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Russian Journal of Bioorganic Chemistry

, Volume 45, Issue 6, pp 608–618 | Cite as

Design and Visualization of DNA/RNA Nanostructures from Branched Oligonucleotides Using Blender Software

  • A. Yu. BakulinaEmail author
  • Z. V. Rad’kova
  • E. A. Burakova
  • E. Benassi
  • T. S. Zatsepin
  • A. A. Fokina
  • D. A. Stetsenko
Article

Abstract

Recently, three-dimensional nucleic acid nanostructures have attracted great interest, which have been made available through the DNA origami technique. We have proposed a different way of constructing nucleic acid nanoobjects, namely, template-directed assembly employing branched oligonucleotides as templates and building blocks, which include nonnucleotidic linkers, particularly, branching units for connecting three or more oligonucleotide chains. For the design and 3D modelling of such nanostructures as DNA tetrahedron, DNA cube and DNA fullerene C24, we have used Blender software. As we found, Blender not only allows one to visualize complex DNA and RNA nanostructures, but also helps to choose the parameters for their synthesis.

Keywords:

nucleic acids DNA nanotechnology template-directed assembly branched oligonucleotides solid-phase synthesis computer modelling click chemistry 

Notes

ACKNOWLEDGMENTS

This work was possible owing to the computation time kindly provided by the Siberian Supercomputer Center (SSCC) SB RAS. The authors are grateful to N.V. Kuchin for technical assistance. E.B. is grateful to Novosibirsk State University and the Advanced Training Program 5-100 of the Ministry of Education and Science of the Russian Federation.

FUNDING

This work was financially supported by the Russian Foundation for Basic Research (grant Nos. 18-29-08062 and 16-03-01055), as well as the Basic Project of the Program of the fundamental scientific research of state academies for 2017–2020. AAAA-A17-117020210024-8 “Therapeutic Nucleic Acids.”

COMPLIANCE WITH ETHICAL STANDARDS

The work has no studies involving humans or animals as subjects of the study.

Conflict of Interests

Authors declare that they have no conflicts of interests.

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Copyright information

© Pleiades Publishing, Ltd. 2019

Authors and Affiliations

  • A. Yu. Bakulina
    • 1
    • 2
    Email author
  • Z. V. Rad’kova
    • 1
    • 2
  • E. A. Burakova
    • 1
    • 3
  • E. Benassi
    • 1
  • T. S. Zatsepin
    • 4
    • 5
  • A. A. Fokina
    • 1
    • 3
  • D. A. Stetsenko
    • 1
    • 3
  1. 1.Novosibirsk State UniversityNovosibirskRussia
  2. 2.State Research Center of Virology and Biotechnology VECTORKoltsovoRussia
  3. 3.Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of SciencesNovosibirskRussia
  4. 4.Skolkovo Institute of Science and Technology, Innovation Centre SKOLKOVOMoscowRussia
  5. 5.Moscow State UniversityMoscowRussia

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