1
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Chu J, Ejaz A, Lin KM, Joseph MR, Coraor AE, Drummond DA, Squires AH. Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01672-8. [PMID: 38750166 DOI: 10.1038/s41565-024-01672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
Multiplexed, real-time fluorescence detection at the single-molecule level can reveal the stoichiometry, dynamics and interactions of multiple molecular species in mixtures and other complex samples. However, fluorescence-based sensing is typically limited to the detection of just 3-4 colours at a time due to low signal-to-noise ratio, high spectral overlap and the need to maintain the chemical compatibility of dyes. Here we engineered a palette of several dozen composite fluorescent labels, called FRETfluors, for multiplexed spectroscopic measurements at the single-molecule level. FRETfluors are compact nanostructures constructed from three chemical components (DNA, Cy3 and Cy5) with tunable spectroscopic properties due to variations in geometry, fluorophore attachment chemistry and DNA sequence. We demonstrate FRETfluor labelling and detection for low-concentration (<100 fM) mixtures of mRNA, dsDNA and proteins using an anti-Brownian electrokinetic trap. In addition to identifying the unique spectroscopic signature of each FRETfluor, this trap differentiates FRETfluors attached to a target from unbound FRETfluors, enabling wash-free sensing. Although usually considered an undesirable complication of fluorescence, here the inherent sensitivity of fluorophores to the local physicochemical environment provides a new design axis complementary to changing the FRET efficiency. As a result, the number of distinguishable FRETfluor labels can be combinatorically increased while chemical compatibility is maintained, expanding prospects for spectroscopic multiplexing at the single-molecule level using a minimal set of chemical building blocks.
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Affiliation(s)
- Jiachong Chu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Ayesha Ejaz
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
- Interdisicplinary Scientist Training Program, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Madeline R Joseph
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Aria E Coraor
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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2
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Chen J, Dai Z, Lv H, Jin Z, Tang Y, Xie X, Shi J, Wang F, Li Q, Liu X, Fan C. Programming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification. Proc Natl Acad Sci U S A 2024; 121:e2312596121. [PMID: 38437555 PMCID: PMC10945798 DOI: 10.1073/pnas.2312596121] [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: 07/27/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.
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Affiliation(s)
- Jielin Chen
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zheze Dai
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hui Lv
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
- Zhangjiang Laboratory, Shanghai201210, China
| | - Zhongchao Jin
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yuqing Tang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jiye Shi
- Division of Physical Biology, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai201800, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
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3
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Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CK. Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.576943. [PMID: 38370628 PMCID: PMC10871237 DOI: 10.1101/2024.02.05.576943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.
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Affiliation(s)
- Johannes Stein
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maria Ericsson
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Michel Nofal
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Lorenzo Magni
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Sarah Aufmkolk
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ryan B. McMillan
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Laura Breimann
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Jens Wohlmann
- Department of Biosciences, University of Oslo, Norway
| | - Laura Arguedas-Jimenez
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Peng Yin
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - George M. Church
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chao-Kng Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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4
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Seabury AG, Khodabocus AJ, Kogan IM, Hoy GR, DeSalvo GA, Wustholz KL. Blinking characteristics of organic fluorophores for blink-based multiplexing. Commun Chem 2024; 7:18. [PMID: 38280979 PMCID: PMC10821931 DOI: 10.1038/s42004-024-01106-5] [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: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
Single-molecule fluorescence experiments have transformed our understanding of complex materials and biological systems. Whether single molecules are used to report on their nano-environment or provide for localization, understanding their blinking dynamics (i.e., stochastic fluctuations in emission intensity under continuous illumination) is paramount. We recently demonstrated another use for blinking dynamics called blink-based multiplexing (BBM), where individual emitters are classified using a single excitation laser based on blinking dynamics, rather than color. This study elucidates the structure-activity relationships governing BBM performance in a series of model rhodamine, BODIPY, and anthraquinone fluorophores that undergo different photo-physical and-chemical processes during blinking. Change point detection and multinomial logistic regression analyses show that BBM can leverage spectral fluctuations, electron and proton transfer kinetics, as well as photostability for molecular classification-even within the context of a shared blinking mechanism. In doing so, we demonstrate two- and three-color BBM with ≥ 93% accuracy using spectrally-overlapped fluorophores.
