1
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Aknine N, Klymchenko AS. Push-Pull Fluorescent Dyes with Trifluoroacetyl Acceptor for High-Fidelity Sensing of Polarity and Heterogeneity of Lipid Droplets. Anal Chem 2024. [PMID: 39083638 DOI: 10.1021/acs.analchem.4c02322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Imaging and sensing of lipid droplets (LDs) attracted significant attention due to growing evidence for their important role in cell life. Solvatochromic dyes are promising tools to probe LDs' local polarity, but this analysis is biased by their non-negligible emission from intracellular membranes and capacity to emit from both the apolar core and polar interface of LDs. Here, we developed two push-pull solvatochromic dyes based on naphthalene and fluorene cores bearing an exceptionally strong electron acceptor, the trifluoroacetyl group. The latter was found to boost the optical properties of the dyes by shifting their absorption and emission to red and increasing their extinction coefficient, photostability, and sensitivity to solvent polarity (solvatochromism). In contrast to classical solvatochromic dyes, such as parent aldehydes and reference Nile Red, the new dyes exhibited strong fluorescence quenching by millimolar water concentrations in organic solvents. In live cells, the trifluoroacetyl dyes exhibited high specificity to LDs, whereas the parent aldehydes and Nile Red showed a detectable backgrounds from intracellular membranes. Experiments in model lipid membranes and nanoemulsion droplets confirmed the high selectivity of new probes to LDs in contrast to classical solvatochromic dyes. Moreover, the new probes were found to be selective to the LDs oil core, where they can sense lipid unsaturation and chain length. Their ratiometric imaging in cells revealed strong heterogeneity in polarity within LDs, which covered the range of polarities of unsaturated triglyceride oils, whereas Nile Red failed to properly estimate the local polarity of LDs. Finally, the probes revealed that LDs core polarity can be altered by fatty acid diets, which correlates with their chain length and unsaturation.
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Affiliation(s)
- Nathan Aknine
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, ITI SysChem, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, ITI SysChem, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch, France
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2
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Archontakis E, Dhiman S, Zhang M, Vleugels MEJ, Meijer EW, Palmans ARA, Zijlstra P, Albertazzi L. Visualizing the Heterogeneity in Homogeneous Supramolecular Polymers. J Am Chem Soc 2024; 146:19974-19985. [PMID: 38986035 PMCID: PMC11273342 DOI: 10.1021/jacs.4c03562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024]
Abstract
The dynamic properties of supramolecular polymers enable new functionality beyond the limitations of conventional polymers. The mechanism of the monomer exchange between different supramolecular polymers is proposed to be closely associated with local disordered domains within the supramolecular polymers. However, a direct detection of such heterogeneity has never been experimentally probed. Here, we present the direct visualization of the local disordered domains in the backbone of supramolecular polymers by a super-resolution microscopy technique: Nile Red-based spectrally resolved point accumulation for imaging in nanoscale topography (NR-sPAINT). We investigate the local disordered domains in trisamide-based supramolecular polymers comprising a (co)assembly of benzene-1,3,5-tricarboxamide (BTA) and a variant with one of the amide bonds inverted (iBTA). The NR-sPAINT allows us to simultaneously map the spatial distribution and polarity of the local disordered domains along the polymers with a spatial precision down to ∼20 nm. Quantitative autocorrelation and cross-correlation analysis show subtle differences in the spatial distribution of the disordered domains between polymers composed of different variants of BTA monomers. Further, statistical analysis unraveled high heterogeneity in monomer packing at both intra- and interpolymer levels. The results reported here demonstrate the necessity of investigating the structures in soft materials at nanoscale to fully understand their intricacy.
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Affiliation(s)
- Emmanouil Archontakis
- Department
of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600MB Eindhoven, The Netherlands
| | - Shikha Dhiman
- Laboratory
of Macromolecular and Organic Chemistry, and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Miao Zhang
- Department
of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600MB Eindhoven, The Netherlands
| | - Marle E. J. Vleugels
- Laboratory
of Macromolecular and Organic Chemistry, and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - E. W. Meijer
- Laboratory
of Macromolecular and Organic Chemistry, and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- School
of Chemistry and RNA Institute, The University
of New South Wales, Sydney, New South Wales 2052, Australia
| | - Anja R. A. Palmans
- Laboratory
of Macromolecular and Organic Chemistry, and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter Zijlstra
- Department
of Applied Physics and Science Education, and Institute for Complex
Molecular Systems, Eindhoven University
of Technology, 5600MB Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Department
of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600MB Eindhoven, The Netherlands
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3
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Manko H, Burton MG, Mély Y, Godet J. Spectral Phasor Applied to Spectrally-Resolved Single Molecule Localization Microscopy. Chemphyschem 2024; 25:e202400101. [PMID: 38563617 DOI: 10.1002/cphc.202400101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Spectrally-resolved single-molecule localization microscopy (srSMLM) has emerged as a powerful tool for exploring the spectral properties of single emitters in localization microscopy. By simultaneously capturing the spatial positions and spectroscopic signatures of individual fluorescent molecules, srSMLM opens up the possibility of investigating an additional dimension in super-resolution imaging. However, appropriate and dedicated tools are required to fully capitalize on the spectral dimension. Here, we propose the application of the spectral phasor analysis as an effective method for summarizing and analyzing the spectral information obtained from srSMLM experiments. The spectral phasor condenses the complete spectrum of a single emitter into a two-dimensional space, preserving key spectral characteristics for single-molecule spectral exploration. We demonstrate the effectiveness of spectral phasor in efficiently classifying single Nile Red fluorescence emissions from largely overlapping cyanine fluorescence signals in dual-color PAINT experiments. Additionally, we employed spectral phasor with srSMLM to reveal subtle alterations occurring in the membrane of Gram-positive Enterococcus hirae in response to gramicidin exposure, a membrane-perturbing antibiotic treatment. Spectral phasor provides a robust, model-free analytic tool for the detailed analysis of the spectral component of srSMLM, enhancing the capabilities of multi-color spectrally-resolved single-molecule imaging.
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Affiliation(s)
- Hanna Manko
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, Illkirch, France
| | - Matthew G Burton
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, Illkirch, France
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Yves Mély
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, Illkirch, France
| | - Julien Godet
- Laboratoire iCube, UMR CNRS 7357, Equipe IMAGeS, Université de Strasbourg, Strasbourg, France
- Groupe Méthodes Recherche Clinique, Hôpitaux Universitaires de trasbourg, France
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4
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Go GE, Jeong U, Park H, Go S, Kim D. Photoswitching Reagent for Super-Resolution Fluorescence Microscopy. Angew Chem Int Ed Engl 2024; 63:e202405246. [PMID: 38622700 DOI: 10.1002/anie.202405246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
Single-molecule localization microscopy (SMLM) has revolutionized optical microscopy by exceeding the diffraction limit and revealing previously unattainable nanoscale details of cellular structures and molecular dynamics. This super-resolution imaging capability relies on fluorophore photoswitching, which is crucial for optimizing the imaging conditions and accurately determining the fluorophore positions. To understand the general on and off photoswitching mechanisms of single dye molecules, various photoswitching reagents were evaluated. Systematic measurement of the single-molecule-level fluorescence on and off rates (kon and koff) in the presence of various photoswitching reagents and theoretical calculation of the structure of the photoswitching reagent-fluorophore pair indicated that the switch-off mechanism is mainly determined by the nucleophilicity of the photoswitching reagent, and the switch-on mechanism is a two-photon-induced dissociation process, which is related to the power of the illuminating laser and bond dissociation energy of this pair. This study contributes to a broader understanding of the molecular photoswitching mechanism in SMLM imaging and provides a basis for designing improved photoswitching reagents with potential applications extending to materials science and chemistry.
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Affiliation(s)
- Ga-Eun Go
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Uidon Jeong
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyunbum Park
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Seokran Go
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Institute of Nano Science and Technology, and Research Institute for Natural Sciences, Seoul, 04763, Republic of Korea
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5
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Lauritsen L, Szomek M, Hornum M, Reinholdt P, Kongsted J, Nielsen P, Brewer JR, Wüstner D. Ratiometric fluorescence nanoscopy and lifetime imaging of novel Nile Red analogs for analysis of membrane packing in living cells. Sci Rep 2024; 14:13748. [PMID: 38877068 PMCID: PMC11178856 DOI: 10.1038/s41598-024-64180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
Subcellular membranes have complex lipid and protein compositions, which give rise to organelle-specific membrane packing, fluidity, and permeability. Due to its exquisite solvent sensitivity, the lipophilic fluorescence dye Nile Red has been used extensively to study membrane packing and polarity. Further improvement of Nile Red can be achieved by introducing electron-donating or withdrawing functional groups. Here, we compare the potential of derivatives of Nile Red with such functional substitutions for super-resolution fluorescence microscopy of lipid packing in model membranes and living cells. All studied Nile Red derivatives exhibit cholesterol-dependent fluorescence changes in model membranes, as shown by spectrally resolved stimulated emission depletion (STED) microscopy. STED imaging of Nile Red probes in cells reveals lower membrane packing in fibroblasts from healthy subjects compared to those from patients suffering from Niemann Pick type C1 (NPC1) disease, a lysosomal storage disorder with accumulation of cholesterol and sphingolipids in late endosomes and lysosomes. We also find small but consistent changes in the fluorescence lifetime of the Nile Red derivatives in NPC1 cells, suggesting altered hydrogen-bonding capacity in their membranes. All Nile Red derivatives are essentially non-fluorescent in water but increase their brightness in membranes, allowing for their use in MINFLUX single molecule tracking experiments. Our study uncovers the potential of Nile Red probes with functional substitutions for nanoscopic membrane imaging.
