In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs

Li, Mo; Zheng, Mengxi; Wu, Shao Peng; Tian, Cheng; Liu, Di; Weizmann, Yossi; Jiang, Wen; Wang, Guansong; Mao, Chengde

doi:10.1038/s41467-018-04652-4

Cited by 81 publications

(84 citation statements)

References 41 publications

(40 reference statements)

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“…Depending on their shape, size, and sequence, RNA nanoparticles can exhibit a strong immunogenicity that can be exploited in drug delivery applications or as adjuvants/reagents for immunotherapy treatments [207]. RNA can be used as a functional scaffold, as in the case of ribozymes, aptamers and siRNA [209]. The suitable spatial arrangement and control of the functional RNA domains allow the development of promising applications in RNA-based therapeutics and nanomedicine [209].…”

Section: Self-assembly Of Oligonucleotides (Dna and Rna)mentioning

confidence: 99%

Self-Assembly of Organic Nanomaterials and Biomaterials: The Bottom-Up Approach for Functional Nanostructures Formation and Advanced Applications

et al. 2020

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In this paper, we survey recent advances in the self-assembly processes of novel functional platforms for nanomaterials and biomaterials applications. We provide an organized overview, by analyzing the main factors that influence the formation of organic nanostructured systems, while putting into evidence the main challenges, limitations and emerging approaches in the various fields of nanotechology and biotechnology. We outline how the building blocks properties, the mutual and cooperative interactions, as well as the initial spatial configuration (and environment conditions) play a fundamental role in the construction of efficient nanostructured materials with desired functional properties. The insertion of functional endgroups (such as polymers, peptides or DNA) within the nanostructured units has enormously increased the complexity of morphologies and functions that can be designed in the fabrication of bio-inspired materials capable of mimicking biological activity. However, unwanted or uncontrollable effects originating from unexpected thermodynamic perturbations or complex cooperative interactions interfere at the molecular level with the designed assembly process. Correction and harmonization of unwanted processes is one of the major challenges of the next decades and requires a deeper knowledge and understanding of the key factors that drive the formation of nanomaterials. Self-assembly of nanomaterials still remains a central topic of current research located at the interface between material science and engineering, biotechnology and nanomedicine, and it will continue to stimulate the renewed interest of biologist, physicists and materials engineers by combining the principles of molecular self-assembly with the concept of supramolecular chemistry.

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Section: Self-assembly Of Oligonucleotides (Dna and Rna)mentioning

confidence: 99%

Self-Assembly of Organic Nanomaterials and Biomaterials: The Bottom-Up Approach for Functional Nanostructures Formation and Advanced Applications

et al. 2020

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“…S8 in the ESM), presumably due to interaction between left (5'-UGUUAUACAG-3') and right (5'-CCGGUCCGGC-3') ssRNA scaffold regions, as previously noted [29]. Finally, smaller nanostructures were imaged as the result of a fragmentation during sample deposition and a disruption by AFM probes [25,54].…”

Section: Rna Origami Co-transcriptional Folding and Afm Imagingmentioning

confidence: 79%

“…Li and coll. [25] developed a different strategy in which the design concept was similar to the approach reported above, but avoiding the use of short "dovetail seams". The RNA nanostructures were designed based on natural motifs: the folding pathway was based on hairpin formation and tertiary interactions of unpaired residues.…”

mentioning

confidence: 99%

Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami

Torelli

Kozyra

Shirt-Ediss

et al. 2019

Preprint

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The scaffolded origami technique has provided an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and staple strands able to correctly fold in high yield into the nanoribbon. Synthesis is successfully confirmed by atomic force microscopy and the unpurified transcription reaction mixture is analyzed by an in gel-imaging assay where the transcribed RNA nanoribbons are able to capture the specific dye through the reconstituted split Broccoli aptamer showing a clear green fluorescent band. Finally, we simulate the RNA origami in silico using the nucleotide-level coarse-grained model oxRNA to investigate the thermodynamic stability of the assembled nanostructure in isothermal conditions over a period of time.Our work suggests that the scaffolded origami technique is a valid, and potentially more powerful, assembly alternative to the single-stranded origami technique for future in vivo applications. KEYWORDSCo-transcriptional folding, scaffolded RNA origami, bio-orthogonal, split Broccoli aptamer, oxRNA simulation 1 Introduction RNA plays sophisticated roles with different and essential coding and noncoding functions. mRNAs, tRNAs, rybozymes, aptamers and CRISPR RNAs are just few examples of RNA species in a vast functional repertoire. Considering the diversity in functional and structural motifs, the emerging field of RNA nanotechnology has been developing rapidly over the past years. As a consequence, a variety of RNA nanostructures with different functionalities, sizes and shapes have

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“…Construction of RNA‐based nanoarchitectures is usually performed in solution containing relatively high concentrations of divalent cations such as Mg 2+ to stabilize the structure. [3a,8] Applications in cells, which is in molecular crowding condition with various biomolecules, are also promising fields . These different conditions impact aptamer function by influencing intermolecular interactions as well as stabilities and structures of RNA aptamer itself.…”

Section: Numbers Of Analyzed Nucleobases At Randomized Position Of R‐mentioning

confidence: 99%

RNA‐Capturing Microsphere Particles (R‐CAMPs) for Optimization of Functional Aptamers

Endoh

Ohyama

Sugimoto

2019

Small

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RNA aptamers are useful building blocks for constructing functional nucleic acid‐based nanoarchitectures. The abilities of aptamers to recognize specific ligands have also been utilized for various biotechnological applications. Solution conditions, which can differ depending on the application, impact the affinity of the aptamers, and thus it is important to optimize the aptamers for the solution conditions to be employed. To simplify the aptamer optimization process, an efficient method that enables re‐selection of an aptamer from a partially randomized library is developed. The process relies on RNA‐capturing microsphere particles (R‐CAMPs): each particle displays different clones of identical DNA and RNA sequences. Using a fluorescence‐activated cell sorter, the R‐CAMPs that are linked to functional aptamers are sorted. It is demonstrated that after a single round of reselection, several functional aptamers, including the wild‐type, are selected from a library of 16 384 sequences. The selection using R‐CAMPs is further performed under the solution containing high concentration of ethylene glycol, suggesting applicability in various conditions to optimize an aptamer for a particular application. As any type of RNA clone can be displayed on the microspheres, the technology demonstrated here will be useful for the selection of RNAs based on diverse functions.

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In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs

Cited by 81 publications

References 41 publications

Self-Assembly of Organic Nanomaterials and Biomaterials: The Bottom-Up Approach for Functional Nanostructures Formation and Advanced Applications

Self-Assembly of Organic Nanomaterials and Biomaterials: The Bottom-Up Approach for Functional Nanostructures Formation and Advanced Applications

Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami

RNA‐Capturing Microsphere Particles (R‐CAMPs) for Optimization of Functional Aptamers

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