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Affiliation(s)
| | | | | | - Grayson R Hoy
- Chemistry Department, William & Mary, Williamsburg, VA, USA
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5
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Sandberg E, Demirbay B, Kulkarni A, Liu H, Piguet J, Widengren J. Fluorescence Bar-Coding and Flowmetry Based on Dark State Transitions in Fluorescence Emitters. J Phys Chem B 2024; 128:125-136. [PMID: 38127267 PMCID: PMC10788918 DOI: 10.1021/acs.jpcb.3c06905] [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: 10/18/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023]
Abstract
Reversible dark state transitions in fluorophores represent a limiting factor in fluorescence-based ultrasensitive spectroscopy, are a necessary basis for fluorescence-based super-resolution imaging, but may also offer additional, largely orthogonal fluorescence-based readout parameters. In this work, we analyzed the blinking kinetics of Cyanine5 (Cy5) as a bar-coding feature distinguishing Cy5 from rhodamine fluorophores having largely overlapping emission spectra. First, fluorescence correlation spectroscopy (FCS) solution measurements on mixtures of free fluorophores and fluorophore-labeled small unilamellar vesicles (SUVs) showed that Cy5 could be readily distinguished from the rhodamines by its reversible, largely excitation-driven trans-cis isomerization. This was next confirmed by transient state (TRAST) spectroscopy measurements, determining the fluorophore dark state kinetics in a more robust manner, from how the time-averaged fluorescence intensity varies upon modulation of the applied excitation light. TRAST was then combined with wide-field imaging of live cells, whereby Cy5 and rhodamine fluorophores could be distinguished on a whole cell level as well as in spatially resolved, multiplexed images of the cells. Finally, we established a microfluidic TRAST concept and showed how different mixtures of free Cy5 and rhodamine fluorophores and corresponding fluorophore-labeled SUVs could be distinguished on-the-fly when passing through a microfluidic channel. In contrast to FCS, TRAST does not rely on single-molecule detection conditions or a high time resolution and is thus broadly applicable to different biological samples. Therefore, we expect that the bar-coding concept presented in this work can offer an additional useful strategy for fluorescence-based multiplexing that can be implemented on a broad range of both stationary and moving samples.
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Affiliation(s)
- Elin Sandberg
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Baris Demirbay
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Abhilash Kulkarni
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Haichun Liu
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Joachim Piguet
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
| | - Jerker Widengren
- Royal Institute of Technology
(KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center, 106 91 Stockholm, Sweden
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6
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Filius M, van Wee R, Joo C. Single-Molecule FRET X. Methods Mol Biol 2024; 2694:203-213. [PMID: 37824006 DOI: 10.1007/978-1-0716-3377-9_10] [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: 10/13/2023]
Abstract
Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon that has been repurposed as a biophysical tool to measure nanometer distances. With FRET by DNA eXchange, or FRET X, many points of interest (POIs) in a single object can be probed, overcoming a major limitation of conventional single-molecule FRET. In FRET X, short fluorescently labeled DNA imager strands specifically and transiently bind their complementary docking strands on a target molecule, such that at most a single FRET pair is formed at each point in time and multiple POIs on a single molecule can be readily probed. Here, we describe the sample preparation, image acquisition, and data analysis for structural analysis of DNA nanostructures with FRET X.
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Affiliation(s)
- Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Raman van Wee
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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7
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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8
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Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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9
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Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
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10
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Tholen MME, Tas RP, Wang Y, Albertazzi L. Beyond DNA: new probes for PAINT super-resolution microscopy. Chem Commun (Camb) 2023; 59:8332-8342. [PMID: 37306078 PMCID: PMC10318573 DOI: 10.1039/d3cc00757j] [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: 02/17/2023] [Accepted: 05/26/2023] [Indexed: 06/13/2023]
Abstract
In the last decade, point accumulation for imaging in nanoscale topography (PAINT) has emerged as a versatile tool for single-molecule localization microscopy (SMLM). Currently, DNA-PAINT is the most widely used, in which a transient stochastically binding DNA docking-imaging pair is used to reconstruct specific characteristics of biological or synthetic materials on a single-molecule level. Slowly, the need for PAINT probes that are not dependent on DNA has emerged. These probes can be based on (i) endogenous interactions, (ii) engineered binders, (iii) fusion proteins, or (iv) synthetic molecules and provide complementary applications for SMLM. Therefore, researchers have been expanding the PAINT toolbox with new probes. In this review, we provide an overview of the currently existing probes that go beyond DNA and their applications and challenges.
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Affiliation(s)
- Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Roderick P Tas
- Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing Soft Matter, Eindhoven University of Technology, Eindhoven, 5612 AP, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB 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, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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11
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Arnould B, Quillin AL, Heemstra JM. Tracking the Message: Applying Single Molecule Localization Microscopy to Cellular RNA Imaging. Chembiochem 2023; 24:e202300049. [PMID: 36857087 PMCID: PMC10192057 DOI: 10.1002/cbic.202300049] [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: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/02/2023]
Abstract
RNA function is increasingly appreciated to be more complex than merely communicating between DNA sequence and protein structure. RNA localization has emerged as a key contributor to the intricate roles RNA plays in the cell, and the link between dysregulated spatiotemporal localization and disease warrants an exploration beyond sequence and structure. However, the tools needed to visualize RNA with precise resolution are lacking in comparison to methods available for studying proteins. In the past decade, many techniques have been developed for imaging RNA, and in parallel super resolution and single-molecule techniques have enabled imaging of single molecules in cells. Of these methods, single molecule localization microscopy (SMLM) has shown significant promise for probing RNA localization. In this review, we highlight current approaches that allow super resolution imaging of specific RNA transcripts and summarize challenges and future opportunities for developing innovative RNA labeling methods that leverage the power of SMLM.
