Skip to main content
SpringerLink
Log in

An Analysis of the Capturing and Passing Ability of a DNA Origami Nanocarrier with the Aid of Molecular Dynamics Simulation

  • Original Paper
  • Published:
Molecular Biotechnology Aims and scope Submit manuscript

Abstract

The present article aims to investigate the ability of a DNA origami nanocarrier to successfully capture a cargo using molecular dynamics (MD) simulation. In addition, the passage of the cargo through the nanocarrier was analyzed by steered molecular dynamics (SMD) simulation. The proposed DNA origami nanocarrier is a nanotube that consists of six double helices in which a positively charged nanocargo was placed. Since the stability of the nanocarrier has been considered one of the obstacles to nanocargo transportation, different cross-sectional areas of the nanocarrier were considered as measures to analyze its structural stability. The results eventually showed that the proposed nanocarrier is able to retain the cargo while maintaining its structural stability. The analysis also revealed that the presence of the cargo increases the structural stability in parts of the nanocarrier. SMD simulation demonstrated that a feasible amount of force is required to separate the cargo and pass it through the nanocarrier, which can provide useful information in the field of smart drug delivery.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13

Similar content being viewed by others

References

  1. Douglas, S. M., Dietz, H., Liedl, T., Högberg, B., Graf, F., & Shih, W. M. (2009). Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 459(7245), 414–418.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Seeman, N. C., & Sleiman, H. F. (2017). DNA nanotechnology. Nature Reviews Materials, 3(1), 17068.

    Article  Google Scholar 

  3. Linko, V., & Dietz, H. (2013). The enabled state of DNA nanotechnology. Current Opinion in Biotechnology, 24(4), 555–561.

    Article  CAS  PubMed  Google Scholar 

  4. Kuzuya, A., & Ohya, Y. (2014). Nanomechanical molecular devices made of DNA origami. ACC Chemical Research, 47, 1742–1749.

    Article  CAS  Google Scholar 

  5. Hong, F., Zhang, F., Liu, Y., & Yan, H. (2017). DNA origami: Scaffolds for creating higher order structures. Chemical Reviews, 117(20), 12584–12640.

    Article  CAS  PubMed  Google Scholar 

  6. Ramakrishnan, S., Ijäs, H., Linko, V., & Keller, V. (2018). Structural stability of DNA Origami nanostructures under application-specific conditions. Computational and Structural Biotechnology Journal, 16, 342–349.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Kim, Y., & Yin, P. (2020). Enhancing biocompatible stability of DNA nanostructures using dendritic oligonucleotides and brick motifs. Angewandte Chemie International Edition, England, 59(2), 700–703.

    Article  CAS  Google Scholar 

  8. Yin, P., Hariadi, R. F., Sahu, S., Choi, H. M. T., Park, S. H., Labean, T. H., & Reif, J. H. (2008). Programming DNA tube circumferences. Science, 321, 824–826.

    Article  CAS  PubMed  Google Scholar 

  9. Andersen, E. S., Dong, M., Nielsen, M. M., Jahn, K., Subramani, R., Mamdouh, W., et al. (2009). Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459(7243), 73–6.

    Article  CAS  PubMed  Google Scholar 

  10. Zadegan, R. M., Jepsen, M. D. E., Thomsen, K. E., Okholm, A. H., Schaffert, D. H., Andersen, E. S., Birkedal, V., & Kjems, J. (2012). Construction of a 4 Zeptoliters switchable 3D DNA box origami. ACS Nano, 6, 10050–10053.

    Article  CAS  PubMed  Google Scholar 

  11. Kang, J. H., Kim, K. R., Lee, H., Ahn, D. R., & Ko, Y. T. (2017). In vitro and in vivo behavior of DNA tetrahedrons as tumor-targeting nanocarriers for doxorubicin delivery. Colloids and Surfaces B: Biointerfaces, 157, 424–431.

