1
|
Nakatani Y, Gaumer S, Shechtman Y, Gustavsson AK. Long axial-range double-helix point spread functions for 3D volumetric super-resolution imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605907. [PMID: 39131321 PMCID: PMC11312577 DOI: 10.1101/2024.07.31.605907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Single-molecule localization microscopy (SMLM) is a powerful tool for observing structures beyond the diffraction limit of light. Combining SMLM with engineered point spread functions (PSFs) enables 3D imaging over an extended axial range, as has been demonstrated for super-resolution imaging of various cellular structures. However, super-resolving structures in 3D in thick samples, such as whole mammalian cells, remains challenging as it typically requires acquisition and post-processing stitching of multiple slices to cover the entire sample volume or more complex analysis of the data. Here, we demonstrate how the imaging and analysis workflows can be simplified by 3D single-molecule super-resolution imaging with long axial-range double-helix (DH)-PSFs. First, we experimentally benchmark the localization precisions of short- and long axial-range DH-PSFs at different signal-to-background ratios by imaging of fluorescent beads. The performance of the DH-PSFs in terms of achievable resolution and imaging speed was then quantified for 3D single-molecule super-resolution imaging of mammalian cells by DNA-PAINT imaging of the nuclear lamina protein lamin B1 in U-2 OS cells. Furthermore, we demonstrate how the use of a deep learning-based algorithm allows the localization of dense emitters, drastically improving the achievable imaging speed and resolution. Our data demonstrate that using long axial-range DH-PSFs offers stitching-free, 3D super-resolution imaging of whole mammalian cells, simplifying the experimental and analysis procedures for obtaining volumetric nanoscale structural information.
Collapse
Affiliation(s)
- Yuya Nakatani
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Scott Gaumer
- Double Helix Optics Inc, 3415 Colorado Ave, Boulder, CO 80303, USA
| | - Yoav Shechtman
- Department of Biomedical Engineering, Technion, 32000 Haifa, Israel
- Department of Mechanical Engineering, University of Texas at Austin, Dean Keeton St, TX 78705, USA
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Department of Biosciences, Rice University, 6100 Main St, Houston, TX, USA
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St, Houston, TX 77005, USA
- Smalley-Curl Institute, Rice University, 6100 Main St, Houston, TX 77005, USA
- Center for Nanoscale Imaging Sciences, Rice University, 6100 Main St, Houston, TX 77005, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| |
Collapse
|
2
|
Rahmani A, Cox T, Achary ATA, Ponjavic A. Astigmatism-based active focus stabilisation with universal objective lens compatibility, extended operating range and nanometer precision. OPTICS EXPRESS 2024; 32:13331-13341. [PMID: 38859306 DOI: 10.1364/oe.520845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/12/2024] [Indexed: 06/12/2024]
Abstract
Focus stabilisation is vital for long-term fluorescence imaging, particularly in the case of high-resolution imaging techniques. Current stabilisation solutions either rely on fiducial markers that can be perturbative, or on beam reflection monitoring that is limited to high-numerical aperture objective lenses, making multimodal and large-scale imaging challenging. We introduce a beam-based method that relies on astigmatism, which offers advantages in terms of precision and the range over which focus stabilisation is effective. This approach is shown to be compatible with a wide range of objective lenses (10x-100x), typically achieving <10 nm precision with >10 μm operating range. Notably, our technique is largely unaffected by pointing stability errors, which in combination with implementation through a standalone Raspberry Pi architecture, offers a versatile focus stabilisation unit that can be added onto most existing microscope setups.
Collapse
|
3
|
Daly S, Ferreira Fernandes J, Bruggeman E, Handa A, Peters R, Benaissa S, Zhang B, Beckwith JS, Sanders EW, Sims RR, Klenerman D, Davis SJ, O'Holleran K, Lee SF. High-density volumetric super-resolution microscopy. Nat Commun 2024; 15:1940. [PMID: 38431671 PMCID: PMC10908787 DOI: 10.1038/s41467-024-45828-5] [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: 05/01/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Volumetric super-resolution microscopy typically encodes the 3D position of single-molecule fluorescence into a 2D image by changing the shape of the point spread function (PSF) as a function of depth. However, the resulting large and complex PSF spatial footprints reduce biological throughput and applicability by requiring lower labeling densities to avoid overlapping fluorescent signals. We quantitatively compare the density dependence of single-molecule light field microscopy (SMLFM) to other 3D PSFs (astigmatism, double helix and tetrapod) showing that SMLFM enables an order-of-magnitude speed improvement compared to the double helix PSF by resolving overlapping emitters through parallax. We demonstrate this optical robustness experimentally with high accuracy ( > 99.2 ± 0.1%, 0.1 locs μm-2) and sensitivity ( > 86.6 ± 0.9%, 0.1 locs μm-2) through whole-cell (scan-free) imaging and tracking of single membrane proteins in live primary B cells. We also exemplify high-density volumetric imaging (0.15 locs μm-2) in dense cytosolic tubulin datasets.