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Affiliation(s)
- Benoît Arnould
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexandria L Quillin
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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12
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Almahayni K, Nestola G, Spiekermann M, Möckl L. Simple, Economic, and Robust Rail-Based Setup for Super-Resolution Localization Microscopy. J Phys Chem A 2023; 127:4553-4560. [PMID: 37163339 DOI: 10.1021/acs.jpca.3c01351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Research during the past 2 decades has showcased the power of single-molecule localization microscopy (SMLM) as a tool for exploring the nanoworld. However, SMLM systems are typically available in specialized laboratories and imaging facilities, owing to their expensiveness as well as complex assembly and alignment procedure. Here, we lay out the blueprint of a sturdy, rail-based, cost-efficient, multicolor SMLM setup that is easy to construct and align in service of simplifying the accessibility of SMLM. We characterize the optical properties of the design and assess its capabilities, robustness, and stability. The performance of the system is assayed using super-resolution imaging of biological samples. We believe that this design will make SMLM more affordable and broaden its availability.
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Affiliation(s)
- Karim Almahayni
- Max Planck Institute for the Science of Light, Staudtstr. 2, 91058 Erlangen, Germany
- Department of Physics, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Gianluca Nestola
- Max Planck Institute for the Science of Light, Staudtstr. 2, 91058 Erlangen, Germany
| | - Malte Spiekermann
- Max Planck Institute for the Science of Light, Staudtstr. 2, 91058 Erlangen, Germany
| | - Leonhard Möckl
- Max Planck Institute for the Science of Light, Staudtstr. 2, 91058 Erlangen, Germany
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13
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Abstract
There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.
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Affiliation(s)
- Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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14
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Reinhardt SCM, Masullo LA, Baudrexel I, Steen PR, Kowalewski R, Eklund AS, Strauss S, Unterauer EM, Schlichthaerle T, Strauss MT, Klein C, Jungmann R. Ångström-resolution fluorescence microscopy. Nature 2023; 617:711-716. [PMID: 37225882 PMCID: PMC10208979 DOI: 10.1038/s41586-023-05925-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/07/2023] [Indexed: 05/26/2023]
Abstract
Fluorescence microscopy, with its molecular specificity, is one of the major characterization methods used in the life sciences to understand complex biological systems. Super-resolution approaches1-6 can achieve resolution in cells in the range of 15 to 20 nm, but interactions between individual biomolecules occur at length scales below 10 nm and characterization of intramolecular structure requires Ångström resolution. State-of-the-art super-resolution implementations7-14 have demonstrated spatial resolutions down to 5 nm and localization precisions of 1 nm under certain in vitro conditions. However, such resolutions do not directly translate to experiments in cells, and Ångström resolution has not been demonstrated to date. Here we introdue a DNA-barcoding method, resolution enhancement by sequential imaging (RESI), that improves the resolution of fluorescence microscopy down to the Ångström scale using off-the-shelf fluorescence microscopy hardware and reagents. By sequentially imaging sparse target subsets at moderate spatial resolutions of >15 nm, we demonstrate that single-protein resolution can be achieved for biomolecules in whole intact cells. Furthermore, we experimentally resolve the DNA backbone distance of single bases in DNA origami with Ångström resolution. We use our method in a proof-of-principle demonstration to map the molecular arrangement of the immunotherapy target CD20 in situ in untreated and drug-treated cells, which opens possibilities for assessing the molecular mechanisms of targeted immunotherapy. These observations demonstrate that, by enabling intramolecular imaging under ambient conditions in whole intact cells, RESI closes the gap between super-resolution microscopy and structural biology studies and thus delivers information key to understanding complex biological systems.
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Affiliation(s)
- Susanne C M Reinhardt
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | | | - Isabelle Baudrexel
- Max Planck Institute of Biochemistry, Planegg, Germany
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Philipp R Steen
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Rafal Kowalewski
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Alexandra S Eklund
- Max Planck Institute of Biochemistry, Planegg, Germany
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Eduard M Unterauer
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Thomas Schlichthaerle
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Maximilian T Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany
| | - Christian Klein
- Department of Chemistry and Biochemistry, Ludwig Maximilian University, Munich, Germany
- Roche Innovation Center Zurich, Roche Pharma Research and Early Development, Schlieren, Switzerland
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany.
- Faculty of Physics and Center for NanoScience, Ludwig Maximilian University, Munich, Germany.
