A mini DNA–RNA hybrid origami nanobrick

Zhou, Lifeng; Chandrasekaran, Arun Richard; Yan, Mengwen; Valsangkar, Vibhav; Feldblyum, Jeremy I.; Sheng, Jia; Halvorsen, Ken

doi:10.1039/d1na00026h

Cited by 13 publications

(19 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S1 ). The TE pH 7.5 + 40 mM NaCl buffer and overnight folding protocol reported for 3D bricklike RNA:DNA origami 59 led to a considerably greater mobility shift with a more diffuse band, indicating a less compactly folded structure for both wireframe particles characterized here ( Supplementary Fig. S1 ).…”

Section: Resultsmentioning

confidence: 82%

“…For RNA:DNA dual-duplex wireframe origami, we adopted an analogous dual-duplex DNA wireframe origami annealing protocol 18 , albeit reducing incubation time at high temperatures, omitting divalent cations (300 mM KCl instead of MgCl2), and lowering the pH (10 mM HEPES pH 7.5 instead of 1x TAE pH 8.0) to minimize RNA instability. We compared our selected protocol to two others employed in published RNA:DNA origami designs, one reported to fold 2D structures 61 and another to fold a 3D bricklike structure 59 . Gel mobility shift Starting with a target polyhedron and scaffold sequence as inputs, we algorithmically route the scaffold through the polyhedron and route and assign staple for I. edges with no scaffold crossover, II.…”

Section: Sequence Design and Biochemical Characterization Of 3d Rna-s...mentioning

confidence: 99%

“…Following the protocol from Wang et al 61 , we mixed 20 nM purified scaffold with 200 nM individual staples in 40 mM Tris pH 8.0 with 20 mM acetic acid, 2 mM EDTA, and 12.5 mM magnesium acetate, and annealed by incubation at 65ºC for 10 min, 50ºC for 10 min, 37ºC for 10 min, 25ºC for 10 min, ending with a hold at 4ºC. Following the protocol from Zhou et al 59 , we mixed 20 nM purified scaffold with 200 nM individual staples in 5 mM Tris pH 7.5 with 1 mM EDTA and 40 mM NaCl, annealed using an overnight folding ramp (Starting at 65ºC, hold for 1.5 min per cycle and cycle 349x, decreasing by 0.1ºC each cycle, then at 30ºC hold for 2 min per cycle and cycle 99x, again decreasing by 0.1ºC each cycle, ending with a hold at 4ºC).…”

Section: Hybrid Rna:dna Nanoparticle Folding and Characterizationmentioning

confidence: 99%

See 2 more Smart Citations

3D RNA-scaffolded wireframe origami

Parsons

Allan

et al. 2022

Preprint

View full text Add to dashboard Cite

Hybrid RNA:DNA origami, in which a long RNA scaffold strand is folded into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of wireframe RNA-scaffolded origami in three dimensions rendered as polyhedra composed of dual-duplex edges. We computationally designed, fabricated, and characterized tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterized secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing for the first time insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.

show abstract

Section: Resultsmentioning

confidence: 82%

Section: Sequence Design and Biochemical Characterization Of 3d Rna-s...mentioning

confidence: 99%

Section: Hybrid Rna:dna Nanoparticle Folding and Characterizationmentioning

confidence: 99%

See 1 more Smart Citation

3D RNA-scaffolded wireframe origami

Parsons

Allan

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…In this way, a short single‐stranded probe is extruded out of the DNA nanoparticle to hybridize with the part of the nucleic acid‐based drugs. This relatively mild condition (usually <37 °C) is not only suitable for RNA‐based drugs, [ 55 ] but also enables the coloading of multiple drugs. [ 56 ] However, the sequence of probe needs to be accurately designed to form stable tethering while minimizing misfolding.…”

Section: Methods Of Loading Various Functional Groupsmentioning

confidence: 99%

Cellular Ingestible DNA Nanostructures for Biomedical Applications

Zhu

et al. 2022

Advanced NanoBiomed Research

View full text Add to dashboard Cite

Delivering functional substances across the cell membrane barriers has been a great challenge in biomedicine. Among various strategies to improve cellular uptake, DNA nanostructures, with different shapes and sizes, supply as suitable platforms for delivering a wide range of functional substances to cells. With great programmability, biocompatibility, and biostability, DNA nanostructure‐based delivery systems have shown and have succeeded in anticancer therapy, antibacterial treatment, gene editing, vaccine development, and stem cell bioengineering. Herein, the development and construction of various cellular ingestible DNA nanostructures are described, the loading strategies of functional substances are summarized, current biomedical applications are overviewed, and finally the remaining challenges and opportunities are discussed.

show abstract

“…24 While many 2D and 3D DNA origami have been designed and visualized, hybrid RNA/DNA origami remains less explored despite the great potential to introduce functional RNA (e.g., RNA aptamers or siRNA) or mRNA as scaffolds. [25][26][27][28][29] Recently, we proposed a custom-made software to select De Bruijn sequences (DBS of order 6) to be used as a scaffold in the origami synthesis. The obtained scaffolds are uniquely addressable and 'bio-orthogonal' by design and can be successfully folded into DNA or RNA origami 13,14 and RNA/DNA hybrid origami.…”

Section: Activation Of the Split Broccoli Aptamer Through A Hybrid Rn...mentioning

confidence: 99%

Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing

Torelli

Shirt-Ediss

Navarro

et al. 2022

Preprint

View full text Add to dashboard Cite

Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence.First, an RNA three-way junction harbouring the split system was assembled in an E. coli based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a ‘bio-orthogonal’ hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect femtomoles of a Campylobacter spp. DNA target sequence.Potential applications of our system include real-time monitoring of the self-assembly of nucleic acid-based devices in vivo and of intracellular delivery of therapeutic nanostructures, as well as in vitro and in vivo detection of different DNA/RNA target.

show abstract

A mini DNA–RNA hybrid origami nanobrick

Abstract: DNA origami is typically used to fold a long single-stranded DNA scaffold into nanostructures with complex geometries using many short DNA staple strands. Integration of RNA into nucleic acid nanostructures...

Cited by 13 publications

References 34 publications

3D RNA-scaffolded wireframe origami

3D RNA-scaffolded wireframe origami

Cellular Ingestible DNA Nanostructures for Biomedical Applications

Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing

Contact Info

Product

Resources

About