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

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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.

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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.”

Author information

Correspondence to A. Yu. Bakulina.

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COMPLIANCE WITH ETHICAL STANDARDS

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

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Authors declare that they have no conflicts of interests.

Additional information

Translated by P. Kuchina

Corresponding author: phone: +7 (383) 363-51-24; fax: +7 (383) 363-42-80; e-mail: bakulina@gmail.com.

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Cite this article

Bakulina, A.Y., Rad’kova, Z.V., Burakova, E.A. et al. Design and Visualization of DNA/RNA Nanostructures from Branched Oligonucleotides Using Blender Software. Russ J Bioorg Chem 45, 608–618 (2019) doi:10.1134/S1068162019060062

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Keywords:

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