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15
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Banerjee A, Anand M, Ganji M. Labeling approaches for DNA-PAINT super-resolution imaging. NANOSCALE 2023; 15:6563-6580. [PMID: 36942769 DOI: 10.1039/d2nr06541j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Super-resolution imaging is becoming a commonly employed tool to visualize biological targets in unprecedented detail. DNA-PAINT is one of the single-molecule localization microscopy-based super-resolution imaging modalities allowing the ultra-high-resolution imaging with superior multiplexing capabilities. We discuss the importance of patterned DNA nanostructures in demonstrating the capabilities of DNA-PAINT and the design of various combinations of imager-docking strand pairs for imaging. Central to the implementation of DNA-PAINT imaging in a biological context is the generation of docking strand-conjugated binders against the target molecules. Several researchers have developed a variety of labelling probes for improving resolution while also providing multiplexing capabilities for the broader application of DNA-PAINT. This review provides a comprehensive summary of the repertoire of labelling probes used for DNA-PAINT in cells and the strategies implemented to chemically modify them with a docking strand.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
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16
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Ferapontov A, Omer M, Baudrexel I, Nielsen JS, Dupont DM, Juul-Madsen K, Steen P, Eklund AS, Thiel S, Vorup-Jensen T, Jungmann R, Kjems J, Degn SE. Antigen footprint governs activation of the B cell receptor. Nat Commun 2023; 14:976. [PMID: 36813795 PMCID: PMC9947222 DOI: 10.1038/s41467-023-36672-0] [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: 01/24/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Antigen binding by B cell receptors (BCR) on cognate B cells elicits a response that eventually leads to production of antibodies. However, it is unclear what the distribution of BCRs is on the naïve B cell and how antigen binding triggers the first step in BCR signaling. Using DNA-PAINT super-resolution microscopy, we find that most BCRs are present as monomers, dimers, or loosely associated clusters on resting B cells, with a nearest-neighbor inter-Fab distance of 20-30 nm. We leverage a Holliday junction nanoscaffold to engineer monodisperse model antigens with precision-controlled affinity and valency, and find that the antigen exerts agonistic effects on the BCR as a function of increasing affinity and avidity. Monovalent macromolecular antigens can activate the BCR at high concentrations, whereas micromolecular antigens cannot, demonstrating that antigen binding does not directly drive activation. Based on this, we propose a BCR activation model determined by the antigen footprint.
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Affiliation(s)
- Alexey Ferapontov
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.,Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark
| | - Marjan Omer
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Isabelle Baudrexel
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jesper Sejrup Nielsen
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Daniel Miotto Dupont
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | | | - Philipp Steen
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Munich, Germany
| | - Alexandra S Eklund
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.,Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark
| | | | - Ralf Jungmann
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Munich, Germany
| | - Jørgen Kjems
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Søren Egedal Degn
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark. .,Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus C, Denmark.
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17
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Kim SH, Li ITS. Super-Resolution Tension PAINT Imaging with a Molecular Beacon. Angew Chem Int Ed Engl 2023; 62:e202217028. [PMID: 36534951 DOI: 10.1002/anie.202217028] [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: 11/24/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
DNA-PAINT enabled super-resolution imaging through the transient binding of fluorescently-labelled single-stranded DNA (ssDNA) imagers to target ssDNA. However, its performance is constrained by imager background fluorescence, resulting in relatively long image acquisition and potential artifacts. We designed a molecular beacon (MB) as the PAINT imager. Unbound MB in solution reduces the background fluorescence due to its natively quenched state. They are fluorogenic upon binding to target DNA to create individual fluorescence events. We demonstrate that MB-PAINT provides localization precision similar to traditional linear imager DNA-PAINT. We also show that MB-PAINT is ideally suited for fast super-resolution imaging of molecular tension probes in living cells, eliminating the potential of artifacts from free-diffusing imagers in traditional DNA-PAINT at the cell-substrate interface.
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Affiliation(s)
- Seong Ho Kim
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
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18
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Chiang HJ, Koo DES, Kitano M, Burkitt S, Unruh JR, Zavaleta C, Trinh LA, Fraser SE, Cutrale F. HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence. Nat Methods 2023; 20:248-258. [PMID: 36658278 PMCID: PMC9911352 DOI: 10.1038/s41592-022-01751-5] [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: 11/12/2021] [Accepted: 12/13/2022] [Indexed: 01/21/2023]
Abstract
The expansion of fluorescence bioimaging toward more complex systems and geometries requires analytical tools capable of spanning widely varying timescales and length scales, cleanly separating multiple fluorescent labels and distinguishing these labels from background autofluorescence. Here we meet these challenging objectives for multispectral fluorescence microscopy, combining hyperspectral phasors and linear unmixing to create Hybrid Unmixing (HyU). HyU is efficient and robust, capable of quantitative signal separation even at low illumination levels. In dynamic imaging of developing zebrafish embryos and in mouse tissue, HyU was able to cleanly and efficiently unmix multiple fluorescent labels, even in demanding volumetric timelapse imaging settings. HyU permits high dynamic range imaging, allowing simultaneous imaging of bright exogenous labels and dim endogenous labels. This enables coincident studies of tagged components, cellular behaviors and cellular metabolism within the same specimen, providing more accurate insights into the orchestrated complexity of biological systems.
