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Hybrid nucleic acid nanostructures partition architectural and functional roles between ribonucleic acid (RNA) joints and deoxyribonucleic acid (DNA) connectors. Nanoshapes self-assemble from nucleic acid modules through synergistic stabilization of marginally stable base pairing interactions within circularly closed polygons. Herein, we report the development of hybrid nanoshapes that include multiple different RNA modules such as internal loop and three-way junction (3WJ) motifs. An iterative mix-and-match screening approach was used to identify suitable DNA connectors that furnished stable nanoshapes for combinations of different RNA modules. The resulting complex multicomponent RNA-DNA hybrid nanoshapes were characterized by atomic force microscopy (AFM) imaging. Our research provides proof of concept for modular design, assembly and screening of RNA-DNA hybrid nanoshapes as building blocks for complex extended nucleic acid materials with features at the sub-10 nm scale.


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Complex RNA-DNA hybrid nanoshapes from iterative mix-and-match screening
Show Author's information Shi Chen3Zhiyuan Zhang1Eugene Alforque1Thomas Hermann1,2( )
Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
Center for Drug Discovery Innovation, University of California, San Diego, CA 92093, USA
Materials Science and Engineering Program, University of California, San Diego, CA 92093, USA
Abstract

Hybrid nucleic acid nanostructures partition architectural and functional roles between ribonucleic acid (RNA) joints and deoxyribonucleic acid (DNA) connectors. Nanoshapes self-assemble from nucleic acid modules through synergistic stabilization of marginally stable base pairing interactions within circularly closed polygons. Herein, we report the development of hybrid nanoshapes that include multiple different RNA modules such as internal loop and three-way junction (3WJ) motifs. An iterative mix-and-match screening approach was used to identify suitable DNA connectors that furnished stable nanoshapes for combinations of different RNA modules. The resulting complex multicomponent RNA-DNA hybrid nanoshapes were characterized by atomic force microscopy (AFM) imaging. Our research provides proof of concept for modular design, assembly and screening of RNA-DNA hybrid nanoshapes as building blocks for complex extended nucleic acid materials with features at the sub-10 nm scale.

Keywords: nucleic acid nanotechnology, nanoshapes, ribonucleic acid (RNA) three-way junction (3WJ), RNA, deoxyribonucleic acid (DNA), sub-10 nm features
Received: 06 June 2020 Revised: 22 July 2020 Accepted: 26 July 2020 Published: 05 January 2021 Issue date: January 2021
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Publication history

Received: 06 June 2020
Revised: 22 July 2020
Accepted: 26 July 2020
Published: 05 January 2021
Issue date: January 2021

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© Tsinghua University Press and Springer-Verlag GmbH Germany, part of Springer Nature

Acknowledgements

This work was supported by the National Science Foundation, Chemical Measurement & Imaging Program, grant number CHE CMI 1608287. We thank A. J. Lushnikov for helping with AFM imaging.

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