TY - JOUR

T1 - Hybrid RNA/DNA Concatemers and Self-Limited Complexes:

T2 - Structure and Prospects for Therapeutic Applications

AU - Kanarskaya, Maria A.

AU - Novikova, Sofia V.

AU - Lomzov, Alexander A.

N1 - Сведения о финансировании Ministry of Education and Science of the Russian Federation 075-15-2022-263

PY - 2024/12/13

Y1 - 2024/12/13

N2 - 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.

AB - 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.

KW - concatemer

KW - hybrid RNA/DNA complex

KW - nucleic acid structure

KW - nucleic acid supramolecular complex

KW - rational design

KW - self-assembly

KW - self-limited complex

KW - hybrid RNA/DNA complex

KW - self-limited complex

KW - concatemer

KW - rational design

KW - self-assembly

KW - nucleic acid supramolecular complex

KW - nucleic acid structure

UR - https://www.mendeley.com/catalogue/73026c9c-b24c-3edf-b577-36dce6cc04ea/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85213248685&origin=inward&txGid=d0fe3b21763db774e02ed5af8a2d02df

U2 - 10.3390/molecules29245896

DO - 10.3390/molecules29245896

M3 - Article

C2 - 39769985

VL - 29

JO - Molecules

JF - Molecules

SN - 1420-3049

IS - 24

M1 - 5896

ER -