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Affiliation(s)
- Hsiao Ju Chiang
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA
| | - Daniel E. S. Koo
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA
| | - Masahiro Kitano
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Molecular and Computational Biology, University of Southern California, Los Angeles, CA USA
| | - Sean Burkitt
- grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA
| | - Jay R. Unruh
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, MO USA
| | - Cristina Zavaleta
- grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA
| | - Le A. Trinh
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Molecular and Computational Biology, University of Southern California, Los Angeles, CA USA
| | - Scott E. Fraser
- grid.42505.360000 0001 2156 6853Translational Imaging Center, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Biomedical Engineering, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Molecular and Computational Biology, University of Southern California, Los Angeles, CA USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA. .,Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA.
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19
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Chen Z, Yin G, Wei J, Qi T, Qian Z, Wang Z, Zong S, Cui Y. Quantitative analysis of multiple breast cancer biomarkers using DNA-PAINT. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:3671-3679. [PMID: 36063064 DOI: 10.1039/d2ay00670g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Immunotherapy has become an efficient treatment method of breast cancer. Detection of proteins such as PD-L1 and CTLA-4, which are important immune checkpoint molecules, is attracting more and more attention as they play key roles in immunotherapy. Here, by combining the high resolution of DNA-PAINT (DNA points accumulation for imaging in nanoscale topography) with the qPAINT quantitative analysis method, accurate spatial localization and absolute quantification of PD-L1 and CTLA-4 on the membrane of breast cancer cells could be achieved. Meanwhile, exchange-PAINT was also conducted to count three other biomarkers (EpCAM, EGFR, and HER2). Simultaneous analysis of these biomarkers can greatly facilitate the differentiation of different kinds of breast cancer. Such a simple quantitative analysis method holds great potential in diagnosis and immunotherapy of cancers.
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Affiliation(s)
- Zengwei Chen
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Gaoqiang Yin
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Jinxiu Wei
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Tongsheng Qi
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Ziting Qian
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Zhuyuan Wang
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Shenfei Zong
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
| | - Yiping Cui
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, China.
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20
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Oleksiievets N, Mathew C, Thiele JC, Gallea JI, Nevskyi O, Gregor I, Weber A, Tsukanov R, Enderlein J. Single-Molecule Fluorescence Lifetime Imaging Using Wide-Field and Confocal-Laser Scanning Microscopy: A Comparative Analysis. NANO LETTERS 2022; 22:6454-6461. [PMID: 35792810 PMCID: PMC9373986 DOI: 10.1021/acs.nanolett.2c01586] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A recent addition to the toolbox of super-resolution microscopy methods is fluorescence-lifetime single-molecule localization microscopy (FL-SMLM). The synergy of SMLM and fluorescence-lifetime imaging microscopy (FLIM) combines superior image resolution with lifetime information and can be realized using two complementary experimental approaches: confocal-laser scanning microscopy (CLSM) or wide-field microscopy. Here, we systematically and comprehensively compare these two novel FL-SMLM approaches in different spectral regions. For wide-field FL-SMLM, we use a commercial lifetime camera, and for CLSM-based FL-SMLM we employ a home-built system equipped with a rapid scan unit and a single-photon detector. We characterize the performances of the two systems in localizing single emitters in 3D by combining FL-SMLM with metal-induced energy transfer (MIET) for localization along the third dimension and in the lifetime-based multiplexed bioimaging using DNA-PAINT. Finally, we discuss advantages and disadvantages of wide-field and confocal FL-SMLM and provide practical advice on rational FL-SMLM experiment design.
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Affiliation(s)
- Nazar Oleksiievets
- III.
Institute of Physics − Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Christeena Mathew
- Laboratory
of Supramolecular Chemistry, EPFL SB ISIC
LCS, BCH 3307, CH-1015 Lausanne, Switzerland
| | - Jan Christoph Thiele
- III.
Institute of Physics − Biophysics, Georg August University, 37077 Göttingen, Germany
| | - José Ignacio Gallea
- III.
Institute of Physics − Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Oleksii Nevskyi
- III.
Institute of Physics − Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Ingo Gregor
- III.
Institute of Physics − Biophysics, Georg August University, 37077 Göttingen, Germany
| | - André Weber
- Combinatorial
NeuroImaging Core Facility, Leibniz Institute
for Neurobiology, Brenneckestraße 6, 39118 Magdeburg, Germany
| | - Roman Tsukanov
- III.
Institute of Physics − Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Jörg Enderlein
- III.
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
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21
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Dai Z, Xie X, Gao Z, Li Q. DNA‐PAINT Super‐Resolution Imaging for Characterization of Nucleic Acid Nanostructures. Chempluschem 2022; 87:e202200127. [DOI: 10.1002/cplu.202200127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Zheze Dai
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Xiaodong Xie
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Zhaoshuai Gao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering Dongchuan Road 800中国 200240 Shanghai CHINA
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22
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Abstract
To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry1-5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F1F0-ATPase6-8, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. 3) and also in artificial molecular motors created by organic chemical synthesis9-12. DNA nanotechnology13 has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems14-17, which can adopt different configurations, for example, triggered by strand-displacement reactions18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins20-26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity27,28 led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as F1F0-ATPase.
