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Nano Research 2019, 12(8): 1952-1958 https://doi.org/10.1007/s12274-019-2463-z
Research Article | Issue | Published: 11 July 2019

Construction of RNA nanotubes

Show Author's Information Hui Li1,†,,, ,§,  Shaoying Wang1,‡,,, ,§,  Zhouxiang Ji1,§,  Congcong Xu1,  Lyudmila S. Shlyakhtenko2,  Peixuan Guo1( )
Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology&Cell Biology, College of Medicine,Dorothy M.Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH,43210,USA;
UNMC Nanoimaging Core Facility, Department of Pharmaceutical Sciences,College of Pharmacy University of Nebraska Medical Center,Omaha, NE,68182,USA;

† Present address: University of California, San Francisco, CA, 94158, USA

§ Hui Li, Shaoying Wang, and Zhouxiang Ji contributed equally to this work.

Keywords:
RNA nanotechnology, peptide sensing, RNA nanotube, nanobiotechnology
Topics:
Atomic force microscopyCholesterol Lipid bilayersNanobiotechnologyPeptidesRNA
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Li H, Wang S, Ji Z, et al. Construction of RNA nanotubes. Nano Research, 2019, 12(8): 1952-1958. https://doi.org/10.1007/s12274-019-2463-z
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Abstract Full text Electronic supplementary material About this article

Nanotubes are miniature materials with significant potential applications in nanotechnological, medical, biological and material sciences. The quest for manufacturing methods of nano-mechanical modules is in progress. For example, the application of carbon nanotubes has been extensively investigated due to the precise width control, but the precise length control remains challenging. Here we report two approaches for the one-pot self-assembly of RNA nanotubes. For the first approach, six RNA strands were used to assemble the nanotube by forming a 11 nm long hollow channel with the inner diameter of 1.7 nm and the outside diameter of 6.3 nm. For the second approach, six RNA strands were designed to hybridize with their neighboring strands by complementary base pairing and formed a nanotube with a six-helix hollow channel similar to the nanotube assembled by the first approach. The fabricated RNA nanotubes were characterized by gel electrophoresis and atomic force microscopy (AFM), confirming the formation of nanotube-shaped RNA nanostructures. Cholesterol molecules were introduced into RNA nanotubes to facilitate their incorporation into lipid bilayer. Incubation of RNA nanotube complex with the free-standing lipid bilayer membrane under applied voltage led to discrete current signatures. Addition of peptides into the sensing chamber revealed discrete steps of current blockage. Polyarginine peptides with different lengths can be detected by current signatures, suggesting that the RNA-cholesterol complex holds the promise of achieving single molecule sensing of peptides.


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Abstract
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Electronic supplementary material
About this article

Construction of RNA nanotubes

Show Author's information Hui Li1,†,,, ,§, Shaoying Wang1,‡,,, ,§, Zhouxiang Ji1,§, Congcong Xu1, Lyudmila S. Shlyakhtenko2, Peixuan Guo1( )
Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology&Cell Biology, College of Medicine,Dorothy M.Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH,43210,USA;
UNMC Nanoimaging Core Facility, Department of Pharmaceutical Sciences,College of Pharmacy University of Nebraska Medical Center,Omaha, NE,68182,USA;

† Present address: University of California, San Francisco, CA, 94158, USA

§ Hui Li, Shaoying Wang, and Zhouxiang Ji contributed equally to this work.

Abstract

Nanotubes are miniature materials with significant potential applications in nanotechnological, medical, biological and material sciences. The quest for manufacturing methods of nano-mechanical modules is in progress. For example, the application of carbon nanotubes has been extensively investigated due to the precise width control, but the precise length control remains challenging. Here we report two approaches for the one-pot self-assembly of RNA nanotubes. For the first approach, six RNA strands were used to assemble the nanotube by forming a 11 nm long hollow channel with the inner diameter of 1.7 nm and the outside diameter of 6.3 nm. For the second approach, six RNA strands were designed to hybridize with their neighboring strands by complementary base pairing and formed a nanotube with a six-helix hollow channel similar to the nanotube assembled by the first approach. The fabricated RNA nanotubes were characterized by gel electrophoresis and atomic force microscopy (AFM), confirming the formation of nanotube-shaped RNA nanostructures. Cholesterol molecules were introduced into RNA nanotubes to facilitate their incorporation into lipid bilayer. Incubation of RNA nanotube complex with the free-standing lipid bilayer membrane under applied voltage led to discrete current signatures. Addition of peptides into the sensing chamber revealed discrete steps of current blockage. Polyarginine peptides with different lengths can be detected by current signatures, suggesting that the RNA-cholesterol complex holds the promise of achieving single molecule sensing of peptides.

Keywords: RNA nanotechnology, peptide sensing, RNA nanotube, nanobiotechnology

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Publication history
Copyright
Acknowledgements

Publication history

Received: 12 February 2019
Revised: 06 June 2019
Accepted: 17 June 2019
Published: 11 July 2019
Issue date: August 2019

Copyright

© Tsinghua University Press and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Acknowledgements

Acknowledgements

The research was supported by NIH grants R01 EB012135 and R01 EB019036. P. G.'s Sylvan G. Frank Endowed Chair position in Pharmaceutics and Drug Delivery is funded by the CM Chen Foundation. We would like to thank Lora McBride and Dr. Catherine Hunt for the manuscript modification.

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