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Czarnecka J, Kwiatkowski M, Wiśniewski M, Roszek K. Protein Corona Hinders N-CQDs Oxidative Potential and Favors Their Application as Nanobiocatalytic System. Int J Mol Sci 2021; 22:ijms22158136. [PMID: 34360901 PMCID: PMC8347256 DOI: 10.3390/ijms22158136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/13/2023] Open
Abstract
The oxidative properties of nanomaterials arouse legitimate concerns about oxidative damage in biological systems. On the other hand, the undisputable benefits of nanomaterials promote them for biomedical applications; thus, the strategies to reduce oxidative potential are urgently needed. We aimed at analysis of nitrogen-containing carbon quantum dots (N-CQDs) in terms of their biocompatibility and internalization by different cells. Surprisingly, N-CQD uptake does not contribute to the increased oxidative stress inside cells and lacks cytotoxic influence even at high concentrations, primarily through protein corona formation. We proved experimentally that the protein coating effectively limits the oxidative capacity of N-CQDs. Thus, N-CQDs served as an immobilization support for three different enzymes with the potential to be used as therapeutics. Various kinetic parameters of immobilized enzymes were analyzed. Regardless of the enzyme structure and type of reaction catalyzed, adsorption on the nanocarrier resulted in increased catalytic efficiency. The enzymatic-protein-to-nanomaterial ratio is the pivotal factor determining the course of kinetic parameter changes that can be tailored for enzyme application. We conclude that the above properties of N-CQDs make them an ideal support for enzymatic drugs required for multiple biomedical applications, including personalized medical therapies.
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Affiliation(s)
- Joanna Czarnecka
- Department of Biochemistry, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Correspondence: (J.C.); (M.W.); (K.R.)
| | - Mateusz Kwiatkowski
- Chair of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland;
| | - Marek Wiśniewski
- Physicochemistry of Carbon Materials Research Group, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Correspondence: (J.C.); (M.W.); (K.R.)
| | - Katarzyna Roszek
- Department of Biochemistry, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Correspondence: (J.C.); (M.W.); (K.R.)
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2
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Single Molecule Characterization of Amyloid Oligomers. Molecules 2021; 26:molecules26040948. [PMID: 33670093 PMCID: PMC7916856 DOI: 10.3390/molecules26040948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
The misfolding and aggregation of polypeptide chains into β-sheet-rich amyloid fibrils is associated with a wide range of neurodegenerative diseases. Growing evidence indicates that the oligomeric intermediates populated in the early stages of amyloid formation rather than the mature fibrils are responsible for the cytotoxicity and pathology and are potentially therapeutic targets. However, due to the low-populated, transient, and heterogeneous nature of amyloid oligomers, they are hard to characterize by conventional bulk methods. The development of single molecule approaches provides a powerful toolkit for investigating these oligomeric intermediates as well as the complex process of amyloid aggregation at molecular resolution. In this review, we present an overview of recent progress in characterizing the oligomerization of amyloid proteins by single molecule fluorescence techniques, including single-molecule Förster resonance energy transfer (smFRET), fluorescence correlation spectroscopy (FCS), single-molecule photobleaching and super-resolution optical imaging. We discuss how these techniques have been applied to investigate the different aspects of amyloid oligomers and facilitate understanding of the mechanism of amyloid aggregation.