    Article  CAS  PubMed  Google Scholar 

  12. Wiraja, C., Zhu, Y., Lio, D. C. S., Yeo, D. C., Xie, M., Li, W. Q., Zheng, M., van Steensel, M., Wang, L., et al. (2019). Framework nucleic acids as programmable carrier for transdermal drug delivery. Nature Communications, 10, 1147.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Liu, J., Song, L., Liu, S., Jiang, Q., Liu, Q., Li, N., Wang, Z. G., & Ding, B. (2018). A DNA-based nanocarrier for efficient gene delivery and combined cancer therapy. Nano Letters, 18, 3328–3334.

    Article  CAS  PubMed  Google Scholar 

  14. Kiviaho, J. K., Linko, V., Ora, A., Tiainen, T., Jarvihaavisto, E., Mikkil, J., Tenhu, H., Nonappa, N., & Kostiainen, M. A. (2016). Cationic polymers for DNA origami coating—examining their binding efficiency and tuning the enzymatic reaction rates. Nanoscale, 8, 11674–80.

    Article  CAS  PubMed  Google Scholar 

  15. Ijas, H., Hakaste, I., Shen, B., Kostiainen, M. A., & Linko, V. (2019). Reconfigurable DNA origami nanocapsule for pH-controlled encapsulation and display of cargo. ACS Nano, 13, 5959–5967.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Grossi, G., Jepsen, M. D. E., Kjems, J., & Andersen, E. S. (2017). Control of enzyme reactions by a reconfigurable DNA nanovault. Nature Communications. https://doi.org/10.1038/s41467-017-01072-8

    Article  PubMed  PubMed Central  Google Scholar 

  17. Douglas, S. M., Bachelet, I., & Church, G. M. (2012). A logic-gated nanorobot for targeted transport of molecular payloads. Science, 335, 831–834.

    Article  CAS  PubMed  Google Scholar 

  18. Kuzuya, A., & Komiyama, M. (2009). Design and construction of a box-shaped 3D-DNA origami. Chemical Communications, 28, 4182–4184.

    Article  Google Scholar 

  19. Maingi, V., Burns, J. R., Uusitalo, J. J., Howorka, S., Marrink, S. J., & Sansom, M. S. P. (2017). Stability and dynamics of membrane-spanning DNA nanopores. Nature Communications, 8, 1–12.

    Article  Google Scholar 

  20. Lee, J. Y., Lee, J. G., Yun, G., Lee, Ch., Kim, Y.-J., Kim, K. S., Kim, T. H., & Kim, D.-N. (2021). Rapid computational analysis of DNA origami assemblies at near-atomic resolution. ACS Nano, 15, 1002–1015.

    Article  CAS  PubMed  Google Scholar 

  21. Mogheiseh, M., Hasanzadeh Ghasemi, R., & Soheilifard, R. (2021). The effect of crossovers on the stability of DNA Origami type nanocarriers. Multidiscipline Modeling in Materials and Structures, 17(2), 426–436.

    Article  CAS  Google Scholar 

  22. Zhang, Q., et al. (2014). DNA Origami as an in vivo drug delivery vehicle for cancer therapy. ACS Nano, 8, 6633–6643.

    Article  CAS  PubMed  Google Scholar 

  23. Keramati, M., & Hasanzadeh Ghasemi, R. (2017). A molecular dynamics investigation of the effects of mutation on prefoldin nano actuator in inhibiting amyloid ˇ42-dimer. Sensors and Actuators B: Chemical, 248, 536–544.

    Article  CAS  Google Scholar 

  24. Weiden, J., & Bastings, M. M. C. (2021). DNA Origami nanostructures for controlled therapeutic drug delivery. Current Opinion in Colloid & Interface Science, 52, 101411.

    Article  CAS  Google Scholar 

  25. Chi, Q., Yang, Z., Xu, K., Wang, Ch., & Liang, H. (2020). DNA nanostructure as an efficient drug delivery platform for immunotherapy. Frontiers in Pharmacology, 10, 1585. https://doi.org/10.3389/fphar.2019.01585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Jiang, Q., Liu, S., Liu, J., Wang, Z.-G., & Ding, B. (2019). Rationally designed dna-origami nanomaterials for drug delivery in vivo. Advance Material, 31(45), 1804785.

