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

Zamoskovtseva, Anastasia A.; Golyshev, Victor M.; Kizilova, Valeria A.; Shevelev, Georgiy Yu.; Пышный, Д. В.; Lomzov, Alexander A.

doi:10.1039/d2ra00155a

Cited by 3 publications

(15 citation statements)

References 62 publications

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“…Distributed trace of stained RNA complexes corresponding to the concatemer can be found for the complexes M-Ui/N (i = 0, 1, 2, 3, 5, 7, and 10), M/N-Uj (j = 1, 2, and 3), and M-Ui/N-Uj (i, j = 1, 2, 3) with exception of M-U3/N-U1 (Figures 2, S4 and S5). A similar observation was made for DNA concatemers [15,23].…”

Section: Gel Shift Assay Analysissupporting

confidence: 78%

“…Moreover, the bands of three molecular M-U5/N-U3/O complexes are less diffuse than the M-U5/N-U3, confirming the formation of a more rigid linear structure at opener adding. We previously observed a similar electropherogram for the bimolecular DNA/DNA complex [15].…”

Section: Gel Shift Assay Analysissupporting

confidence: 63%

“…The ability to change and control complexes' shape and molecularity is an important task in nucleic acid nanoarchitectonics and nanomachine building. Here and in our previous works [15,24], we have shown the possibility of purposefully changing self-limited complexes to linear ones or controllable ones by reducing the size of concatemer complexes by adding an opener oligonucleotide. We formulated principles for the efficient regulation of this process.…”

Section: Rna Nanomaachines Topology Regulationmentioning

confidence: 66%

“…Distributed trace of stained RNA complexes corresponding to the conca can be found for the complexes M-Ui/N (i = 0, 1, 2, 3, 5, 7, and 10), M/N-Uj (j = 1, 2, a and M-Ui/N-Uj (i, j = 1, 2, 3) with exception of M-U3/N-U1 (Figures 2, S4 and S5). A s observation was made for DNA concatemers[15,23].For a number of these complexes formed by M-Ui with i > 0, well-defined addi bands with mobility in the range of 200-300 bp of dsDNA were found (Figures2, S S5). These bands correspond to the self-limited complexes of various molecularitie blow).All other complexes have single or multiple well-defined bands on the electrop…”

mentioning

confidence: 92%

“…Molecules 2024, 29, x FOR PEER REVIEW 2 We recently demonstrated the ability to construct a variety of linear and cyclic ( limited) DNA complexes using a pair of oligonucleotides (Figure 1a,b) [15]. This appr is based on the self-association of a pair of oligonucleotides with two transp complementary blocks.…”

Section: Introductionmentioning

confidence: 99%

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Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines

Kanarskaya,

Pyshnyi,

Lomzov

2023

Molecules

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New tool development for various nucleic acid applications is an essential task in RNA nanotechnology. Here, we determined the ability of self-limited complex formation by a pair of oligoribonucleotides carrying two pairwise complementary blocks connected by a linker of different lengths in each chain. The complexes were analyzed using UV melting, gel shift assay analysis, and molecular dynamics (MD) simulations. We have demonstrated the spontaneous formation of various self-limited and concatemer complexes. The linear concatemer complex is formed by a pair of oligomers without a linker in at least one of them. Longer linkers resulted in the formation of circular complexes. The self-limited complexes formation was confirmed using the toehold strand displacement. The MD simulations indicate the reliability of the complexes’ structure and demonstrate their dynamics, which increase with the rise of complex size. The linearization of 2D circular complexes into 1D structures and a reverse cyclization process were demonstrated using a toehold-mediated approach. The approach proposed here for the construction and directed modification of the molecularity and shape of complexes will be a valuable tool in RNA nanotechnology, especially for the rational design of therapeutic nucleic acids with high target specificity and the programmable response of the immune system of organisms.

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Section: Gel Shift Assay Analysissupporting

confidence: 78%

Section: Gel Shift Assay Analysissupporting

confidence: 63%

Section: Rna Nanomaachines Topology Regulationmentioning

confidence: 66%

mentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines

Kanarskaya,

Pyshnyi,

Lomzov

2023

Molecules

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Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies

Chubarov,

Endeward,

Kanarskaya

et al. 2024

Biomolecules

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Pulsed electron–electron double resonance (PELDOR) spectroscopy is a powerful method for determining nucleic acid (NA) structure and conformational dynamics. PELDOR with molecular dynamics (MD) simulations opens up unique possibilities for defining the conformational ensembles of flexible, three-dimensional, self-assembled complexes of NA. Understanding the diversity and structure of these complexes is vital for uncovering matrix and regulative biological processes in the human body and artificially influencing them for therapeutic purposes. To explore the reliability of PELDOR and MD simulations, we site-specifically attached nitroxide spin labels to oligonucleotides, which form self-assembled complexes between NA chains and exhibit significant conformational flexibility. The DNA complexes assembled from a pair of oligonucleotides with different linker sizes showed excellent agreement between the distance distributions obtained from PELDOR and calculated from MD simulations, both for the mean inter-spin distance and the distance distribution width. These results prove that PELDOR with MD simulations has significant potential for studying the structure and dynamics of conformational flexible complexes of NA.

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Hybrid RNA/DNA Concatemers and Self-Limited Complexes: Structure and Prospects for Therapeutic Applications

Kanarskaya,

Novikova,

Lomzov

2024

Molecules

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The development of new convenient tools for the design of multicomponent nucleic acid (NA) complexes is one of the challenges in biomedicine and NA nanotechnology. In this paper, we analyzed the formation of hybrid RNA/DNA concatemers and self-limited complexes by a pair of oligonucleotides using UV melting, circular dichroism spectroscopy, and a gel shift assay. Effects of the size of the linker between duplex-forming segments of the oligonucleotides on complexes’ shape and number of subunits were compared and systematized for RNA/DNA, DNA/DNA, and RNA/RNA assemblies. The data on complex types summarized here as heat maps offer a convenient tool for the design of NA constructs. General rules found for RNA/DNA, DNA/DNA, and RNA/RNA complexes allow not only designing complexes with desired structures but also purposefully transforming their geometry. The A-form of the double helix of the studied RNA/DNA complexes was confirmed by circular dichroism analysis. Moreover, we show for the first time efficient degradation of RNA in hybrid self-limited complexes by RNase H and imidazole. The results open up new prospects for the design of supramolecular complexes as tools for nanotechnology, nanomachinery, and biomedical applications.

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

Abstract: 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.

Cited by 3 publications

References 62 publications

Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines

Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines

Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies

Hybrid RNA/DNA Concatemers and Self-Limited Complexes: Structure and Prospects for Therapeutic Applications

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