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

A. Yu Bakulina; Z. V. Rad’kova; E. A. Burakova; E. Benassi; T. S. Zatsepin; A. A. Fokina; D. A. Stetsenko

doi:10.1134/S1068162019060062

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

A. Yu Bakulina, Z. V. Rad’kova, E. A. Burakova, E. Benassi, T. S. Zatsepin, A. A. Fokina, D. A. Stetsenko

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	608-618
Number of pages	11
Journal	Russian Journal of Bioorganic Chemistry
Volume	45
Issue number	6
DOIs	https://doi.org/10.1134/S1068162019060062
Publication status	Published - 1 Nov 2019

Keywords

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

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10.1134/S1068162019060062

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title = "Design and Visualization of DNA/RNA Nanostructures from Branched Oligonucleotides Using Blender Software",

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

author = "Bakulina, {A. Yu} and Rad{\textquoteright}kova, {Z. V.} and Burakova, {E. A.} and E. Benassi and Zatsepin, {T. S.} and Fokina, {A. A.} and Stetsenko, {D. A.}",

year = "2019",

month = nov,

day = "1",

doi = "10.1134/S1068162019060062",

language = "English",

volume = "45",

pages = "608--618",

journal = "Russian Journal of Bioorganic Chemistry",

issn = "1068-1620",

publisher = "MAIK NAUKA/INTERPERIODICA/SPRINGER",

number = "6",

}

Design and Visualization of DNA/RNA Nanostructures from Branched Oligonucleotides Using Blender Software. / Bakulina, A. Yu; Rad’kova, Z. V.; Burakova, E. A.; Benassi, E.; Zatsepin, T. S.; Fokina, A. A.; Stetsenko, D. A.

In: Russian Journal of Bioorganic Chemistry, Vol. 45, No. 6, 01.11.2019, p. 608-618.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Design and Visualization of DNA/RNA Nanostructures from Branched Oligonucleotides Using Blender Software

AU - Bakulina, A. Yu

AU - Rad’kova, Z. V.

AU - Burakova, E. A.

AU - Benassi, E.

AU - Zatsepin, T. S.

AU - Fokina, A. A.

AU - Stetsenko, D. A.

PY - 2019/11/1

Y1 - 2019/11/1

N2 - 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.

AB - 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.

KW - branched oligonucleotides

KW - click chemistry

KW - computer modelling

KW - DNA nanotechnology

KW - nucleic acids

KW - solid-phase synthesis

KW - template-directed assembly

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DO - 10.1134/S1068162019060062

M3 - Article

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JO - Russian Journal of Bioorganic Chemistry

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SN - 1068-1620

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