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Template-Assisted Assembly of DNA Nanostructures from Branched Oligonucleotides

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Abstract

We have proposed previously a template-assisted method for 3D assembly of nucleic acid nanostructures. The method involved a branched oligonucleotide as a template and a building block, which incorporates non-nucleotidic linkers, in particular, branching foci connecting two or three oligonucleotide chains. In this work, we have attempted the synthesis of branched oligonucleotide templates for the assembly of a DNA tetrahedron and a DNA cube, a branched oligonucleotide building block (“starlet”), and studied the assembly of a DNA tetrahedron.

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Funding

The work was supported by the Russian Foundation for Basic Research (grant nos. 16-03-01055 and 18-29-08062), and the Ministry of Science and Higher Education of the Russian Federation (Novosibirsk State University project FSUS-2020-0035).

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Authors and Affiliations

  1. Novosibirsk State University, 630090, Novosibirsk, Russia

    A. A. Fokina, E. A. Burakova, A. Yu. Bakulina, E. I. Ryabchikova & D. A. Stetsenko

  2. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

    A. A. Fokina, E. A. Burakova & D. A. Stetsenko

  3. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

    Yu. E. Poletaeva & E. I. Ryabchikova

  4. State Research Center of Virology and Biotechnology VECTOR, 630559, Koltsovo, Novosibirsk oblast, Russia

    A. Yu. Bakulina

  5. Skolkovo Institute of Science and Technology, 121205, Innovation Centre SKOLKOVO, Moscow oblast, Russia

    T. S. Zatsepin

  6. Moscow State University, 119991, Moscow, Russia

    T. S. Zatsepin

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  1. A. A. Fokina
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Correspondence to D. A. Stetsenko.

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This work contains no description of studies carried out by any of the authors that involve humans or animals.

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Additional information

Abbreviations: BCN, bicyclо[6.1.0]non-4-yne; ВР, Bromophenol Blue; DMTr, 4,4'-dimethoxytrityl; EtBr, ethidium bromide; MMTr, 4-methoxytrityl; NPOM, 1-(2-nitropiperonyl)ethoxymethyl; SPAAC, strain-promoted azide-alkyne [3+2]cycloaddition; TEAA, triethylammonium acetate; THPTA, tris-hydroxypropyltriazolylmethylamine; ОN, oligonucleotide; BО, branched oligonucleotide; BОT, branched oligonucleotide template; BОB, branched oligonucleotide building block; DE, disconnecting element; prefixes d and r in deoxy- and 2'-O-methylribonucleotides are omitted.

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Fokina, A.A., Poletaeva, Y.E., Burakova, E.A. et al. Template-Assisted Assembly of DNA Nanostructures from Branched Oligonucleotides. Russ J Bioorg Chem 47, 700–712 (2021). https://doi.org/10.1134/S1068162021030067

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