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Affiliation(s)
- Line Lauritsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jonathan R Brewer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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6
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Sun B, Ding T, Zhou W, Porter TS, Lew MD. Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay. NANO LETTERS 2024. [PMID: 38828968 DOI: 10.1021/acs.nanolett.4c01263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Amyloid-beta (Aβ42) aggregates are characteristic Alzheimer's disease signatures, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational "wobble" of Nile blue (NB) molecules transiently binding to Aβ42 fibrils. We correlate fibril architectures measured by SMOLM with their growth and decay over the course of 5 to 20 min visualized by single-molecule localization microscopy (SMLM). We discover that stable Aβ42 fibrils tend to be well-ordered and signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order and disorder are signatures of growing and decaying fibrils, respectively. We also observe SMLM-invisible fibril remodeling, including steady growth and decay patterns that conserve β-sheet organization. SMOLM reveals that increased fibril architectural heterogeneity is correlated with dynamic remodeling and that large-scale fibril remodeling tends to originate from strongly heterogeneous local regions.
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Affiliation(s)
- Brian Sun
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tianben Ding
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Weiyan Zhou
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tara S Porter
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Matthew D Lew
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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7
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Steves MA, He C, Xu K. Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells. Annu Rev Phys Chem 2024; 75:163-183. [PMID: 38360526 DOI: 10.1146/annurev-physchem-070623-034225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information-such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond-for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit.
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Affiliation(s)
- Megan A Steves
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Changdong He
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California, USA;
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8
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Fang R, He L, Wang Y, Wang L, Qian H, Yang S. The Investigation of the Subtle Structural Discrepancies between Oryza Sativa Recombinant and Plasma-Derived Human Serum Albumins to Design a Novel Nanoparticle as a Taxane Delivery System. Protein J 2024; 43:544-558. [PMID: 38581543 DOI: 10.1007/s10930-024-10194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 04/08/2024]
Abstract
To solve the large size faultiness of Oryza sativa recombinant human serum albumin nanoparticle (OsrHSA NP), the structural discrepancies between OsrHSA and plasma-derived human serum albumin (pdHSA) were analyzed deeply in this research. It demonstrated that there were some subtle structural discrepancies located in subdomain IA and IIA between OsrHSA and pdHSA, which included peptide backbone, disulphide bridge and some amino acids. Firstly, the structural discrepancies were investigated through literature comparison, it inferred that the structural discrepancies resulted from the fatty acid (FA) binding to OsrHSA at site 2 of subdomain IA and IIA. To form a cavity for accommodation of FA molecule in OsrHSA, the peptide backbone structure of subdomain IA and IIA would change, accompanied by the conformational transition of disulphide bridges and side chain structure change of some amino acids in subdomain IA and IIA. These alterations induced the exposure of tryptophan (Trp) and tyrosine (Tyr) residues in subdomain IA and IIA and the decrease of net negative charges of molecular surface. The former would promote more OsrHSA molecules aggregate, and the latter would weaken the electrostatic repulsion. As a result, the size of OsrHSA NP was more extensive than that of pdHSA NP (175.84 ± 15.63 nm vs. 31.67 ± 1.31 nm) when the concentration of Dimethyl Sulphoxide (DMSO) was 30% (v/v). In this study, the experimental scheme of OsrHSA NP preparation was improved. There were two changes in the enhanced preparation scheme: pH 8.2 PBS buffer and 63% DMSO. It indicated that the improved OsrHSA NP carrier was comparable to the pdHSA NP carrier. The size and drug loading of paclitaxel-loaded improved OsrHSA NP were 53.57 ± 3.63 nm and 7.25 ± 0.46% (w/w), and those of docetaxel-loaded improved OsrHSA NP were 44.75 ± 2.26 nm and 8.43 ± 0.74% (w/w). Moreover, both NPs exhibited good stability for 168 h at 7.4 pH values. It is established that the improved OsrHSA NP is comparable to the pdHSA NP as a taxane delivery system.
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Affiliation(s)
- Ru Fang
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Liang He
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Yanbin Wang
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Liling Wang
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Hua Qian
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | - Shaozong Yang
- Institute of Forest Food, Zhejiang Academy of Forestry, Hangzhou, 310023, China.
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9
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YEO WEIHONG, BRENNER BENJAMIN, LEE YOUNGSEOP, KWEON JUNGHUN, SUN CHENG, ZHANG HAOF. Maximizing photon utilization in spectroscopic single-molecule localization microscopy using symmetrically dispersed dual-wedge prisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593746. [PMID: 38798392 PMCID: PMC11118294 DOI: 10.1101/2024.05.12.593746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Single-molecule localization microscopy (SMLM) enables super-resolution imaging on conventional fluorescent microscopes. Spectroscopic SMLM (sSMLM) further allows highly multiplexed super-resolution imaging. We report an easy-to-implement symmetrically dispersed dual-wedge prism (SDDWP)-sSMLM design that maximizes photon utilization. We first symmetrically dispersed photons to the -1st and +1st orders in an optical assembly using two identical dual-wedge prisms (DWPs). Then we computationally extracted the fluorophores' spatial position and spectral characteristics using photons in both the -1st and +1st orders. Theoretical analysis and experimental validation showed lateral and spectral precisions of 10.1 nm and 0.3 nm, respectively, representing improvements of 28% and 48% over our previous DWP-based system, where emitted photons are divided separately for spatial and spectral analyses.
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Affiliation(s)
- WEI-HONG YEO
- Department of Biomedical Engineering, Northwestern University, Evanston IL 60201, USA
| | - BENJAMIN BRENNER
- Department of Biomedical Engineering, Northwestern University, Evanston IL 60201, USA
| | - YOUNGSEOP LEE
- Department of Biomedical Engineering, Northwestern University, Evanston IL 60201, USA
| | - JUNGHUN KWEON
- Department of Biomedical Engineering, Northwestern University, Evanston IL 60201, USA
| | - CHENG SUN
- Department of Mechanical Engineering, Northwestern University, Evanston IL 60201, USA
| | - HAO F. ZHANG
- Department of Biomedical Engineering, Northwestern University, Evanston IL 60201, USA
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10
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Batey JE, Kim GW, Yang M, Heffer DC, Pott ED, Giang H, Dong B. High throughput spectrally resolved super-resolution fluorescence microscopy with improved photon usage. Analyst 2024; 149:2801-2805. [PMID: 38682955 DOI: 10.1039/d4an00343h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Single-molecule localization microscopy (SMLM), a type of super-resolution fluorescence microscopy, has become a strong technique in the toolbox of chemists, biologists, physicists, and engineers in recent years for its unique ability to resolve characteristic features at the nanoscopic level. It drastically improves the resolution of optical microscopes beyond the diffraction limit, with which previously unresolvable structures can now be studied. Spectrally resolved super-resolution fluorescence microscopy via multiplexing of different fluorophores is one of the greatest advancements among SMLM techniques. However, current spectrally resolved SMLM (SR-SMLM) methodologies present low spatial resolution due to loss of photons, low throughput due to spectral interferences, or require complex optical systems. Here, we overcome these drawbacks by developing a SR-SMLM methodology using a color glass filter. It enables high throughput and improved photon usage for hyperspectral imaging at the nanoscopic level. Our methodology can readily distinguish fluorophores of close spectral emission and achieves sub-10 nm localization and sub-5 nm spectral precisions.
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Affiliation(s)
- James Ethan Batey
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Geun Wan Kim
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Meek Yang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Darby Claire Heffer
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Elric Dion Pott
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Hannah Giang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Bin Dong
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
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11
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Sun B, Ding T, Zhou W, Porter TS, Lew MD. Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.24.586510. [PMID: 38585908 PMCID: PMC10996564 DOI: 10.1101/2024.03.24.586510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Amyloid-beta ( A β 42 ) aggregates are characteristic signatures of Alzheimer's disease, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational "wobble" of Nile blue (NB) molecules transiently binding to A β 42 fibrils. We quantify correlations between fibril architectures, measured by SMOLM, and their growth and decay visualized by single-molecule localization microscopy (SMLM). We discover that stable A β 42 fibrils tend to be well-ordered, signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order and disorder are signatures of growing and decaying A β 42 fibrils, respectively. We also observe SMLM-invisible fibril remodeling, including steady growth and decay patterns that conserve β -sheet organization. SMOLM reveals that increased heterogeneity in fibril architectures is correlated with more dynamic remodeling and that large-scale fibril remodeling tends to originate from local regions that exhibit strong heterogeneity.
