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Noble JE, Hsiao YW, Kepiro IE, De Santis E, Hoose A, Augagneur C, Lamarre B, Briones A, Hammond K, Bray DJ, Crain J, Ryadnov MG. A Nonlinear Peptide Topology for Synthetic Virions. ACS NANO 2024; 18:29956-29967. [PMID: 39402499 DOI: 10.1021/acsnano.4c10662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2024]
Abstract
a nonlinear de novo peptide topology for the assembly of synthetic virions is reported. The topology is a backbone cyclized amino-acid sequence in which polar l- and hydrophobic d-amino acid residues of the same-type alternate. This arrangement introduces pseudo C4 symmetries of side chains within the same cyclopeptide ring, allowing for the lateral propagation of cyclopeptides into networks with a [3/6, 4]-fold rotational symmetry closing into virus-like shells. A combination of computational and experimental approaches was used to establish that the topology forms morphologically uniform, nonaggregating and nontoxic nanoscale shells. These effectively encapsulate genetic cargo and promote its intracellular delivery and a target genetic response. The design introduces a nanotechnology inspired solution for engineering virus-like systems thereby expanding traditional molecular biology approaches used to create artificial biology to chemical space.
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Affiliation(s)
- James E Noble
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Ya-Wen Hsiao
- The Hartree Centre, STFC Daresbury Laboratory, Warrington WA4 4AD, U.K
| | - Ibolya E Kepiro
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | | | - Alex Hoose
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | | | | | - Andrea Briones
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - David J Bray
- The Hartree Centre, STFC Daresbury Laboratory, Warrington WA4 4AD, U.K
| | - Jason Crain
- IBM Research Europe, Hartree Centre, Daresbury WA4 4AD, U.K
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Physics, King's College London, Strand Lane, London WC2R 2LS, U.K
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Noble JE, Vila-Gómez P, Rey S, Dondi C, Briones A, Aggarwal P, Hoose A, Baran M, Ryadnov MG. Folding-Mediated DNA Delivery by α-Helical Amphipathic Peptides. ACS Biomater Sci Eng 2023; 9:2584-2595. [PMID: 37014978 DOI: 10.1021/acsbiomaterials.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The renaissance gene therapy experiences these days requires specialist biomaterials and a systemic understanding of major factors influencing their ability to deliver genetic material. Peptide transfection systems represent a major class of such biomaterials. Several peptidic reagents have been commercialized to date. However, a comparative assessment of peptide sequences alone without auxiliary support or excipients against a common determinant for their ability to complex and deliver DNA has been lacking. This study cross-compares commercial and experimental transfection reagents from the same family of helical amphiphiles. Factors defining the efficacy of DNA delivery including cell uptake and gene expression are assessed along with cytotoxicity and DNA complexation. The results show that despite differences in sequence composition, length, and origin, peptide reagents of the same structural family exhibit similar characteristics and limitations with common variability trends. The cross-comparison revealed that functional DNA delivery is independent of the peptide sequence used but is mediated by the ability of the reagents to co-fold with DNA. Peptide folding proved to be the common determinant for DNA complexation and delivery by peptidic transfection reagents.
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Affiliation(s)
- James E Noble
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Paula Vila-Gómez
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Brain Sciences, Imperial College London, London W12 0TR, U.K
| | - Stephanie Rey
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Camilla Dondi
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Andrea Briones
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Purnank Aggarwal
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Alex Hoose
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Maryana Baran
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Physics, King's College London, London WC2R 2LS, U.K
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Rey S, Faruqui N, Hoose A, Dondi C, Ryadnov MG. Designer protein pseudo-capsids targeting intracellular bacteria. Biomater Sci 2021; 9:6807-6812. [PMID: 34491257 DOI: 10.1039/d1bm01235e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of multidrug-resistant bacteria stimulates the search for antimicrobial materials capable of addressing challenges conventional antibiotics fail to address. The ability to target intracellular bacteria remains one of the most fundamental tasks for contemporary antimicrobial treatments. Here we report engineered protein pseudo-capsids targeting bacteria internalised in macrophages. Using a combination of live-cell imaging and single-cell electron microscopy analysis we show that these materials effectively disrupt the bacteria without affecting the host cells. The study offers a disruptive antimicrobial strategy demonstrating potential for developing principally more challenging mechanisms for bacteria to overcome.
