Dual-probe RNA FRET-FISH in Yeast

Wadsworth, Gable M.; Parikh, Rasesh Y.; Kim, Harold D.

doi:10.21769/bioprotoc.2867

Cited by 1 publication

(1 citation statement)

References 6 publications

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“…The fluorogenic RNA aptamers, also known as “light-up” aptamers, activate small fluorophore molecules upon binding. , These reporters have shown some advantages over other imaging techniques such as FRET, FISH, and molecular beacons. , While the latest methods are limited to only exogenously introduced NANPs, the fluorescent dyes must be covalently linked to either the 5′- or 3′-end of nucleic acids, and the light-up RNA aptamers offer excellent real-time imaging that is label-free, protein-free, has a high signal-to-noise ratio, and possess modularity for simple sequence incorporation and tagging. ,− This opens endless possibilities to program functional NANPs and nucleic acid nanodevices for logical operation in vitro and in vivo. − …”

Section: Introductionmentioning

confidence: 99%

Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles

Hartung,

McCann,

Doe

et al. 2023

ACS Appl. Mater. Interfaces

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We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamersmalachite green (MG), broccoli, and mangowere embedded within NANPs as reporter domains to confirm shape transitions. While MG “lights up” within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.

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