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23
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DeSalvo GA, Hoy GR, Kogan IM, Li JZ, Palmer ET, Luz-Ricca E, de Gialluly PS, Wustholz KL. Blinking-Based Multiplexing: A New Approach for Differentiating Spectrally Overlapped Emitters. J Phys Chem Lett 2022; 13:5056-5060. [PMID: 35652798 DOI: 10.1021/acs.jpclett.2c01252] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Multicolor single-molecule imaging is widely applied to answer questions in biology and materials science. However, most studies rely on spectrally distinct fluorescent probes or time-intensive sequential imaging strategies to multiplex. Here, we introduce blinking-based multiplexing (BBM), a simple approach to differentiate spectrally overlapped emitters based solely on their intrinsic blinking dynamics. The blinking dynamics of hundreds of rhodamine 6G and CdSe/ZnS quantum dots on glass are obtained using the same acquisition settings and analyzed with a change point detection algorithm. Although substantial blinking heterogeneity is observed, the analysis yields a blinking metric with 93.5% classification accuracy. We further show that BBM with up to 96.6% accuracy is achieved by using a deep learning algorithm for classification. This proof-of-concept study demonstrates that a single emitter can be accurately classified based on its intrinsic blinking dynamics and without the need to probe its spectral color.
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Affiliation(s)
- Grace A DeSalvo
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Grayson R Hoy
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Isabelle M Kogan
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - John Z Li
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Elise T Palmer
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Emilio Luz-Ricca
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Paul Scemama de Gialluly
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Kristin L Wustholz
- Department of Chemistry, William & Mary, P.O. Box 8795, Williamsburg, Virginia 23187, United States
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24
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Yang Q, Chang X, Lee JY, Olivera TR, Saji M, Wisniewski H, Kim S, Zhang F. Recent Advances in Self-Assembled DNA Nanostructures for Bioimaging. ACS APPLIED BIO MATERIALS 2022; 5:4652-4667. [PMID: 35559619 DOI: 10.1021/acsabm.2c00128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA nanotechnology has been proven to be a powerful platform to assist the development of imaging probes for biomedical research. The attractive features of DNA nanostructures, such as nanometer precision, controllable size, programmable functions, and biocompatibility, have enabled researchers to design and customize DNA nanoprobes for bioimaging applications. However, DNA probes with low molecular weights (e.g., 10-100 nt) generally suffer from low stability in physiological buffer environments. To improve the stability of DNA nanoprobes in such environments, DNA nanostructures can be designed with relatively larger sizes and defined shapes. In addition, the established modification methods for DNA nanostructures are also essential in enhancing their properties and performances in a physiological environment. In this review, we begin with a brief recap of the development of DNA nanostructures including DNA tiles, DNA origami, and multifunctional DNA nanostructures with modifications. Then we highlight the recent advances of DNA nanostructures for bioimaging, emphasizing the latest developments in probe modifications and DNA-PAINT imaging. Multiple imaging modules for intracellular biomolecular imaging and cell membrane biomarkers recognition are also summarized. In the end, we discuss the advantages and challenges of applying DNA nanostructures in bioimaging research and speculate on its future developments.
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Affiliation(s)
- Qi Yang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Tiffany R Olivera
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Henry Wisniewski
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Suchan Kim
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
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25
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Chung KKH, Zhang Z, Kidd P, Zhang Y, Williams ND, Rollins B, Yang Y, Lin C, Baddeley D, Bewersdorf J. Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. Nat Methods 2022; 19:554-559. [PMID: 35501386 PMCID: PMC9133131 DOI: 10.1038/s41592-022-01464-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/23/2022] [Indexed: 11/21/2022]
Abstract
DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful super-resolution microscopy method that can acquire high-fidelity images at nanometer resolution. It suffers, however, from high background and slow imaging speed, both of which can be attributed to the presence of unbound fluorophores in solution. Here we present two-color fluorogenic DNA-PAINT, which uses improved imager probe and docking strand designs to solve these problems. These self-quenching single-stranded DNA probes are conjugated with a fluorophore and quencher at the terminals, which permits an increase in fluorescence by up to 57-fold upon binding and unquenching. In addition, the engineering of base pair mismatches between the fluorogenic imager probes and docking strands allowed us to achieve both high fluorogenicity and the fast binding kinetics required for fast imaging. We demonstrate a 26-fold increase in imaging speed over regular DNA-PAINT and show that our new implementation enables three-dimensional super-resolution DNA-PAINT imaging without optical sectioning.
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Affiliation(s)
- Kenny K H Chung
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Zhao Zhang
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Phylicia Kidd
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Nathan D Williams
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Bennett Rollins
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Yang Yang
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Chenxiang Lin
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - David Baddeley
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University, New Haven, CT, USA.