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Affiliation(s)
- Brian Sun
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Tianben Ding
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Weiyan Zhou
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Tara S. Porter
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
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12
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the Nanoscale Structure of β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation-Localization Microscopy. ACS NANO 2024; 18:8798-8810. [PMID: 38478911 PMCID: PMC11025465 DOI: 10.1021/acsnano.3c11771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize by using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8L and KFE8D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) ribbon structure of both KFE8 and Aβ42 and quantifies the precise tilt of the fibrils' inner and outer backbones in relevant buffer conditions without the need for covalent labeling or sequence mutations. SMOLM also distinguishes polymorphic branched and curved morphologies of KFE8, whose backbones exhibit much more heterogeneity than those of typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross-β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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13
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Wüstner D, Egebjerg JM, Lauritsen L. Dynamic Mode Decomposition of Multiphoton and Stimulated Emission Depletion Microscopy Data for Analysis of Fluorescent Probes in Cellular Membranes. SENSORS (BASEL, SWITZERLAND) 2024; 24:2096. [PMID: 38610307 PMCID: PMC11013970 DOI: 10.3390/s24072096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
An analysis of the membrane organization and intracellular trafficking of lipids often relies on multiphoton (MP) and super-resolution microscopy of fluorescent lipid probes. A disadvantage of particularly intrinsically fluorescent lipid probes, such as the cholesterol and ergosterol analogue, dehydroergosterol (DHE), is their low MP absorption cross-section, resulting in a low signal-to-noise ratio (SNR) in live-cell imaging. Stimulated emission depletion (STED) microscopy of membrane probes like Nile Red enables one to resolve membrane features beyond the diffraction limit but exposes the sample to a lot of excitation light and suffers from a low SNR and photobleaching. Here, dynamic mode decomposition (DMD) and its variant, higher-order DMD (HoDMD), are applied to efficiently reconstruct and denoise the MP and STED microscopy data of lipid probes, allowing for an improved visualization of the membranes in cells. HoDMD also allows us to decompose and reconstruct two-photon polarimetry images of TopFluor-cholesterol in model and cellular membranes. Finally, DMD is shown to not only reconstruct and denoise 3D-STED image stacks of Nile Red-labeled cells but also to predict unseen image frames, thereby allowing for interpolation images along the optical axis. This important feature of DMD can be used to reduce the number of image acquisitions, thereby minimizing the light exposure of biological samples without compromising image quality. Thus, DMD as a computational tool enables gentler live-cell imaging of fluorescent probes in cellular membranes by MP and STED microscopy.
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Affiliation(s)
- Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (J.M.E.); (L.L.)
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14
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Jana S, Nevskyi O, Höche H, Trottenberg L, Siemes E, Enderlein J, Fürstenberg A, Wöll D. Local Water Content in Polymer Gels Measured with Super-Resolved Fluorescence Lifetime Imaging. Angew Chem Int Ed Engl 2024; 63:e202318421. [PMID: 38165135 DOI: 10.1002/anie.202318421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/03/2024]
Abstract
Water molecules play an important role in the structure, function, and dynamics of (bio-) materials. A direct access to the number of water molecules in nanoscopic volumes can thus give new molecular insights into materials and allow for fine-tuning their properties in sophisticated applications. The determination of the local water content has become possible by the finding that H2 O quenches the fluorescence of red-emitting dyes. Since deuterated water, D2 O, does not induce significant fluorescence quenching, fluorescence lifetime measurements performed in different H2 O/D2 O-ratios yield the local water concentration. We combined this effect with the recently developed fluorescence lifetime single molecule localization microscopy imaging (FL-SMLM) in order to nanoscopically determine the local water content in microgels, i.e. soft hydrogel particles consisting of a cross-linked polymer swollen in water. The change in water content of thermo-responsive microgels when changing from their swollen state at room temperature to a collapsed state at elevated temperature could be analyzed. A clear decrease in water content was found that was, to our surprise, rather uniform throughout the entire microgel volume. Only a slightly higher water content around the dye was found in the periphery with respect to the center of the swollen microgels.
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Affiliation(s)
- Sankar Jana
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Oleksii Nevskyi
- Third Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Hannah Höche
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Leon Trottenberg
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Eric Siemes
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, 37077, Göttingen, Germany
| | - Alexandre Fürstenberg
- Department of Physical Chemistry and Department of Inorganic and Analytical Chemistry, University of Geneva, 1211, Geneva, Switzerland
| | - Dominik Wöll
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074, Aachen, Germany
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15
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Ma J, Sun R, Xia K, Xia Q, Liu Y, Zhang X. Design and Application of Fluorescent Probes to Detect Cellular Physical Microenvironments. Chem Rev 2024; 124:1738-1861. [PMID: 38354333 DOI: 10.1021/acs.chemrev.3c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The microenvironment is indispensable for functionality of various biomacromolecules, subcellular compartments, living cells, and organisms. In particular, physical properties within the biological microenvironment could exert profound effects on both the cellular physiology and pathology, with parameters including the polarity, viscosity, pH, and other relevant factors. There is a significant demand to directly visualize and quantitatively measure the fluctuation in the cellular microenvironment with spatiotemporal resolution. To satisfy this need, analytical methods based on fluorescence probes offer great opportunities due to the facile, sensitive, and dynamic detection that these molecules could enable in varying biological settings from in vitro samples to live animal models. Herein, we focus on various types of small molecule fluorescent probes for the detection and measurement of physical parameters of the microenvironment, including pH, polarity, viscosity, mechanical force, temperature, and electron potential. For each parameter, we primarily describe the chemical mechanisms underlying how physical properties are correlated with changes of various fluorescent signals. This review provides both an overview and a perspective for the development of small molecule fluorescent probes to visualize the dynamic changes in the cellular environment, to expand the knowledge for biological process, and to enrich diagnostic tools for human diseases.
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Affiliation(s)
- Junbao Ma
- Department of Chemistry and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, Zhejiang Province, China
| | - Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Kaifu Xia
- Department of Chemistry and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, Zhejiang Province, China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, Chinese Academy of Sciences Dalian Liaoning 116023, China
| | - Xin Zhang
- Department of Chemistry and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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16
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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17
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Mahato J, Mukherjee R, Bose A, Mehra S, Gadhe L, Maji SK, Chowdhury A. Sensitized Emission Imaging Allows Nanoscale Surface Polarity Mapping of α-Synuclein Amyloid Fibrils. ACS Chem Neurosci 2024; 15:108-118. [PMID: 38099928 DOI: 10.1021/acschemneuro.3c00467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024] Open
Abstract
When misfolded, α-Synuclein (α-Syn), a natively disordered protein, aggregates to form amyloid fibrils responsible for the neurodegeneration observed in Parkinson's disease. Structural studies revealed distinct molecular packing of α-Syn in different fibril polymorphs and variations of interprotofilament connections in the fibrillar architecture. Fibril polymorphs have been hypothesized to exhibit diverse surface polarities depending on the folding state of the protein during aggregation; however, the spatial variation of surface polarity in amyloid fibrils remains unexplored. To map the local polarity (or hydrophobicity) along α-Syn fibrils, we visualized the spectral characteristics of two dyes with distinct polarities-hydrophilic Thioflavin T (ThT) and hydrophobic Nile red (NR)─when both are bound to α-Syn fibrils. Dual-channel fluorescence imaging reveals uneven partitioning of ThT and NR along individual fibrils, implying that relatively more polar/hydrophobic patches are spread over a few hundred nanometers. Remarkably, spectrally resolved sensitized emission imaging of α-Syn fibrils provides unambiguous evidence of energy transfer from ThT to NR, implying that dyes of dissimilar polarity are in close proximity. Furthermore, spatially resolved fluorescence spectroscopy of the solvatochromic probe NR allowed us to quantitatively map the range and variation of the polarity parameter ET30 along individual fibrils. Our results suggest the existence of interlaced polar and nonpolar nanoscale domains throughout the fibrils; however, the relative populations of these patches vary considerably over larger length scales likely due to heterogeneous packing of α-Syn during fibrilization and dissimilar exposed polarities of polymorphic segments. The employed method may provide a foundation for imaging modalities of other similar structurally unresolved systems with diverse hydrophobic-hydrophilic topology.
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Affiliation(s)
- Jaladhar Mahato
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Rajat Mukherjee
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Abhik Bose
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
- Sunita Sanghi Centre of Ageing and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
- Sunita Sanghi Centre of Ageing and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
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18
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Song KH, Zhang Y. Spectral precision improvement with demagnifying spectral images in spectroscopic nanoscopy. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2024; 41:39-44. [PMID: 38175128 PMCID: PMC10768805 DOI: 10.1364/josaa.497634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024]
Abstract
Spectroscopic nanoscopy (SN) has been recognized as a key functional imaging tool in cell biology and chemistry because it offers the unique capability to simultaneously obtain the spatial and spectral information for single molecules. However, it has an intrinsic issue in using the limited photon budget from single emitters divided into two imaging channels to concurrently acquire spatial and spectral images. Accordingly, this issue lowers the spatial localization and spectral precision. Although several techniques have been introduced to improve the spatial precision in SN, improving the spectral precision has been overlooked so far. Here we propose a method to improve the spectral precision by optically manipulating the width of the spectroscopic signatures using a demagnifier. We evaluate its performance using numerical simulations with systematic investigations of several underlying optimal parameters such as the demagnification factor and the integration width in the proposed configuration. We also present achievable spectral precision values with different signal and background levels. Compared to the existing SN system, the 3× demagnifier-based configuration shows an approximate 35% improvement, from 2.9 nm to 1.9 nm, in the spectral precision at the 1000 photons signal level.
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Affiliation(s)
- Ki-Hee Song
- Quantum Optics Research Division, Korea Atomic Energy Research Institute, Daedeok-daero 989 beon-gil, Yuseong-gu, Daejeon 34057, Republic of Korea
| | - Yang Zhang
- Molecular Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering, Chemistry and Science, North Carolina State University, Raleigh, NC 27606, USA
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19
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He C, Wu CY, Li W, Xu K. Multidimensional Super-Resolution Microscopy Unveils Nanoscale Surface Aggregates in the Aging of FUS Condensates. J Am Chem Soc 2023; 145:24240-24248. [PMID: 37782826 PMCID: PMC10691933 DOI: 10.1021/jacs.3c08674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remains unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here, we uncover nanoscale heterogeneities in FUS condensates and elucidate their evolution over aging. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SMdM), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems at the nanoscale.