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McGraw E, Dissanayaka RH, Vaughan JC, Kunte N, Mills G, Laurent GM, Avila LA. Laser-Assisted Delivery of Molecules in Fungal Cells. ACS APPLIED BIO MATERIALS 2020; 3:6167-6176. [PMID: 35021749 DOI: 10.1021/acsabm.0c00720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fungal infections are becoming a global health problem. A major limiting factor for the development of antifungals is the high impermeability of the rigid and thick fungal cell wall. Compared to mammalian cells, fungal cells are more resilient to perforation due to the presence of this carbohydrate armor. While a few methods have been reported to penetrate the fungal cell wall, such as electroporation, biolistics, glass beads, and the use of monovalent cations, such methods are generally time-consuming, compromise cell viability, and often lead to low permeation rates. In addition, their use remains limited to in vitro applications due to the collateral damage that these techniques could cause to healthy living tissues. Presented in this study is a delivery approach based on the generation of transient breaks, or pores, in the cell wall. Breaks are generated by cavitation and shock waves resulting from the irradiation of gold nanoparticles with a femtosecond infrared laser. Such an approach enabled the delivery of membrane impermeable molecules (i.e., calcein and plasmid DNA) into Saccharomyces cerevisiae, a fungal model organism. This method is expected to exhibit high biocompatibility and holds potential for clinical applications for the treatment of fungal infections given that neither the laser irradiation nor the nanoparticles have been found to damage cells. Mechanistical aspects of photoporation, such as the proximity needed between the nanoparticle and the cell membrane for these processes to take place, are also discussed. Hence, the laser-assisted drug delivery approach described here is suitable for further preclinical evaluation in oral, vaginal, and skin mycoses where current treatments are insufficient due to host-related adverse reactions, poor fungal cell penetration, or risk of developing antifungal resistance.
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Affiliation(s)
- Erin McGraw
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, United States
| | - Radini H Dissanayaka
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - John C Vaughan
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Nitish Kunte
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, United States
| | - G Mills
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Guillaume M Laurent
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - L Adriana Avila
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, United States
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4
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Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N. Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon. Sci Rep 2018; 8:6989. [PMID: 29725066 PMCID: PMC5934368 DOI: 10.1038/s41598-018-25270-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022] Open
Abstract
RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
| | - Jerzy Wieslaw Kozyra
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom
| | - Jing-Ying Gu
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Ulrich Stimming
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Luca Piantanida
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Kislon Voïtchovsky
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
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5
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A peptide tag-specific nanobody enables high-quality labeling for dSTORM imaging. Nat Commun 2018; 9:930. [PMID: 29500346 PMCID: PMC5834503 DOI: 10.1038/s41467-018-03191-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/26/2018] [Indexed: 11/08/2022] Open
Abstract
Dense fluorophore labeling without compromising the biological target is crucial for genuine super-resolution microscopy. Here we introduce a broadly applicable labeling strategy for fixed and living cells utilizing a short peptide tag-specific nanobody (BC2-tag/bivBC2-Nb). BC2-tagging of ectopically introduced or endogenous proteins does not interfere with the examined structures and bivBC2-Nb staining results in a close-grained fluorophore labeling with minimal linkage errors. This allowed us to perform high-quality dSTORM imaging of various targets in mammalian and yeast cells. We expect that this versatile strategy will render many more demanding cellular targets amenable to dSTORM imaging.
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Lerner E, Cordes T, Ingargiol A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 2018; 359:eaan1133. [PMID: 29348210 PMCID: PMC6200918 DOI: 10.1126/science.aan1133] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Antonino Ingargiol
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yazan Alhadid
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
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7
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Kozyra J, Ceccarelli A, Torelli E, Lopiccolo A, Gu JY, Fellermann H, Stimming U, Krasnogor N. Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami. ACS Synth Biol 2017; 6:1140-1149. [PMID: 28414914 DOI: 10.1021/acssynbio.6b00271] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as a bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e., "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimized for high-yield folding. We demonstrate our fully synthetic scaffold design with both DNA and RNA origamis and describe a protocol to produce these bio-orthogonal and uniquely addressable origami scaffolds.
