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Complex RNA-DNA hybrid nanoshapes from iterative mix-and-match screening

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.

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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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Correspondence to Thomas Hermann.

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Chen, S., Zhang, Z., Alforque, E. et al. Complex RNA-DNA hybrid nanoshapes from iterative mix-and-match screening. Nano Res. 14, 46–51 (2021). https://doi.org/10.1007/s12274-020-3008-1

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  • DOI: https://doi.org/10.1007/s12274-020-3008-1

Keywords

  • nucleic acid nanotechnology
  • nanoshapes
  • ribonucleic acid (RNA) three-way junction (3WJ)
  • RNA
  • deoxyribonucleic acid (DNA)
  • sub-10 nm features