate DNA origami nanopore is designed and investigated using molecular dynamics simulation. The thin plate is designed using caDNAno software along with the square lattice method and the molecular dynamics simulation is performed using GROMACS software. The model is simulated in a wide temperature range and its stability is investigated. The shape and dimensions of the nanopore are also compared at these temperatures. The results indicate that the designed nanopore exhibits decent stability at these temperatures and no breakdown was observed despite some distortions in the structure at high temperatures. In addition, the effect of the number of staple strands on the structure, stability, and deformation of the DNA origami plate is investigated and it is found that addition of staple strands have a significant positive effect on the stability of nanopore’s shape. By the results of analyzing the shape of the nanopore, it suggests that the proposed nanopore can be used to pass a wide range of molecules, macromolecules, and drug cargoes.

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Authors and Affiliations

  1. M.S. Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran

    Raheleh Khosravi

  2. Department of Mechanical Engineering, Hakim Sabzevari University, 397, Sabzevar, Iran

    Reza Hasanzadeh Ghasemi & Reza Soheilifard

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  1. Raheleh Khosravi
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  2. Reza Hasanzadeh Ghasemi
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  3. Reza Soheilifard
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Correspondence to Reza Hasanzadeh Ghasemi.

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Khosravi, R., Ghasemi, R.H. & Soheilifard, R. Design and Simulation of a DNA Origami Nanopore for Large Cargoes. Mol Biotechnol 62, 423–432 (2020). https://doi.org/10.1007/s12033-020-00261-z

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  • DOI: https://doi.org/10.1007/s12033-020-00261-z

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