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Affiliation(s)
- Jerzy Kozyra
- Interdisciplinary
Computing and Complex BioSystems (ICOS), School
of Computing Science, ‡Centre for Synthetic Biology and the Bioeconomy (CSBB), ¶Centre for Bacterial
Cell Biology (CBCB), and §School of Chemistry, Newcastle University, Newcastle
upon Tyne, NE1 7RU, U.K
| | - Alessandro Ceccarelli
- Interdisciplinary
Computing and Complex BioSystems (ICOS), School
of Computing Science, ‡Centre for Synthetic Biology and the Bioeconomy (CSBB), ¶Centre for Bacterial
Cell Biology (CBCB), and §School of Chemistry, Newcastle University, Newcastle
upon Tyne, NE1 7RU, U.K
| | - Emanuela Torelli
- Interdisciplinary
Computing and Complex BioSystems (ICOS), School
of Computing Science, ‡Centre for Synthetic Biology and the Bioeconomy (CSBB), ¶Centre for Bacterial
Cell Biology (CBCB), and §School of Chemistry, Newcastle University, Newcastle
upon Tyne, NE1 7RU, U.K
| | - Annunziata Lopiccolo
- Interdisciplinary
Computing and Complex BioSystems (ICOS), School
of Computing Science, ‡Centre for Synthetic Biology and the Bioeconomy (CSBB), ¶Centre for Bacterial
Cell Biology (CBCB), and §School of Chemistry, Newcastle University, Newcastle
upon Tyne, NE1 7RU, U.K
| | - Jing-Ying Gu
- Interdisciplinary
Computing and Complex BioSystems (ICOS), School
of Computing Science, ‡Centre for Synthetic Biology and the Bioeconomy (CSBB), ¶Centre for Bacterial
Cell Biology (CBCB), and §School of Chemistry, Newcastle University, Newcastle
upon Tyne, NE1 7RU, U.K
| | - Harold Fellermann
- Interdisciplinary
Computing and Complex BioSystems (ICOS), School
of Computing Science, ‡Centre for Synthetic Biology and the Bioeconomy (CSBB), ¶Centre for Bacterial
Cell Biology (CBCB), and §School of Chemistry, Newcastle University, Newcastle
upon Tyne, NE1 7RU, U.K
| | - Ulrich Stimming
- Interdisciplinary
Computing and Complex BioSystems (ICOS), School
of Computing Science, ‡Centre for Synthetic Biology and the Bioeconomy (CSBB), ¶Centre for Bacterial
Cell Biology (CBCB), and §School of Chemistry, Newcastle University, Newcastle
upon Tyne, NE1 7RU, U.K
| | - Natalio Krasnogor
- Interdisciplinary
Computing and Complex BioSystems (ICOS), School
of Computing Science, ‡Centre for Synthetic Biology and the Bioeconomy (CSBB), ¶Centre for Bacterial
Cell Biology (CBCB), and §School of Chemistry, Newcastle University, Newcastle
upon Tyne, NE1 7RU, U.K
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8
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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9
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Plochowietz A, Farrell I, Smilansky Z, Cooperman BS, Kapanidis AN. In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria. Nucleic Acids Res 2016; 45:926-937. [PMID: 27625389 PMCID: PMC5314786 DOI: 10.1093/nar/gkw787] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 07/29/2016] [Accepted: 08/20/2016] [Indexed: 11/21/2022] Open
Abstract
Transfer RNA (tRNA) links messenger RNA nucleotide sequence with amino acid sequence during protein synthesis. Despite the importance of tRNA for translation, its subcellular distribution and diffusion properties in live cells are poorly understood. Here, we provide the first direct report on tRNA diffusion localization in live bacteria. We internalized tRNA labeled with organic fluorophores into live bacteria, applied single-molecule fluorescence imaging with single-particle tracking and localized and tracked single tRNA molecules over seconds. We observed two diffusive species: fast (with a diffusion coefficient of ∼8 μm2/s, consistent with free tRNA) and slow (consistent with tRNA bound to larger complexes). Our data indicate that a large fraction of internalized fluorescent tRNA (>70%) appears to diffuse freely in the bacterial cell. We also obtained the subcellular distribution of fast and slow diffusing tRNA molecules in multiple cells by normalizing for cell morphology. While fast diffusing tRNA is not excluded from the bacterial nucleoid, slow diffusing tRNA is localized to the cell periphery (showing a 30% enrichment versus a uniform distribution), similar to non-uniform localizations previously observed for mRNA and ribosomes.
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Affiliation(s)
- Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
| | - Ian Farrell
- Anima Inc, 75 Claremont Road, Suite 102, Bernardsville, NJ 07924-2270, USA.,Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104-6323, USA
| | - Zeev Smilansky
- Anima Inc, 75 Claremont Road, Suite 102, Bernardsville, NJ 07924-2270, USA
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104-6323, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
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