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Affiliation(s)
- Stephanie Rey
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Nilofar Faruqui
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Alex Hoose
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Camilla Dondi
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK. .,Department of Physics, King's College London, London, WC2R 2LS, UK
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Vila-Gómez P, Noble JE, Ryadnov MG. Peptide Nanoparticles for Gene Packaging and Intracellular Delivery. Methods Mol Biol 2021; 2208:33-48. [PMID: 32856254 DOI: 10.1007/978-1-0716-0928-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Efficient gene transfer is necessary for advanced biotechnologies ranging from gene therapy to synthetic biology. Peptide nanoparticles provide suitable packaging systems promoting targeted gene expression or silencing. Though these systems have yet to match the transfection efficacy of viruses, they are typically devoid of drawbacks characteristic of virus-based vectors, including insertional mutagenesis, low packaging capacities, and strong immune responses. Given the promise nanoparticle formulations hold for gene delivery, methods of their preparation and accurate analysis of their physicochemical and biological properties become indispensable for progress toward systems that seek to outperform viral vectors. Herein, we report a comprehensive protocol for the preparation and characterization of archetypal peptide nanoparticles resulting from nonspecific and noncovalent complexation with RNA and DNA.
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Affiliation(s)
| | - James E Noble
- National Physical Laboratory, Teddington, Middlesex, UK
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Revealing Sources of Variation for Reproducible Imaging of Protein Assemblies by Electron Microscopy. MICROMACHINES 2020; 11:mi11030251. [PMID: 32120860 PMCID: PMC7143348 DOI: 10.3390/mi11030251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/27/2022]
Abstract
Electron microscopy plays an important role in the analysis of functional nano-to-microstructures. Substrates and staining procedures present common sources of variation for the analysis. However, systematic investigations on the impact of these sources on data interpretation are lacking. Here we pinpoint key determinants associated with reproducibility issues in the imaging of archetypal protein assemblies, protein shells, and filaments. The effect of staining on the morphological characteristics of the assemblies was assessed to reveal differential features for anisotropic (filaments) and isotropic (shells) forms. Commercial substrates and coatings under the same staining conditions gave comparable results for the same model assembly, while highlighting intrinsic sample variations including the density and heterogenous distribution of assemblies on the substrate surface. With no aberrant or disrupted structures observed, and putative artefacts limited to substrate-associated markings, the study emphasizes that reproducible imaging must correlate with an optimal combination of substrate stability, stain homogeneity, accelerating voltage, and magnification.
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Whitehouse WL, Noble JE, Ryadnov MG, Howorka S. Cholesterol Anchors Enable Efficient Binding and Intracellular Uptake of DNA Nanostructures. Bioconjug Chem 2019; 30:1836-1844. [PMID: 30821443 DOI: 10.1021/acs.bioconjchem.9b00036] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA nanostructures constitute a rapidly advancing tool-set for exploring cell-membrane functions and intracellular sensing or advancing delivery of biomolecular cargo into cells. Chemical conjugation with lipid anchors can mediate binding of DNA nanostructures to synthetic lipid bilayers, yet how such structures interact with biological membranes and internalize cells has not been shown. Here, an archetypal 6-duplex nanobundle is used to investigate how lipid conjugation influences DNA cell binding and internalization kinetics. Cellular interactions of DNA nanobundles modified with one and three cholesterol anchors were assessed using flow cytometry and confocal microscopy. Nuclease digestion was used to distinguish surface-bound DNA, which is nuclease accessible, from internalized DNA. Three cholesterol anchors were found to enhance cellular association by up to 10-fold when compared with unmodified DNA. The bundles were endocytosed efficiently within 24 h. The results can help design controlled DNA binding and trafficking into cells.
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Affiliation(s)
- William L Whitehouse
- Department of Chemistry, Institute of Structural and Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
| | - James E Noble
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| | - Stefan Howorka
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
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Hayouka Z, Bella A, Stern T, Ray S, Jiang H, Grovenor CRM, Ryadnov MG. Binary Encoding of Random Peptide Sequences for Selective and Differential Antimicrobial Mechanisms. Angew Chem Int Ed Engl 2017; 56:8099-8103. [DOI: 10.1002/anie.201702313] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/08/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition; The Hebrew University of Jerusalem; Rehovot 76100 Israel
| | - Angelo Bella
- National Physical Laboratory; Teddington TW11 0LW UK
| | - Tal Stern
- Institute of Biochemistry, Food Science and Nutrition; The Hebrew University of Jerusalem; Rehovot 76100 Israel
| | - Santanu Ray
- SET; University of Brighton; Brighton BN2 4GJ UK
| | - Haibo Jiang
- CMCA; University of Western Australia; Perth 6009 Australia
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Hayouka Z, Bella A, Stern T, Ray S, Jiang H, Grovenor CRM, Ryadnov MG. Binary Encoding of Random Peptide Sequences for Selective and Differential Antimicrobial Mechanisms. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition; The Hebrew University of Jerusalem; Rehovot 76100 Israel
| | - Angelo Bella
- National Physical Laboratory; Teddington TW11 0LW UK
| | - Tal Stern
- Institute of Biochemistry, Food Science and Nutrition; The Hebrew University of Jerusalem; Rehovot 76100 Israel
| | - Santanu Ray
- SET; University of Brighton; Brighton BN2 4GJ UK
| | - Haibo Jiang
- CMCA; University of Western Australia; Perth 6009 Australia
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