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Affiliation(s)
- Changdong He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Chun Ying Wu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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20
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Shi Y, Ruan H, Xu Y, Zou C. Cholesterol, Eukaryotic Lipid Domains, and an Evolutionary Perspective of Transmembrane Signaling. Cold Spring Harb Perspect Biol 2023; 15:a041418. [PMID: 37604587 PMCID: PMC10626259 DOI: 10.1101/cshperspect.a041418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Transmembrane signaling is essential for complex life forms. Communication across a bilayer lipid barrier is elaborately organized to convey precision and to fine-tune strength. Looking back, the steps that it has taken to enable this seemingly mundane errand are breathtaking, and with our survivorship bias, Darwinian. While this review is to discuss eukaryotic membranes in biological functions for coherence and theoretical footing, we are obliged to follow the evolution of the biological membrane through time. Such a visit is necessary for our hypothesis that constraints posited on cellular functions are mainly via the biomembrane, and relaxation thereof in favor of a coordinating membrane environment is the molecular basis for the development of highly specialized cellular activities, among them transmembrane signaling. We discuss the obligatory paths that have led to eukaryotic membrane formation, its intrinsic ability to signal, and how it set up the platform for later integration of protein-based receptor activation.
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Affiliation(s)
- Yan Shi
- Department of Basic Medical Sciences, Tsinghua-Peking University Joint Center for Life Sciences, School of Medicine; Institute for Immunology, Tsinghua University, Beijing 100084, China
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Hefei Ruan
- Department of Basic Medical Sciences, Tsinghua-Peking University Joint Center for Life Sciences, School of Medicine; Institute for Immunology, Tsinghua University, Beijing 100084, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanni Xu
- Department of Basic Medical Sciences, Tsinghua-Peking University Joint Center for Life Sciences, School of Medicine; Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Chunlin Zou
- Department of Basic Medical Sciences, Tsinghua-Peking University Joint Center for Life Sciences, School of Medicine; Institute for Immunology, Tsinghua University, Beijing 100084, China
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21
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Hsu CC, Rückel M, Bonn D, Brouwer AM. Super-resolution Fluorescence Imaging of Recycled Polymer Blends via Hydrogen Bond-Assisted Adsorption of a Nile Red Derivative. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:14652-14659. [PMID: 37788122 PMCID: PMC10586370 DOI: 10.1021/acs.langmuir.3c01976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/19/2023] [Indexed: 10/05/2023]
Abstract
A key challenge in the recycling of multilayer plastic films of polyethylene and polyamide, as typically used for food packaging, is to assess and control the phase separation of the two types of polymers in the recycled material, the specifics of which determine the mechanical strength of the recycled material. However, visualizing the polyamide-in-polyethylene domains with conventional fluorescence methods or electron microscopy is challenging. We present a new approach that combines the point accumulation in nanoscale topography (PAINT) super-resolution method with a newly synthesized Nile Red probe (diOHNR) as the fluorescent label. The molecule was modified to undergo a hydrogen bond-assisted interaction with the polyamide phase in the blend due to its two additional hydroxyl groups but preserves the spectral properties of Nile Red. As a result, the localization density of the probe in the PAINT image is 13 times larger at the polyamide phase than at the polyethylene phase, enabling quantitative evaluation of the spatial polyamide/polyethylene distribution down to the nanoscale. The method achieved a spatial resolution of 18.8 nm, and we found that over half of the polyamide particles in a recycled sample were smaller than the optical diffraction limit. Being able to image the blends with nanoscopic resolution can help to optimize the composition and mechanical properties of recycled materials and thus contribute to an increased reuse of plastics.
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Affiliation(s)
- Chao-Chun Hsu
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Markus Rückel
- Group
Research, BASF SE, Ludwigshafen D-67056, Germany
| | - Daniel Bonn
- van
der Waals-Zeeman Institute, Institute of
Physics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Albert M. Brouwer
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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22
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Fernando SI, Martineau JT, Hobson RJ, Vu TN, Baker B, Mueller BD, Menon R, Jorgensen EM, Gerton JM. Simultaneous spectral differentiation of multiple fluorophores in super-resolution imaging using a glass phase plate. OPTICS EXPRESS 2023; 31:33565-33581. [PMID: 37859135 PMCID: PMC10544955 DOI: 10.1364/oe.499929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 10/21/2023]
Abstract
By engineering the point-spread function (PSF) of single molecules, different fluorophore species can be imaged simultaneously and distinguished by their unique PSF patterns. Here, we insert a silicon-dioxide phase plate at the Fourier plane of the detection path of a wide-field fluorescence microscope to produce distinguishable PSFs (X-PSFs) at different wavelengths. We demonstrate that the resulting PSFs can be localized spatially and spectrally using a maximum-likelihood estimation algorithm and can be utilized for hyper-spectral super-resolution microscopy of biological samples. We produced superresolution images of fixed U2OS cells using X-PSFs for dSTORM imaging with simultaneous illumination of up to three fluorophore species. The species were distinguished only by the PSF pattern. We achieved ∼21-nm lateral localization precision (FWHM) and ∼17-nm axial precision (FWHM) with an average of 1,800 - 3,500 photons per PSF and a background as high as 130 - 400 photons per pixel. The modified PSF distinguished fluorescent probes with ∼80 nm separation between spectral peaks.
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Affiliation(s)
- Sanduni I. Fernando
- University of Utah Department of Physics and Astronomy, 201 James Fletcher Bldg. 115 S. 1400 E Salt Lake City, UT 84112-0830, USA
| | - Jason T. Martineau
- University of Utah Department of Physics and Astronomy, 201 James Fletcher Bldg. 115 S. 1400 E Salt Lake City, UT 84112-0830, USA
| | - Robert J. Hobson
- University of Utah School of Biological Sciences, 257 South 1400 East Salt Lake City, Utah 84112, USA
| | - Thien N. Vu
- University of Utah School of Biological Sciences, 257 South 1400 East Salt Lake City, Utah 84112, USA
| | - Brian Baker
- University of Utah Nanofab 36 S. Wasatch Drive, SMBB Room 2500 Salt Lake City, UT 84112, USA
| | - Brian D. Mueller
- University of Utah School of Biological Sciences, 257 South 1400 East Salt Lake City, Utah 84112, USA
| | - Rajesh Menon
- University of Utah Department of Electrical and Computer Engineering 50 S. Central Campus Drive, MEB Room 2110 Salt Lake City, UT 84112, USA
| | - Erik M. Jorgensen
- University of Utah School of Biological Sciences, 257 South 1400 East Salt Lake City, Utah 84112, USA
| | - Jordan M. Gerton
- University of Utah Department of Physics and Astronomy, 201 James Fletcher Bldg. 115 S. 1400 E Salt Lake City, UT 84112-0830, USA
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23
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the nanoscale structure of β-sheet assemblies using single-molecule orientation-localization microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557571. [PMID: 37745382 PMCID: PMC10515885 DOI: 10.1101/2023.09.13.557571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils have remarkable utility as engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarity to amyloid species has been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers, KFE8L and KFE8D, and the pathological amyloid-beta peptide Aβ42. SMOLM reveals that the orientations of Nile red, as it transiently binds to both KFE8 and Aβ42, are consistent with a helical (bilayer) ribbon structure and convey the precise tilt of the fibrils' inner and outer backbones. SMOLM also finds polymorphic branched and curved morphologies of KFE8 whose backbones exhibit much more heterogeneity than those of more typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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24
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Liu Y, Shahid MA, Mao H, Chen J, Waddington M, Song KH, Zhang Y. Switchable and Functional Fluorophores for Multidimensional Single-Molecule Localization Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:403-413. [PMID: 37655169 PMCID: PMC10466381 DOI: 10.1021/cbmi.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 09/02/2023]
Abstract
Multidimensional single-molecule localization microscopy (mSMLM) represents a paradigm shift in the realm of super-resolution microscopy techniques. It affords the simultaneous detection of single-molecule spatial locations at the nanoscale and functional information by interrogating the emission properties of switchable fluorophores. The latter is finely tuned to report its local environment through carefully manipulated laser illumination and single-molecule detection strategies. This Perspective highlights recent strides in mSMLM with a focus on fluorophore designs and their integration into mSMLM imaging systems. Particular interests are the accomplishments in simultaneous multiplexed super-resolution imaging, nanoscale polarity and hydrophobicity mapping, and single-molecule orientational imaging. Challenges and prospects in mSMLM are also discussed, which include the development of more vibrant and functional fluorescent probes, the optimization of optical implementation to judiciously utilize the photon budget, and the advancement of imaging analysis and machine learning techniques.
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Affiliation(s)
- Yunshu Liu
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Md Abul Shahid
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Hongjing Mao
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Jiahui Chen
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Michael Waddington
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Ki-Hee Song
- Quantum
Optics Research Division, Korea Atomic Energy
Research Institute, Yuseong-gu, Daejeon 34057, Republic of Korea
| | - Yang Zhang
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
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25
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Manko H, Mély Y, Godet J. Advancing Spectrally-Resolved Single Molecule Localization Microscopy with Deep Learning. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300728. [PMID: 37093225 DOI: 10.1002/smll.202300728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Spectrally-resolved single molecule localization microscopy (srSMLM) is a recent technique enriching single molecule localization microscopy with the simultaneous recording of spectra of the single emitters. srSMLM resolution is limited by the number of photons collected per emitters. Sharing a photon budget to record the localization and the spectroscopic information results in a loss of spatial and spectral resolution-or forces the sacrifice of one at the expense of the other. Here, srUnet-a deep-learning Unet-based image processing routine trained to increase the spectral and spatial signals to compensate for the resolution loss inherent in additionally recording the spectral component is reported. Both localization and spectral precision are improved by srUnet-particularly for the low-emitting species. srUnet increases the fraction of localization whose signal can be both spatially and spectrally characterized. It preserves spectral shifts and the linearity of the dispersion of light. It strongly facilitates wavelength assignment in multicolor experiments. srUnet is a simple post-processing add-on boosting srSMLM performance close to conventional SMLM with the potential to turn srSMLM into the new standard for multicolor single molecule imaging.