    Article  CAS  Google Scholar 

  27. Yoo, J., & Aksimentiev, A. (2013). In situ structure and dynamics of DNA Origami determined through molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America, 110, 20099–20104.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Khosravi, R., Ghasemi, R. H., & Soheilifard, R. (2020). Design and simulation of a DNA origami nanopore for large cargoes. Mol Biotechnol, 62(9), 423–432.

    Article  CAS  PubMed  Google Scholar 

  29. Dastorani, S., Mogheiseh, M., Ghasemi, R. H., & Soheilifard, R. (2020). Modeling and Structural Investigation of a New DNA Origami Based Flexible Bio-Nano Joint. Molecular Simulation. https://doi.org/10.1080/08927022.2020.1797019

    Article  Google Scholar 

  30. Dastorani, S., Hasanzadeh Ghasemi, R., & Soheilifard, R. (2021). A study on the bending stiffness of a new DNA origami nano-joint. Molecular Biotechnology, 63, 1057–1067.

    Article  CAS  PubMed  Google Scholar 

  31. Douglas, S. M., Marblestonen, A. H., Teerapittayanon, S., Vazquez, A., Church, G. M., & Shih, W. M. (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research, 37(15), 5001–5006.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ghaffari, A., Shokuhfar, A., & Hasanzadeh Ghasemi, R. (2012). Capturing and releasing a nano cargo by Prefoldin nano actuator. Sensors and Actuators B: Chemical, 171, 1199–1206.

    Article  Google Scholar 

  33. Auvinen, H., et al. (2017). Protein coating of DNA nanostructures for enhanced stability and immunocompatibility. Advanced Healthcare Materials. https://doi.org/10.1002/adhm.201700692

    Article  PubMed  Google Scholar 

  34. Samanta, S., Mukherjee, S., Chakrabarti, J., & Bhattacharyya, D. (2009). Structural properties of polymeric DNA from molecular dynamics simulations. The Journal of Chemical Physics, 130, 1–14.

    Article  Google Scholar 

  35. Cheatham, T. E., Crowley, M. F., Fox, T., & Kollman, P. A. (1997). A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions. Proceedings of the National Academy of Sciences, 94, 9626–9630.

    Article  CAS  Google Scholar 

  36. Abidi, M., Soheilifard, R., & HasanzadehGhasemi, R. (2021). The effect of temperature on the binding affinity of Remdesivir and RdRp enzyme of SARS-COV-2 virus using steered molecular dynamics simulation. Journal of Control, 14(5), 39–47.

    Article  Google Scholar 

  37. Nguyen, H. L., Thai, N. Q., Truong, D. T., & Li, M. S. (2020). Remdesivir strongly binds to both RNA-dependent RNA polymerase and main protease of SARS-CoV-2: evidence from molecular simulations. The Journal of Physical Chemistry B, 124, 11337–11348.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Abidi, M., Soheilifard, R., & Hasanzadeh Ghasemi, R. (2020). Comparison of the unbinding process of RBD-ACE2 complex between SARS-CoV-2 new variants (Delta, Delta plus and Lambda): A steered molecular dynamics simulation. Molecular Simulation.

  39. Kim, S., Liu, Y., Lei, Z., Dicker, J., Cao, Y., & Zhang, X. F. (2021). Differential interactions between human ACE2 and spike RBD of SARS- CoV-2 variants of concern. Journal of Chemical Theory and Computation, 17(12), 7972–7979.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

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

    Maryam Mogheiseh & Reza Hasanzadeh Ghasemi

Authors
  1. Maryam Mogheiseh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Reza Hasanzadeh Ghasemi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Reza Hasanzadeh Ghasemi.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mogheiseh, M., Ghasemi, R.H. An Analysis of the Capturing and Passing Ability of a DNA Origami Nanocarrier with the Aid of Molecular Dynamics Simulation. Mol Biotechnol 65, 1287–1295 (2023). https://doi.org/10.1007/s12033-022-00636-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12033-022-00636-4

Keywords

Search

Navigation