- Nanobiology Institute, Yale University, West Haven, CT, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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26
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Gimber N, Strauss S, Jungmann R, Schmoranzer J. Simultaneous Multicolor DNA-PAINT without Sequential Fluid Exchange Using Spectral Demixing. NANO LETTERS 2022; 22:2682-2690. [PMID: 35290738 PMCID: PMC9011399 DOI: 10.1021/acs.nanolett.1c04520] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Several variants of multicolor single-molecule localization microscopy (SMLM) have been developed to resolve the spatial relationship of nanoscale structures in biological samples. The oligonucleotide-based SMLM approach "DNA-PAINT" robustly achieves nanometer localization precision and can be used to count binding sites within nanostructures. However, multicolor DNA-PAINT has primarily been realized by "Exchange-PAINT", which requires sequential exchange of the imaging solution and thus leads to extended acquisition times. To alleviate the need for fluid exchange and to speed up the acquisition of current multichannel DNA-PAINT, we here present a novel approach that combines DNA-PAINT with simultaneous multicolor acquisition using spectral demixing (SD). By using newly designed probes and a novel multichannel registration procedure, we achieve simultaneous multicolor SD-DNA-PAINT with minimal crosstalk. We demonstrate high localization precision (3-6 nm) and multicolor registration of dual- and triple-color SD-DNA-PAINT by resolving patterns on DNA origami nanostructures and cellular structures.
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Affiliation(s)
- Niclas Gimber
- Advanced
Medical Bioimaging Core Facility, Charité-Universitätsmedizin, 10117 Berlin, Germany
- . Phone +49 30 450 536331
| | - Sebastian Strauss
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80799 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80799 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jan Schmoranzer
- Advanced
Medical Bioimaging Core Facility, Charité-Universitätsmedizin, 10117 Berlin, Germany
- . Phone +49
30 450 536331
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27
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Abstract
Due to its sensitivity and versatility, fluorescence is widely used to detect specifically labeled biomolecules. However, fluorescence is currently limited by label discrimination, which suffers from the broad full width of the absorption/emission bands and the narrow lifetime distribution of the bright fluorophores. We overcome this limitation by introducing extra kinetic dimensions through illuminations of reversibly photoswitchable fluorophores (RSFs) at different light intensities. In this expanded space, each RSF is characterized by a chromatic aberration-free kinetic fingerprint of photochemical reactivity, which can be recovered with limited hardware, excellent photon budget, and minimal data processing. This fingerprint was used to identify and discriminate up to 20 among 22 spectrally similar reversibly photoswitchable fluorescent proteins (RSFPs) in less than 1s. This strategy opens promising perspectives for expanding the multiplexing capabilities of fluorescence imaging. Label discrimination is challenging in fluorescence microscopy due to broad spectra and narrow lifetime distribution. Here, the authors introduce extra kinetic dimensions by illuminating reversibly photoswitchable fluorophores with different intensities, and discriminate 20 spectrally similar fluorophores.
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28
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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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29
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Bond C, Santiago-Ruiz AN, Tang Q, Lakadamyali M. Technological advances in super-resolution microscopy to study cellular processes. Mol Cell 2022; 82:315-332. [PMID: 35063099 PMCID: PMC8852216 DOI: 10.1016/j.molcel.2021.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/22/2023]
Abstract
Since its initial demonstration in 2000, far-field super-resolution light microscopy has undergone tremendous technological developments. In parallel, these developments have opened a new window into visualizing the inner life of cells at unprecedented levels of detail. Here, we review the technical details behind the most common implementations of super-resolution microscopy and highlight some of the recent, promising advances in this field.
