Complex RNA-DNA hybrid nanoshapes from iterative mix-and-match screening
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Complex RNA–DNA hybrid nanoshapes from iterative mix-andmatch screening Shi Chen3, Zhiyuan Zhang1, Eugene Alforque1, and Thomas Hermann1,2 () 1
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 3 Materials Science and Engineering Program, University of California, San Diego, CA 92093, USA 2
© Tsinghua University Press and Springer-Verlag GmbH Germany, part of Springer Nature 2020 Received: 6 June 2020 / Revised: 22 July 2020 / Accepted: 26 July 2020
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
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Introduction
Applications of nucleic acids in soft materials nanotechnology exploit the predictable folding and self-assembly of the biopolymer through predominantly base pair formation between sequencecomplementary oligonucleotide segments. Designing nanostructures that include predetermined folds of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) modules is in many cases reduced to defining the overall topology of the desired architecture which, in turn, establishes connection of the building blocks [1–4]. While RNA and DNA had been used largely separately to create nucleic acid nano-materials, RNA–DNA hybrid assemblies have recently emerged as a promising carrier material for functional biomolecules and the dynamic construction of reversible nano-objects [5–9]. We have previously introduced a versatile kit of hybrid nanoshapes that assemble from both RNA architectural joints derived from a single type of RNA motif and double-helical DNA modules as functional connector modules [10]. Hybrid nucleic acid architectures combine RNA modules that introduce structural complexity wit h DNA components t hat allow for straightforward chemical modification and inclusion of diverse protein binding sites as a toolkit for the creation of composite soft materials. Robust hybrid nanoshapes self-assemble from R
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