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Affiliation(s)
- Hanna Manko
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, Illkirch, 67401, France
| | - Yves Mély
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, Université de Strasbourg, Illkirch, 67401, France
| | - Julien Godet
- Groupe Méthodes Recherche Clinique, Hôpitaux Universitaires de Strasbourg, Strasbourg, 67091, France
- Laboratoire iCube, UMR CNRS 7357, Equipe IMAGeS, Université de Strasbourg, Illkirch, 67400, France
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26
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He C, Wu CY, Li W, Xu K. Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548239. [PMID: 37503034 PMCID: PMC10369965 DOI: 10.1101/2023.07.12.548239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remain unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here we uncover nanoscale heterogeneities in the aging process of FUS condensates. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SM d M), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating nanoscale structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems.
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Frawley AT, Leslie KG, Wycisk V, Galiani S, Shrestha D, Eggeling C, Anderson HL. A Photoswitchable Solvatochromic Dye for Probing Membrane Ordering by RESOLFT Super-resolution Microscopy. Chemphyschem 2023; 24:e202300125. [PMID: 36946252 DOI: 10.1002/cphc.202300125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/23/2023]
Abstract
A switchable solvatochromic fluorescent dyad can be used to map ordering of lipids in vesicle membranes at a resolution better than the diffraction limit. Combining a Nile Red fluorophore with a photochromic spironaphthoxazine quencher allows the fluorescence to be controlled using visible light, via photoswitching and FRET quenching. Synthetic lipid vesicles of varying composition were imaged with an average 2.5-fold resolution enhancement, compared to the confocal images. Ratiometric detection was used to probe the membrane polarity, and domains of different lipid ordering were distinguished within the same membrane.
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Affiliation(s)
- Andrew T Frawley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kathryn G Leslie
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Virginia Wycisk
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Dilip Shrestha
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien-Platz 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745, Jena, Germany
- Jena Center for Soft Matter (JCSM), Philosophenweg 7, 07743, Jena, Germany
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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28
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Pelletier R, Danylchuk DI, Benaissa H, Broch F, Vauchelles R, Gautier A, Klymchenko AS. Genetic Targeting of Solvatochromic Dyes for Probing Nanoscale Environments of Proteins in Organelles. Anal Chem 2023. [PMID: 37229557 DOI: 10.1021/acs.analchem.3c00515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A variety of protein tags are available for genetically encoded protein labeling, which allow their precise localization and tracking inside the cells. A new dimension in protein imaging can be offered by combining protein tags with polarity-sensitive fluorescent probes, which provide information about local nanoscale environments of target proteins within the subcellular compartments (organelles). Here, we designed three fluorescent probes based on solvatochromic nile red dye, conjugated to a HaloTag reactive targeting group through polyethylene glycol linkers of varying lengths. The probe with medium linker length, NR12-Halo, was found to label specifically a large variety of proteins localized in defined cell compartments, such as plasma membranes (outer and inner leaflets), endoplasmic reticulum, Golgi apparatus, cytosol, microtubules, actin, and chromatin. Owing to its polarity-sensitive fluorophore, the probe clearly distinguished the proteins localized within apolar lipid membranes from other proteins. Moreover, it revealed dramatic changes in the environment during the life cycle of proteins from biosynthesis to their expected localization and, finally, to recycling inside lysosomes. Heterogeneity in the local polarity of some membrane proteins also suggested a formation of low-polar protein aggregates, for example, within cell-cell contacts. The approach also showed that mechanical stress (cell shrinking by osmotic shock) induced a general polarity decrease in membrane proteins, probably due to the condensation of biomolecules. Finally, the nanoenvironment of some membrane proteins was affected by a polyunsaturated fatty acid diet, which provided the bridge between organization of lipids and proteins. The developed solvatochromic HaloTag probe constitutes a promising tool for probing nanoscale environments of proteins and their interactions within subcellular structures.
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Affiliation(s)
- Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Hela Benaissa
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Fanny Broch
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Romain Vauchelles
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Arnaud Gautier
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
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29
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Sarkar A, Namboodiri V, Kumbhakar M. Single-Molecule Orientation Imaging Reveals Two Distinct Binding Configurations on Amyloid Fibrils. J Phys Chem Lett 2023:4990-4996. [PMID: 37220418 DOI: 10.1021/acs.jpclett.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fluorescence readouts for an amyloid fibril sensor critically depend on its molecular interaction and local environment offered by the available structural motifs. Here we employ polarized points accumulation for imaging in nanoscale topography with intramolecular charge transfer probes transiently bound to amyloid fibrils to investigate the organization of fibril nanostructures and probe binding configurations. Besides the in-plane (θ ≈ 90°) mode for binding on the fibril surface parallel to the long fibril axis, we also observed a sizable population of over 60% out-of-plane (θ < 60°) dipoles for rotor probes experiencing a varying degree of orientational mobility. Highly confined dipoles exhibiting an out-of-plane configuration probably reflect tightly bound dipoles in the inner channel grooves, while the weakly bound ones on amyloid enjoy rotational flexibility. Our observation of an out-of-plane binding mode emphasizes the pivotal role played by the electron donor amino group toward fluorescence detection and hence the emergence of anchored probes alongside conventional groove binders.
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Affiliation(s)
- Aranyak Sarkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Vinu Namboodiri
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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30
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Brenner B, Sun C, Raymo FM, Zhang HF. Spectroscopic single-molecule localization microscopy: applications and prospective. NANO CONVERGENCE 2023; 10:14. [PMID: 36943541 PMCID: PMC10030755 DOI: 10.1186/s40580-023-00363-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/05/2023] [Indexed: 05/25/2023]
Abstract
Single-molecule localization microscopy (SMLM) breaks the optical diffraction limit by numerically localizing sparse fluorescence emitters to achieve super-resolution imaging. Spectroscopic SMLM or sSMLM further allows simultaneous spectroscopy and super-resolution imaging of fluorescence molecules. Hence, sSMLM can extract spectral features with single-molecule sensitivity, higher precision, and higher multiplexity than traditional multicolor microscopy modalities. These new capabilities enabled advanced multiplexed and functional cellular imaging applications. While sSMLM suffers from reduced spatial precision compared to conventional SMLM due to splitting photons to form spatial and spectral images, several methods have been reported to mitigate these weaknesses through innovative optical design and image processing techniques. This review summarizes the recent progress in sSMLM, its applications, and our perspective on future work.
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Affiliation(s)
- Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Françisco M Raymo
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
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31
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Song KH, Sun C, Zhang HF. Design strategy for a dual-wedge prism imaging spectrometer in spectroscopic nanoscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:023706. [PMID: 36859048 DOI: 10.1063/5.0122692] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Spectroscopic single-molecule localization microscopy (sSMLM, or spectroscopic nanoscopy) has been established as a key tool in functional super-resolution imaging by providing spatial and spectral information of single molecules at nanoscale resolution. A recently developed dual-wedge prism (DWP) imaging spectrometer, a monolithic optical component, has broadened the accessibility of sSMLM with an improved imaging resolution of more than 40%. It also improved the system reliability by reducing the number of discrete optical components. However, achieving its optimal performance requires the comprehensive understanding of the underlying constraints of the key system parameters, such as the refractive index of the DWP, spectral dispersion (SD), axial separation for three-dimensional (3D) biplane reconstruction, and the overall dimensional constraints. In this work, we present a generalized design principle for the DWP imaging spectrometer. Specifically, we develop the theoretical framework capturing the influence of the primary design parameters, including the achievable SD and localization performance, for different design cases. It further establishes the workflow to design and optimize the DWP imaging spectrometer for better multi-color functional imaging. This will give practical guidance for users to easily design the DWP imaging spectrometer, allowing for straightforward 3D sSMLM implementation.
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Affiliation(s)
- Ki-Hee Song
- Korea Atomic Energy Research Institute, 111, Daedeok-daero 989beon-gil, Yuseong-gu, Daejeon 34057, Republic of Korea
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
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32
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Yang L, Chen Q, Wang Z, Zhang H, Sun H. Small-molecule fluorescent probes for plasma membrane staining: Design, mechanisms and biological applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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33
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Archontakis E, Deng L, Zijlstra P, Palmans ARA, Albertazzi L. Spectrally PAINTing a Single Chain Polymeric Nanoparticle at Super-Resolution. J Am Chem Soc 2022; 144:23698-23707. [PMID: 36516974 PMCID: PMC9801428 DOI: 10.1021/jacs.2c11940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Folding a polymer chain into a well-defined single-chain polymeric nanoparticle (SCPN) is a fascinating approach to obtaining structured and functional nanoparticles. Like all polymeric materials, SCPNs are heterogeneous in their nature due to the polydispersity of their synthesis: the stochastic synthesis of polymer backbone length and stochastic functionalization with hydrophobic and hydrophilic pendant groups make structural diversity inevitable. Therefore, in a single batch of SCPNs, nanoparticles with different physicochemical properties are present, posing a great challenge to their characterization at a single-particle level. The development of techniques that can elucidate differences between SCPNs at a single-particle level is imperative to capture their potential applications in different fields such as catalysis and drug delivery. Here, a Nile Red based spectral point accumulation for imaging in nanoscale topography (NR-sPAINT) super-resolution fluorescence technique was implemented for the study of SCPNs at a single-particle level. This innovative method allowed us to (i) map the small-molecule binding rates on individual SCPNs and (ii) map the polarity of individual SCPNs for the first time. The SCPN designs used here have the same polymeric backbone but differ in the number of hydrophobic groups. The experimental results show notable interparticle differences in the binding rates within the same polymer design. Moreover, a marked polarity shift between the different designs is observed. Interestingly, interparticle polarity heterogeneity was unveiled, as well as an intraparticle diversity, information which has thus far remained hidden by ensemble techniques. The results indicate that the addition of hydrophobic pendant groups is vital to determine binding properties and induces single-particle polarity diversity. Overall, NR-sPAINT represents a powerful approach to quantifying the single-particle polarity of SCPNs and paves the way to relate the structural heterogeneity to functionality at the single-particle level. This provides an important step toward the aim of rationally designing SCPNs for the desired application.
