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

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

Journal

International Journal of Molecular Sciences
, E-ISSN: 1422-0067

Output data

Year: 2023, Volume: 24, Number: 21, Article number : 15978, Pages count : DOI: 10.3390/ijms242115978

Tags

nucleic acids; DNA nanotechnology; solid-phase synthesis; branched oligonucleotide; photolabile protecting group

Authors

Fokina A.A. ^1,2 , Poletaeva Y. ³ , Dukova S. ⁴ , Klabenkova K.V. ^1,2 , Rad’kova Z.V. ⁵ , Bakulina A. ⁵ , Zatsepin T.S. ⁶ , Ryabchikova E.I. ³ , Стеценко Д.А. ^1,2

Affiliations

1	Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
2	Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
3	Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
4	JSC Genterra, Moscow 129085, Russia
5	Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
6	Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia

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 20 -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

Fokina A.A. , Poletaeva Y. , Dukova S. , Klabenkova K.V. , Rad’kova Z.V. , Bakulina A. , Zatsepin T.S. , Ryabchikova E.I. , Стеценко Д.А.
Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides
International Journal of Molecular Sciences. 2023. V.24. N21. 15978 . DOI: 10.3390/ijms242115978 WOS Scopus OpenAlex

Published print:

Nov 5, 2023

Web of science:	WOS:001100506700001
Scopus:	2-s2.0-85176296586
OpenAlex:	W4388380426

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