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Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides. / Fokina, Alesya; Poletaeva, Yulia; Dukova, Svetlana et al.

In: International Journal of Molecular Sciences, Vol. 24, No. 21, 15978, 05.11.2023.

Research output: Contribution to journalArticlepeer-review

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Vancouver

Fokina A, Poletaeva Y, Dukova S, Klabenkova K, Rad'kova Z, Bakulina A et al. Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides. International Journal of Molecular Sciences. 2023 Nov 5;24(21):15978. doi: 10.3390/ijms242115978

Author

Fokina, Alesya ; Poletaeva, Yulia ; Dukova, Svetlana et al. / Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides. In: International Journal of Molecular Sciences. 2023 ; Vol. 24, No. 21.

BibTeX

@article{25eb9892600444a99a67916e86f6b14b,
title = "Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides",
abstract = "A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.",
author = "Alesya Fokina and Yulia Poletaeva and Svetlana Dukova and Kristina Klabenkova and Zinaida Rad'kova and Anastasia Bakulina and Timofei Zatsepin and Elena Ryabchikova and Dmitry Stetsenko",
note = "This work was funded by the Russian Science Foundation (grant no. 22-13-00212, oligonucleotide synthesis) and, in part, by the Russian Foundation for Basic Research (grant no. 18-29-08062, molecular modeling and TEM) and the Ministry of Science and Higher Education of the Russian Federation (project of Novosibirsk State University no. FSUS-2020-0035).",
year = "2023",
month = nov,
day = "5",
doi = "10.3390/ijms242115978",
language = "English",
volume = "24",
journal = "International Journal of Molecular Sciences",
issn = "1661-6596",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
number = "21",

}

RIS

TY - JOUR

T1 - Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides

AU - Fokina, Alesya

AU - Poletaeva, Yulia

AU - Dukova, Svetlana

AU - Klabenkova, Kristina

AU - Rad'kova, Zinaida

AU - Bakulina, Anastasia

AU - Zatsepin, Timofei

AU - Ryabchikova, Elena

AU - Stetsenko, Dmitry

N1 - This work was funded by the Russian Science Foundation (grant no. 22-13-00212, oligonucleotide synthesis) and, in part, by the Russian Foundation for Basic Research (grant no. 18-29-08062, molecular modeling and TEM) and the Ministry of Science and Higher Education of the Russian Federation (project of Novosibirsk State University no. FSUS-2020-0035).

PY - 2023/11/5

Y1 - 2023/11/5

N2 - A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.

AB - A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85176296586&origin=inward&txGid=8e9b5628b61801f7b200360b632e7d23

U2 - 10.3390/ijms242115978

DO - 10.3390/ijms242115978

M3 - Article

C2 - 37958961

VL - 24

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 21

M1 - 15978

ER -

ID: 57638511