Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: Concatemers and self-limited complexes

Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: Concatemers and self-limited complexes Full article

Journal

RSC Advances
ISSN: 2046-2069

Output data

Year: 2022, Volume: 12, Number: 11, Pages: 6416-6431 Pages count : 16 DOI: 10.1039/d2ra00155a

Authors

Zamoskovtseva A.A. ^1,2 , Golyshev V.M. ¹ , Kizilova V.A. ¹ , Shevelev G.Y. ¹ , Pyshnyi D.V. ¹ , Lomzov A.A. ¹

Affiliations

1	Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
2	Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, 141701, Russian Federation

The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging. We conducted a comprehensive study on the formation of various complexes from a pair of oligonucleotides with two transposed complementary blocks that can be linked through a nucleotide or non-nucleotide linker. A methodology is proposed to prove the formation of a self-limited complex and to determine its molecularity. It is based on the opening of a self-limited complex with an oligonucleotide that effectively binds to a duplex-forming block. The complexes assembled from a pair of oligonucleotides with different block length and different linker sizes and types were investigated by theoretical analysis, several experimental methods (a gel shift assay, atomic force microscopy, and ultraviolet melting analysis), and molecular dynamics simulations. The results showed a variety of complexes formed by only a pair of oligonucleotides. Self-limited associates, concatemer complexes, or mixtures thereof can arise if we change the length of a duplex and loop-forming blocks in oligonucleotides or via introduction of overhangs and chemical modifications. We postulated basic principles of rational design of native self-limited DNA complexes of desired structure, shape, and molecularity. Our foundation makes self-limited complexes useful tools for nanotechnology, biological studies, and therapeutics. © 2022 Royal Society of Chemistry. All rights reserved.

Zamoskovtseva A.A. , Golyshev V.M. , Kizilova V.A. , Shevelev G.Y. , Pyshnyi D.V. , Lomzov A.A.
Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: Concatemers and self-limited complexes
RSC Advances. 2022. V.12. N11. P.6416-6431. DOI: 10.1039/d2ra00155a WOS Scopus РИНЦ OpenAlex

Submitted:	Jan 10, 2022
Accepted:	Feb 15, 2022

Web of science:	WOS:000759691600001
Scopus:	2-s2.0-85126961103
Elibrary:	48272029
OpenAlex:	W4212844618

DB	Citing
Scopus	1
Web of science	2
Elibrary	5
OpenAlex	2