Collapse
Affiliation(s)
- Sam Daly
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - João Ferreira Fernandes
- Radcliffe Department of Medicine and MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Ezra Bruggeman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Anoushka Handa
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ruby Peters
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Sarah Benaissa
- Cambridge Advanced Imaging Centre, Downing Site, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Boya Zhang
- Cambridge Advanced Imaging Centre, Downing Site, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Joseph S Beckwith
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Edward W Sanders
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ruth R Sims
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Simon J Davis
- Radcliffe Department of Medicine and MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Kevin O'Holleran
- Cambridge Advanced Imaging Centre, Downing Site, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Steven F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| |
Collapse
|
4
|
Niederauer C, Nguyen C, Wang-Henderson M, Stein J, Strauss S, Cumberworth A, Stehr F, Jungmann R, Schwille P, Ganzinger KA. Dual-color DNA-PAINT single-particle tracking enables extended studies of membrane protein interactions. Nat Commun 2023; 14:4345. [PMID: 37468504 DOI: 10.1038/s41467-023-40065-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
DNA-PAINT based single-particle tracking (DNA-PAINT-SPT) has recently significantly enhanced observation times in in vitro SPT experiments by overcoming the constraints of fluorophore photobleaching. However, with the reported implementation, only a single target can be imaged and the technique cannot be applied straight to live cell imaging. Here we report on leveraging this technique from a proof-of-principle implementation to a useful tool for the SPT community by introducing simultaneous live cell dual-color DNA-PAINT-SPT for quantifying protein dimerization and tracking proteins in living cell membranes, demonstrating its improved performance over single-dye SPT.
Collapse
Affiliation(s)
| | - Chikim Nguyen
- Autonomous Matter Department, AMOLF, Amsterdam, The Netherlands
| | | | - Johannes Stein
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Florian Stehr
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | |
Collapse
|
5
|
Bhaskar H, Kleinjan D, Oi C, Gidden Z, Rosser SJ, Horrocks MH, Regan L. Live-cell super-resolution imaging of actin using LifeAct-14 with a PAINT-based approach. Protein Sci 2023; 32:e4558. [PMID: 36585831 PMCID: PMC9878614 DOI: 10.1002/pro.4558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
We present direct-LIVE-PAINT, an easy-to-implement approach for the nanoscopic imaging of protein structures in live cells using labeled binding peptides. We demonstrate the feasibility of direct-LIVE-PAINT with an actin-binding peptide fused to EGFP, the location of which can be accurately determined as it transiently binds to actin filaments. We show that direct-LIVE-PAINT can be used to image actin structures below the diffraction-limit of light and have used it to observe the dynamic nature of actin in live cells. We envisage a similar approach could be applied to imaging other proteins within live mammalian cells.
Collapse
Affiliation(s)
- Haresh Bhaskar
- The School of Biological SciencesUniversity of EdinburghEdinburghUK,EaStCHEM School of ChemistryUniversity of EdinburghEdinburghUK
| | - Dirk‐Jan Kleinjan
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Curran Oi
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Zoe Gidden
- The School of Biological SciencesUniversity of EdinburghEdinburghUK,EaStCHEM School of ChemistryUniversity of EdinburghEdinburghUK
| | - Susan J. Rosser
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | | | - Lynne Regan
- The School of Biological SciencesUniversity of EdinburghEdinburghUK
| |
Collapse
|
6
|
de Moliner F, Konieczna Z, Mendive-Tapia L, Saleeb RS, Morris K, Gonzalez-Vera JA, Kaizuka T, Grant SGN, Horrocks MH, Vendrell M. Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging. Angew Chem Int Ed Engl 2023; 62:e202216231. [PMID: 36412996 PMCID: PMC10108274 DOI: 10.1002/anie.202216231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/23/2022]
Abstract
The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.
Collapse
Affiliation(s)
- Fabio de Moliner
- Centre for Inflammation Research, The University of Edinburgh, UK
| | | | | | | | - Katie Morris
- EaStCHEM School of Chemistry, The University of Edinburgh, UK
| | | | - Takeshi Kaizuka
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | | | - Marc Vendrell
- Centre for Inflammation Research, The University of Edinburgh, UK
| |
Collapse
|
7
|
de Moliner F, Konieczna Z, Mendive‐Tapia L, Saleeb RS, Morris K, Gonzalez‐Vera JA, Kaizuka T, Grant SGN, Horrocks MH, Vendrell M. Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202216231. [PMID: 38515539 PMCID: PMC10952862 DOI: 10.1002/ange.202216231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 11/23/2022]
Abstract
The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.
Collapse
Affiliation(s)
| | | | | | | | - Katie Morris
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | | | - Takeshi Kaizuka
- Centre for Clinical Brain SciencesThe University of EdinburghUK
| | | | | | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghUK
| |
Collapse
|