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Affiliation(s)
- Emmanouil Archontakis
- Department
of Biomedical Engineering and Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Linlin Deng
- Institute
for Complex Molecular Systems (ICMS), Laboratory of Macromolecular
and Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter Zijlstra
- Department
of Applied Physics, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands,
| | - Anja R. A. Palmans
- Institute
for Complex Molecular Systems (ICMS), Laboratory of Macromolecular
and Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands,
| | - Lorenzo Albertazzi
- Department
of Biomedical Engineering and Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands,Nanoscopy
for Nanomedicine, Institute for Bioengineering of Catalonia, 08028 Barcelona, Spain,
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A Multichannel Fluorescent Tongue for Amyloid- β Aggregates Detection. Int J Mol Sci 2022; 23:ijms232314562. [PMID: 36498895 PMCID: PMC9739152 DOI: 10.3390/ijms232314562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Attention has been paid to the early diagnosis of Alzheimer's disease, due to the maximum benefit acquired from the early-stage intervention and treatment. However, the sensing techniques primarily depended upon for neuroimaging and immunological assays for the detection of AD biomarkers are expensive, time-consuming and instrument dependent. Here, we developed a multichannel fluorescent tongue consisting of four fluorescent dyes and GO through electrostatic and π-π interaction. The array distinguished multiple aggregation states of 1 µM Aβ40/Aβ42 with 100% prediction accuracy via 10-channel signal outputs, illustrating the rationality of the array design. Screening vital sensor elements for the simplified sensor array and the optimization of sensing system was achieved by machine learning algorithms. Moreover, our sensing tongue was able to detect the aggregation states of Aβ40/Aβ42 in serum, demonstrating the great potential of multichannel array in diagnosing the Alzheimer's diseases.
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35
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Kovacs T, Nagy P, Panyi G, Szente L, Varga Z, Zakany F. Cyclodextrins: Only Pharmaceutical Excipients or Full-Fledged Drug Candidates? Pharmaceutics 2022; 14:pharmaceutics14122559. [PMID: 36559052 PMCID: PMC9788615 DOI: 10.3390/pharmaceutics14122559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Cyclodextrins, representing a versatile family of cyclic oligosaccharides, have extensive pharmaceutical applications due to their unique truncated cone-shaped structure with a hydrophilic outer surface and a hydrophobic cavity, which enables them to form non-covalent host-guest inclusion complexes in pharmaceutical formulations to enhance the solubility, stability and bioavailability of numerous drug molecules. As a result, cyclodextrins are mostly considered as inert carriers during their medical application, while their ability to interact not only with small molecules but also with lipids and proteins is largely neglected. By forming inclusion complexes with cholesterol, cyclodextrins deplete cholesterol from cellular membranes and thereby influence protein function indirectly through alterations in biophysical properties and lateral heterogeneity of bilayers. In this review, we summarize the general chemical principles of direct cyclodextrin-protein interactions and highlight, through relevant examples, how these interactions can modify protein functions in vivo, which, despite their huge potential, have been completely unexploited in therapy so far. Finally, we give a brief overview of disorders such as Niemann-Pick type C disease, atherosclerosis, Alzheimer's and Parkinson's disease, in which cyclodextrins already have or could have the potential to be active therapeutic agents due to their cholesterol-complexing or direct protein-targeting properties.
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Affiliation(s)
- Tamas Kovacs
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lajos Szente
- CycloLab Cyclodextrin R & D Laboratory Ltd., H-1097 Budapest, Hungary
| | - Zoltan Varga
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Florina Zakany
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
- Correspondence:
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36
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Martens KJA, Gobes M, Archontakis E, Brillas RR, Zijlstra N, Albertazzi L, Hohlbein J. Enabling Spectrally Resolved Single-Molecule Localization Microscopy at High Emitter Densities. NANO LETTERS 2022; 22:8618-8625. [PMID: 36269936 PMCID: PMC9650776 DOI: 10.1021/acs.nanolett.2c03140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Single-molecule localization microscopy (SMLM) is a powerful super-resolution technique for elucidating structure and dynamics in the life- and material sciences. Simultaneously acquiring spectral information (spectrally resolved SMLM, sSMLM) has been hampered by several challenges: an increased complexity of the optical detection pathway, lower accessible emitter densities, and compromised spatio-spectral resolution. Here we present a single-component, low-cost implementation of sSMLM that addresses these challenges. Using a low-dispersion transmission grating positioned close to the image plane, the +1stdiffraction order is minimally elongated and is analyzed using existing single-molecule localization algorithms. The distance between the 0th and 1st order provides accurate information on the spectral properties of individual emitters. This method enables a 5-fold higher emitter density while discriminating between fluorophores whose peak emissions are less than 15 nm apart. Our approach can find widespread use in single-molecule applications that rely on distinguishing spectrally different fluorophores under low photon conditions.
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Affiliation(s)
- Koen J. A. Martens
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martijn Gobes
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Emmanouil Archontakis
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands
| | - Roger R. Brillas
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands
| | - Niels Zijlstra
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Lorenzo Albertazzi
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands
- Nanoscopy
for Nanomedicine, Institute for Bioengineering
of Catalonia, 08028 Barcelona, Spain
| | - Johannes Hohlbein
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Microspectroscopy
Research Facility, Wageningen University
and Research, Stippeneng
4, 6708 WE Wageningen, The Netherlands
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37
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Danial JSH, Lam JYL, Wu Y, Woolley M, Dimou E, Cheetham MR, Emin D, Klenerman D. Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging. Nat Protoc 2022; 17:2570-2619. [PMID: 36002768 DOI: 10.1038/s41596-022-00730-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 05/24/2022] [Indexed: 11/09/2022]
Abstract
Single-molecule localization microscopy (SMLM) leverages the power of modern optics to unleash ultra-precise structural nanoscopy of complex biological machines in their native environments as well as ultra-sensitive and high-throughput medical diagnostics with the sensitivity of a single molecule. To achieve this remarkable speed and resolution, SMLM setups are either built by research laboratories with strong expertise in optical engineering or commercially sold at a hefty price tag. The inaccessibility of SMLM to life scientists for technical or financial reasons is detrimental to the progress of biological and biomedical discoveries reliant on super-resolution imaging. In this work, we present the NanoPro, an economic, high-throughput, high-quality and easy-to-assemble SMLM for super-resolution imaging. We show that our instrument performs similarly to the most expensive, best-in-class commercial microscopes and rivals existing open-source microscopes at a lower price and construction complexity. To facilitate its wide adoption, we compiled a step-by-step protocol, accompanied by extensive illustrations, to aid inexperienced researchers in constructing the NanoPro as well as assessing its performance by imaging ground-truth samples as small as 20 nm. The detailed visual instructions make it possible for students with little expertise in microscopy engineering to construct, validate and use the NanoPro in <1 week, provided that all components are available.
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Affiliation(s)
- John S H Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK.
| | - Jeff Y L Lam
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Yunzhao Wu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Matthew Woolley
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Eleni Dimou
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Matthew R Cheetham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Derya Emin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK.
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38
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Park Y, Jeong D, Jeong U, Park H, Yoon S, Kang M, Kim D. Polarity Nano-Mapping of Polymer Film Using Spectrally Resolved Super-Resolution Imaging. ACS APPLIED MATERIALS & INTERFACES 2022; 14:46032-46042. [PMID: 36103715 DOI: 10.1021/acsami.2c11958] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
With the rapid development of the nanofabrication of polymer materials, the local measurement of the chemical properties of polymer nanostructures has become crucial because they can be highly heterogeneous at the nanoscale. We developed a spectroscopic imaging approach to characterize the nanoscale local polarity of polymer films via spectrally resolved super-resolution microscopy. We demonstrate the capability of the recently developed single-molecule sensing and imaging method to probe the polarity of polymers either inside a polymer matrix or on the external surface of a polymer. The nanoscale polarity sensing capability of our method facilitates the differentiation of various polymer surfaces based on chemical polarities, and it can further differentiate the polarity of functional side chain groups. Moreover, we demonstrate that a two-component polymer mixture can be locally distinguished based on the contrasting polarities of the lateral phase separation, further allowing for the investigation of nanoscale phase separation depending on the composition of the polymer blend film. This approach is anticipated to open the door to further characterizations of various nanocomposite materials.
