Nanocages for virus inhibition

Chauhan, Neha; Wang, Xing

doi:10.1038/s41563-021-01088-y

Cited by 6 publications

(5 citation statements)

References 10 publications

(10 reference statements)

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“…There is an urgent need to improve the performance of virus diagnostics both in point-of-care (POC) settings and with high sensitivities to help curb the spread of highly contagious diseases like COVID-19. − Nanomaterials and nanotechnology have provided promising solutions to tackling infectious diseases. − We have previously demonstrated a “DNA Star” strategy for creating a biosensor by targeting the immobile envelope protein clusters (called ED3) exposed on the outer surface of the dengue virus (DENV) . DENV envelope proteins are rigid and arranged into a shell-like structure on the viral surface, making them suitable for a star-shaped rigid matching.…”

Section: Introductionmentioning

confidence: 99%

Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus

et al. 2022

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We present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for selective recognition and high-affinity capture of intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild-type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers release fluorescence signals upon virus binding that are easily read with a handheld fluorimeter for a rapid (in 10 min), simple (mix-and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼$1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1 × 10 3 -fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

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Section: Introductionmentioning

confidence: 99%

Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus

et al. 2022

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“…Potential ligands include proteins, nanoparticles, oligonucleotides, fluorophores, and other biomolecules. 256 − 260 Further, the biocompatibility, biostability and nontoxicity of DNA nanostructures have made them useful in biosensing and drug delivery applications.…”

Section: Role Of Dna Nanotechnology In Viral Diagnostics and Therapymentioning

confidence: 99%

“…Moreover, the chemical nature and predictability of DNA base pairing allow for the precise decoration of DNA nanostructures with ligands at sub-nanometer resolution. Potential ligands include proteins, nanoparticles, oligonucleotides, fluorophores, and other biomolecules. − Further, the biocompatibility, biostability and nontoxicity of DNA nanostructures have made them useful in biosensing and drug delivery applications.…”

Section: Role Of Dna Nanotechnology In Viral Diagnostics and Therapymentioning

confidence: 99%

Aptamers for Viral Detection and Inhibition

et al. 2022

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Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus–aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.

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“…Many spherical viral capsids adopt icosahedral structures, which is fully characterized by 60 symmetry operations. To elucidate the mechanism of self-assembly of molecules 1,2 and also the rational design of capsid-based nanocontainers [3][4][5][6] , it is important to understand how icosahedral symmetry imposes geometric constraints on the interaction patterns between subunit proteins. The Caspar-Klug (CK) theory is currently used as a major tool for classifying capsid structures 7 .…”

Section: Introductionmentioning

confidence: 99%

Explicit description of viral capsid subunit shapes by unfolding dihedrons

Toyooka,

Nishimoto,

Tendo

et al. 2024

Preprint

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Viral capsid assembly and the design of capsid-based nanocontainers critically depend on understanding the shapes and interfaces of constituent protein subunits. However, a comprehensive framework for characterizing these features is still lacking. Here, we introduce a novel approach based on spherical tiling theory that explicitly describes the 2D shapes and interfaces of subunits in icosahedral capsids. Our method unfolds spherical dihedrons defined by icosahedral symmetry axes, enabling systematic characterization of all possible subunit geometries. Applying this framework to real T=1 capsid structures reveals distinct interface groups within this single classification, with variations in interaction patterns around 3-fold and 5-fold symmetry axes. We validate our classification through molecular docking simulations, demonstrating its consistency with physical subunit interactions. This analysis suggests different assembly pathways for capsid nucleation. Our general framework is applicable to other triangular numbers, paving the way for broader studies in structural virology and nanomaterial design.

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Nanocages for virus inhibition

Cited by 6 publications

References 10 publications

Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus

Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus

Aptamers for Viral Detection and Inhibition

Explicit description of viral capsid subunit shapes by unfolding dihedrons

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