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Issue 5, 2020
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RNA–DNA hybrid nanoshapes that self-assemble dependent on ligand binding

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Abstract

Self-assembly of nucleic acid nanostructures is driven by selective association of oligonucleotide modules through base pairing between complementary sequences. Herein, we report the development of RNA–DNA hybrid nanoshapes that conditionally assemble under the control of an adenosine ligand. The design concept for the nanoshapes relies on ligand-dependent stabilization of DNA aptamers that serve as connectors between marginally stable RNA corner modules. Ligand-dependent RNA–DNA nanoshapes self-assemble in an all-or-nothing process by coupling adenosine binding to the formation of circularly closed structures which are stabilized through continuous base stacking in the resulting polygons. By screening combinations of various DNA aptamer constructs with RNA corner modules for the formation of stable complexes, we identified adenosine-dependent nanosquares whose shape was confirmed by atomic force microscopy. As a proof-of-concept for sensor applications, adenosine-responsive FRET-active nanosquares were obtained by dye conjugation of the DNA aptamer components.

Graphical abstract: RNA–DNA hybrid nanoshapes that self-assemble dependent on ligand binding

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Supplementary files

Article information


Submitted
14 Nov 2019
Accepted
20 Jan 2020
First published
21 Jan 2020

Nanoscale, 2020,12, 3302-3307
Article type
Paper

RNA–DNA hybrid nanoshapes that self-assemble dependent on ligand binding

S. Chen and T. Hermann, Nanoscale, 2020, 12, 3302
DOI: 10.1039/C9NR09706F

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