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39
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Archontakis E, Woythe L, van Hoof B, Albertazzi L. Mapping the relationship between total and functional antibodies conjugated to nanoparticles with spectrally-resolved direct stochastic optical reconstruction microscopy (SR-dSTORM). NANOSCALE ADVANCES 2022; 4:4402-4409. [PMID: 36321150 PMCID: PMC9552925 DOI: 10.1039/d2na00435f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Antibody-functionalized nanoparticles (NPs) have shown numerous benefits in drug delivery and biosensing, improving the specificity of cell targeting and analyte detection, respectively. However, one of the main challenges is the lack of control over antibody orientation on the NP surface. Popular and easy conjugation strategies, such as carbodiimide-based conjugations, lead to a random orientation of antibodies on the NPs, compromising ligand functionality and contributing to undesired biological effects and reduced target recognition. While new methods for more controlled NP functionalization have been proposed, there is a lack of techniques that can elucidate the orientation of the antibodies at the single-particle level to determine the conjugation outcome and, therefore, the NPs' potential in selective targeting. Here, spectrally-resolved direct stochastic optical reconstruction microscopy (SR-dSTORM), an optical super-resolution technique, is introduced to quantify the relationship between total and functional NP conjugated cetuximab antibodies at the single-particle level. An evident single-particle heterogeneity in total and functional cetuximab is observed, leading to particles with different functional : total ratios. Additionally, the results indicate that the functional : total ratio of cetuximab highly depends on the conjugated cetuximab concentration. Overall, SR-dSTORM represents a direct approach for the NP structure-functionality relationship quantification, providing a platform to improve antibody-conjugated NPs characterization and facilitating their rational design.
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Affiliation(s)
- Emmanouil Archontakis
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Laura Woythe
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Bas van Hoof
- Department of Applied Physics, Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Nanoscopy for Nanomedicine, Institute for Bioengineering of Catalonia Barcelona Spain
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40
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Zhang Y, Wang G, Huang P, Sun E, Kweon J, Li Q, Zhe J, Ying LL, Zhang HF. Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy. Anal Chem 2022; 94:13834-13841. [PMID: 36165784 PMCID: PMC9859736 DOI: 10.1021/acs.analchem.2c02417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Super-resolution microscopy can capture spatiotemporal organizations of protein interactions with resolution down to 10 nm; however, the analyses of more than two proteins involving low-abundance protein are challenging because spectral crosstalk and heterogeneities of individual fluorescent labels result in molecular misidentification. Here we developed a deep learning-based imaging analysis method for spectroscopic single-molecule localization microscopy to minimize molecular misidentification in three-color super-resolution imaging. We characterized the 3-fold reduction of molecular misidentification in the new imaging method using pure samples of different photoswitchable fluorophores and visualized three distinct subcellular proteins in U2-OS cell lines. We further validated the protein counts and interactions of TOMM20, DRP1, and SUMO1 in a well-studied biological process, Staurosporine-induced apoptosis, by comparing the imaging results with Western-blot analyses of different subcellular portions.
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Affiliation(s)
- Yang Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Gaoxiang Wang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Hematology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan Hubei, 430030, China
| | - Peizhou Huang
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Edison Sun
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Junghun Kweon
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
| | - Qianru Li
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago IL, 60611, USA
| | - Ji Zhe
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
- Department of Pharmacology, Northwestern University, Chicago IL, 60611, USA
| | - Leslie L. Ying
- Department of Biomedical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
- Department of Electrical Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston IL, 60208, USA
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41
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Aparin IO, Yan R, Pelletier R, Choi AA, Danylchuk DI, Xu K, Klymchenko AS. Fluorogenic Dimers as Bright Switchable Probes for Enhanced Super-Resolution Imaging of Cell Membranes. J Am Chem Soc 2022; 144:18043-18053. [PMID: 36153973 DOI: 10.1021/jacs.2c07542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Super-resolution fluorescence imaging based on single-molecule localization microscopy (SMLM) enables visualizing cellular structures with nanometric precision. However, its spatial and temporal resolution largely relies on the brightness of ON/OFF switchable fluorescent dyes. Moreover, in cell plasma membranes, the single-molecule localization is hampered by the fast lateral diffusion of membrane probes. Here, to address these two fundamental problems, we propose a concept of ON/OFF switchable probes for SMLM (points accumulation for imaging in nanoscale topography, PAINT) based on fluorogenic dimers of bright cyanine dyes. In these probes, the two cyanine units connected with a linker were modified at their extremities with low-affinity membrane anchors. Being self-quenched in water due to intramolecular dye H-aggregation, they displayed light up on reversible binding to lipid membranes. The charged group in the linker further decreased the probe affinity to the lipid membranes, thus accelerating its dynamic reversible ON/OFF switching. The concept was validated on cyanines 3 and 5. SMLM of live cells revealed that the new probes provided higher brightness and ∼10-fold slower diffusion at the cell surface, compared to reference probes Nile Red and DiD, which boosted axial localization precision >3-fold down to 31 nm. The new probe allowed unprecedented observation of nanoscale fibrous protrusions on plasma membranes of live cells with 40 s time resolution, revealing their fast dynamics. Thus, going beyond the brightness limit of single switchable dyes by cooperative dequenching in fluorogenic dimers and slowing down probe diffusion in biomembranes open the route to significant enhancement of super-resolution fluorescence microscopy of live cells.
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Affiliation(s)
- Ilya O Aparin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
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42
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Shoup D, Scarpitti BT, Schultz ZD. A Wide-Field Imaging Approach for Simultaneous Super-Resolution Surface-Enhanced Raman Scattering Bioimaging and Spectroscopy. ACS MEASUREMENT SCIENCE AU 2022; 2:332-341. [PMID: 35996539 PMCID: PMC9389649 DOI: 10.1021/acsmeasuresciau.2c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
High spatial resolution imaging and chemical-specific detection in living organisms is important in a wide range of fields from medicine to catalysis. In this work, we characterize a wide-field surface-enhanced Raman scattering (SERS) imaging approach capable of simultaneously capturing images and SERS spectra from nanoparticle SERS tags in cancer cells. By passing the image through a transmission diffraction grating before it reaches an array detector, we record the image and wavelength dispersed signal simultaneously on the camera sensor. Optimization of the experiment provides an approach with better spectral resolution and more rapid acquisition than liquid crystal tunable filters commonly used for wide-field SERS imaging. Intensity fluctuations inherent to SERS enabled localization algorithms to be applied to both the spatial and spectral domain, providing super-resolution SERS images that are correlated with improved peak positions identified in the spectrum of the SERS tag. The detected Raman signal is shown to be sensitive to the focal plane, providing three-dimensional (3D) sectioning abilities for the detected nanoparticles. Our work demonstrates spectrally resolved super-resolution SERS imaging that has the potential to be applied to complex physical and biological imaging applications.
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Affiliation(s)
- Deben
N. Shoup
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Brian T. Scarpitti
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Zachary D. Schultz
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
- Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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43
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Schultz ZD, Shoup DN, Smith AE. Super-Resolution SERS Spectral Bioimaging. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2022; 12203:1220304. [PMID: 37431396 PMCID: PMC10329846 DOI: 10.1117/12.2632824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Advances in nanotechnology enable the detection of trace molecules from the enhanced Raman signal generated at the surface of plasmonic nanoparticles. We have developed technology to enable super-resolution imaging of plasmonic nanoparticles, where the fluctuations in the surface enhanced Raman scattering (SERS) signal can be analyzed with localization microscopy techniques to provide nanometer spatial resolution of the emitting molecule's location. Additional work now enables the super-resolved SERS image and the corresponding spectrum to be acquired simultaneously. Here we will discuss how this approach can be applied to provide new insights into biological cells.
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Affiliation(s)
- Zachary D. Schultz
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH, USA 43210-1173
| | - Deben N. Shoup
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH, USA 43210-1173
| | - Abigail E. Smith
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W. 18 Avenue, Columbus, OH, USA 43210-1173
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44
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Lee Y, Kim D, Park SB. Systematic Exploration of Furoindolizine‐Based Molecular Frameworks towards a Versatile Fluorescent Platform. Chemistry 2022; 28:e202200533. [DOI: 10.1002/chem.202200533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Youngjun Lee
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Dahham Kim
- CRI Center for Chemical Proteomics, Department of Chemistry Seoul National University Seoul 08826 Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry Seoul National University Seoul 08826 Korea
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45
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Butler C, Saraceno GE, Kechkar A, Bénac N, Studer V, Dupuis JP, Groc L, Galland R, Sibarita JB. Multi-Dimensional Spectral Single Molecule Localization Microscopy. FRONTIERS IN BIOINFORMATICS 2022; 2:813494. [PMID: 36304321 PMCID: PMC9580959 DOI: 10.3389/fbinf.2022.813494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Single molecule localization (SML) and tracking (SPT) techniques, such as (spt)PALM, (u/DNA)PAINT and quantum dot tracking, have given unprecedented insight into the nanoscale molecular organization and dynamics in living cells. They allow monitoring individual proteins with millisecond temporal resolution and high spatial resolution (<30 nm) by precisely localizing the point spread function (PSF) of individual emitters and tracking their position over time. While SPT methods have been extended to study the temporal dynamics and co-organization of multiple proteins, conventional experimental setups are restricted in the number of proteins they can probe simultaneously and usually have to tradeoff between the number of colors, the spatio-temporal resolution, and the field of view. Yet, localizing and tracking several proteins simultaneously at high spatial and temporal resolution within large field of views can provide important biological insights. By employing a dual-objective spectral imaging configuration compatible with live cell imaging combined with dedicated computation tools, we demonstrate simultaneous 3D single particle localization and tracking of multiple distinct species over large field of views to be feasible without compromising spatio-temporal resolution. The dispersive element introduced into the second optical path induces a spectrally dependent displacement, which we used to analytically separate up to five different fluorescent species of single emitters based on their emission spectra. We used commercially available microscope bodies aligned one on top of the other, offering biologists with a very ergonomic and flexible instrument covering a broad range of SMLM applications. Finally, we developed a powerful freely available software, called PALMTracer, which allows to quantitatively assess 3D + t + λ SMLM data. We illustrate the capacity of our approach by performing multi-color 3D DNA-PAINT of fixed samples, and demonstrate simultaneous tracking of multiple receptors in live fibroblast and neuron cultures.
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Affiliation(s)
- Corey Butler
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297F-33000, F-33000, Bordeaux, France
- Imagine Optic, Orsay, France
| | - G Ezequiel Saraceno
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297F-33000, F-33000, Bordeaux, France
| | - Adel Kechkar
- Ecole Nationale Supérieure de Biotechnologie, Laboratoire de Bioengineering, Constantine, El Khroub, Algeria
| | - Nathan Bénac
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297F-33000, F-33000, Bordeaux, France
| | - Vincent Studer
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297F-33000, F-33000, Bordeaux, France
| | - Julien P. Dupuis
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297F-33000, F-33000, Bordeaux, France
| | - Laurent Groc
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297F-33000, F-33000, Bordeaux, France
| | - Rémi Galland
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297F-33000, F-33000, Bordeaux, France
- *Correspondence: Rémi Galland, ; Jean-Baptiste Sibarita,
| | - Jean-Baptiste Sibarita
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297F-33000, F-33000, Bordeaux, France
- *Correspondence: Rémi Galland, ; Jean-Baptiste Sibarita,
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46
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Song KH, Brenner B, Yeo WH, Kweon J, Cai Z, Zhang Y, Lee Y, Yang X, Sun C, Zhang HF. Monolithic dual-wedge prism-based spectroscopic single-molecule localization microscopy. NANOPHOTONICS 2022; 11:1527-1535. [PMID: 35873202 PMCID: PMC9307059 DOI: 10.1515/nanoph-2021-0541] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
By manipulating the spectral dispersion of detected photons, spectroscopic single-molecule localization microscopy (sSMLM) permits concurrent high-throughput single-molecular spectroscopic analysis and imaging. Despite its promising potential, using discrete optical components and managing the delicate balance between spectral dispersion and spatial localization compromise its performance, including non-uniform spectral dispersion, high transmission loss of grating, high optical alignment demands, and reduced precision. We designed a dual-wedge prism (DWP)-based monolithic imaging spectrometer to overcome these challenges. We optimized the DWP for spectrally dispersing focused beam without deviation and with minimal wavefront error. We integrated all components into a compact assembly, minimizing total transmission loss and significantly reducing optical alignment requirements. We show the feasibility of DWP using ray-tracing and numerical simulations. We validated our numerical simulations by experimentally imaging individual nanospheres and confirmed that DWP-sSMLM achieved much improved spatial and spectral precisions of grating-based sSMLM. We also demonstrated DWP-sSMLM in 3D multi-color imaging of cells.
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Affiliation(s)
- Ki-Hee Song
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Wei-Hong Yeo
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Junghun Kweon
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Zhen Cai
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Yang Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Youngseop Lee
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Xusan Yang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - Hao F. Zhang
- Corresponding authors: Hao F. Zhang, Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA,
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47
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Dhiman S, Andrian T, Gonzalez BS, Tholen MME, Wang Y, Albertazzi L. Can super-resolution microscopy become a standard characterization technique for materials chemistry? Chem Sci 2022; 13:2152-2166. [PMID: 35310478 PMCID: PMC8864713 DOI: 10.1039/d1sc05506b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
The characterization of newly synthesized materials is a cornerstone of all chemistry and nanotechnology laboratories. For this purpose, a wide array of analytical techniques have been standardized and are used routinely by laboratories across the globe. With these methods we can understand the structure, dynamics and function of novel molecular architectures and their relations with the desired performance, guiding the development of the next generation of materials. Moreover, one of the challenges in materials chemistry is the lack of reproducibility due to improper publishing of the sample preparation protocol. In this context, the recent adoption of the reporting standard MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature) for material characterization and details of experimental protocols aims to provide complete, reproducible and reliable sample preparation for the scientific community. Thus, MIRIBEL should be immediately adopted in publications by scientific journals to overcome this challenge. Besides current standard spectroscopy and microscopy techniques, there is a constant development of novel technologies that aim to help chemists unveil the structure of complex materials. Among them super-resolution microscopy (SRM), an optical technique that bypasses the diffraction limit of light, has facilitated the study of synthetic materials with multicolor ability and minimal invasiveness at nanometric resolution. Although still in its infancy, the potential of SRM to unveil the structure, dynamics and function of complex synthetic architectures has been highlighted in pioneering reports during the last few years. Currently, SRM is a sophisticated technique with many challenges in sample preparation, data analysis, environmental control and automation, and moreover the instrumentation is still expensive. Therefore, SRM is currently limited to expert users and is not implemented in characterization routines. This perspective discusses the potential of SRM to transition from a niche technique to a standard routine method for material characterization. We propose a roadmap for the necessary developments required for this purpose based on a collaborative effort from scientists and engineers across disciplines.
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Affiliation(s)
- Shikha Dhiman
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| | - Teodora Andrian
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology Barcelona Spain
| | - Beatriz Santiago Gonzalez
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
- Department of Applied Physics, Eindhoven University of Technology Postbus 513 5600 MB Eindhoven The Netherlands
| | - Lorenzo Albertazzi
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology Barcelona Spain
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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48
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Filbrun SL, Zhao F, Chen K, Huang TX, Yang M, Cheng X, Dong B, Fang N. Imaging Dynamic Processes in Multiple Dimensions and Length Scales. Annu Rev Phys Chem 2022; 73:377-402. [PMID: 35119943 DOI: 10.1146/annurev-physchem-090519-034100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optical microscopy has become an invaluable tool for investigating complex samples. Over the years, many advances to optical microscopes have been made that have allowed us to uncover new insights into the samples studied. Dynamic changes in biological and chemical systems are of utmost importance to study. To probe these samples, multidimensional approaches have been developed to acquire a fuller understanding of the system of interest. These dimensions include the spatial information, such as the three-dimensional coordinates and orientation of the optical probes, and additional chemical and physical properties through combining microscopy with various spectroscopic techniques. In this review, we survey the field of multidimensional microscopy and provide an outlook on the field and challenges that may arise. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Seth L Filbrun
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Fei Zhao
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Kuangcai Chen
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA.,Imaging Core Facility, Georgia State University, Atlanta, Georgia, USA
| | - Teng-Xiang Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Meek Yang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA;
| | - Xiaodong Cheng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen Key Laboratory of Analytical Molecular Nanotechnology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, China; ,
| | - Bin Dong
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA;
| | - Ning Fang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen Key Laboratory of Analytical Molecular Nanotechnology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, China; ,
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Bhangu SK, Charchar P, Noble BB, Kim CJ, Pan S, Yarovsky I, Cavalieri F, Caruso F. Origins of Structural Elasticity in Metal-Phenolic Networks Probed by Super-Resolution Microscopy and Multiscale Simulations. ACS NANO 2022; 16:98-110. [PMID: 34843208 DOI: 10.1021/acsnano.1c08192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Metal-phenolic networks (MPNs) are amorphous materials that can be used to engineer functional films and particles. A fundamental understanding of the heat-driven structural reorganization of MPNs can offer opportunities to rationally tune their properties (e.g., size, permeability, wettability, hydrophobicity) for applications such as drug delivery, sensing, and tissue engineering. Herein, we use a combination of single-molecule localization microscopy, theoretical electronic structure calculations, and all-atom molecular dynamics simulations to demonstrate that MPN plasticity is governed by both the inherent flexibility of the metal (FeIII)-phenolic coordination center and the conformational elasticity of the phenolic building blocks (tannic acid, TA) that make up the metal-organic coordination complex. Thermal treatment (heating to 150 °C) of the flexible TA/FeIII networks induces a considerable increase in the number of aromatic π-π interactions formed among TA moieties and leads to the formation of hydrophobic domains. In the case of MPN capsules, 15 min of heating induces structural rearrangements that cause the capsules to shrink (from ∼4 to ∼3 μm), resulting in a thicker (3-fold), less porous, and higher protein (e.g., bovine serum albumin) affinity MPN shell. In contrast, when a simple polyphenol such as gallic acid is complexed with FeIII to form MPNs, rigid materials that are insensitive to temperature changes are obtained, and negligible structural rearrangement is observed upon heating. These findings are expected to facilitate the rational engineering of versatile TA-based MPN materials with tunable physiochemical properties for diverse applications.
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Affiliation(s)
- Sukhvir Kaur Bhangu
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
- School of Science, RMIT University, Victoria 3001, Australia
| | - Patrick Charchar
- School of Engineering, RMIT University, Victoria 3001, Australia
| | - Benjamin B Noble
- School of Engineering, RMIT University, Victoria 3001, Australia
| | - Chan-Jin Kim
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shuaijun Pan
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Victoria 3001, Australia
| | - Francesca Cavalieri
- School of Science, RMIT University, Victoria 3001, Australia
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma "Tor Vergata", via della ricerca scientifica 1, 00133 Rome, Italy
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
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50
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Jeong D, Kim D. Super‐resolution fluorescence microscopy‐based single‐molecule spectroscopy. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dokyung Jeong
- Department of Chemistry Hanyang University Seoul Republic of Korea
| | - Doory Kim
- Department of Chemistry Hanyang University Seoul Republic of Korea
- Research Institute for Convergence of Basic Science, Institute of Nano Science and Technology, and Research Institute for Natural Sciences Hanyang University Seoul Republic of Korea
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