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Affiliation(s)
- Charles Bond
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adriana N. Santiago-Ruiz
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qing Tang
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Correspondence should be sent to M.L.:
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30
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Arista-Romero M, Delcanale P, Pujals S, Albertazzi L. Nanoscale Mapping of Recombinant Viral Proteins: From Cells to Virus-Like Particles. ACS PHOTONICS 2022; 9:101-109. [PMID: 35083366 PMCID: PMC8778639 DOI: 10.1021/acsphotonics.1c01154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 05/17/2023]
Abstract
Influenza recombinant proteins and virus-like particles (VLPs) play an important role in vaccine development (e.g., CadiFlu-S). However, their production from mammalian cells suffers from low yields and lack of control of the final VLPs. To improve these issues, characterization techniques able to visualize and quantify the different steps of the process are needed. Fluorescence microscopy represents a powerful tool able to image multiple protein targets; however, its limited resolution hinders the study of viral constructs. Here, we propose the use of super-resolution microscopy and in particular of DNA-point accumulation for imaging in nanoscale topography (DNA-PAINT) microscopy as a characterization method for recombinant viral proteins on both cells and VLPs. We were able to quantify the amount of the three main influenza proteins (hemagglutinin (HA), neuraminidase (NA), and ion channel matrix protein 2 (M2)) per cell and per VLP with nanometer resolution and single-molecule sensitivity, proving that DNA-PAINT is a powerful technique to characterize recombinant viral constructs.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
| | - Pietro Delcanale
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco area delle Scienze 7/A, 43124 Parma, Italy
| | - Silvia Pujals
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering
of Catalonia (IBEC), The Barcelona Institute of Science and Technology, C\Baldiri Reixac 15-21, Helix Building, 08028 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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31
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Oleksiievets N, Sargsyan Y, Thiele JC, Mougios N, Sograte-Idrissi S, Nevskyi O, Gregor I, Opazo F, Thoms S, Enderlein J, Tsukanov R. Fluorescence lifetime DNA-PAINT for multiplexed super-resolution imaging of cells. Commun Biol 2022; 5:38. [PMID: 35017652 PMCID: PMC8752799 DOI: 10.1038/s42003-021-02976-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 12/08/2021] [Indexed: 11/08/2022] Open
Abstract
DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful super-resolution technique highly suitable for multi-target (multiplexing) bio-imaging. However, multiplexed imaging of cells is still challenging due to the dense and sticky environment inside a cell. Here, we combine fluorescence lifetime imaging microscopy (FLIM) with DNA-PAINT and use the lifetime information as a multiplexing parameter for targets identification. In contrast to Exchange-PAINT, fluorescence lifetime PAINT (FL-PAINT) can image multiple targets simultaneously and does not require any fluid exchange, thus leaving the sample undisturbed and making the use of flow chambers/microfluidic systems unnecessary. We demonstrate the potential of FL-PAINT by simultaneous imaging of up to three targets in a cell using both wide-field FLIM and 3D time-resolved confocal laser scanning microscopy (CLSM). FL-PAINT can be readily combined with other existing techniques of multiplexed imaging and is therefore a perfect candidate for high-throughput multi-target bio-imaging.
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Affiliation(s)
- Nazar Oleksiievets
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Yelena Sargsyan
- Department of Child and Adolescent Health, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Jan Christoph Thiele
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Nikolaos Mougios
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Oleksii Nevskyi
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Ingo Gregor
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
- NanoTag Biotechnologies GmbH, 37079, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center Göttingen, 37073, Göttingen, Germany
- Biochemistry and Molecular Medicine, Medical School, Bielefeld University, 33615, Bielefeld, Germany
| | - Jörg Enderlein
- III. 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, Göttingen, Germany.
| | - Roman Tsukanov
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany.
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32
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Andrian T, Pujals S, Albertazzi L. Quantifying the effect of PEG architecture on nanoparticle ligand availability using DNA-PAINT. NANOSCALE ADVANCES 2021; 3:6876-6881. [PMID: 34977461 PMCID: PMC8650147 DOI: 10.1039/d1na00696g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/01/2021] [Indexed: 06/14/2023]
Abstract
The importance of PEG architecture on nanoparticle (NP) functionality is known but still difficult to investigate, especially at a single particle level. Here, we apply DNA Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT), a super-resolution microscopy (SRM) technique, to study the surface functionality in poly(lactide-co-glycolide)-poly(ethylene glycol) (PLGA-PEG) NPs with different PEG structures. We demonstrated how the length of the PEG spacer can influence the accessibility of surface chemical functionality, highlighting the importance of SRM techniques to support the rational design of functionalized NPs.
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Affiliation(s)
- Teodora Andrian
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology Baldiri Reixac 15-21 08028 Barcelona Spain
| | - Silvia Pujals
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology Baldiri Reixac 15-21 08028 Barcelona Spain
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology Baldiri Reixac 15-21 08028 Barcelona Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology 5612AZ Eindhoven The Netherlands
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33
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Barrantes FJ. Fluorescence sensors for imaging membrane lipid domains and cholesterol. CURRENT TOPICS IN MEMBRANES 2021; 88:257-314. [PMID: 34862029 DOI: 10.1016/bs.ctm.2021.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Lipid membrane domains are supramolecular lateral heterogeneities of biological membranes. Of nanoscopic dimensions, they constitute specialized hubs used by the cell as transient signaling platforms for a great variety of biologically important mechanisms. Their property to form and dissolve in the bulk lipid bilayer endow them with the ability to engage in highly dynamic processes, and temporarily recruit subpopulations of membrane proteins in reduced nanometric compartments that can coalesce to form larger mesoscale assemblies. Cholesterol is an essential component of these lipid domains; its unique molecular structure is suitable for interacting intricately with crevices and cavities of transmembrane protein surfaces through its rough β face while "talking" to fatty acid acyl chains of glycerophospholipids and sphingolipids via its smooth α face. Progress in the field of membrane domains has been closely associated with innovative improvements in fluorescence microscopy and new fluorescence sensors. These advances enabled the exploration of the biophysical properties of lipids and their supramolecular platforms. Here I review the rationale behind the use of biosensors over the last few decades and their contributions towards elucidation of the in-plane and transbilayer topography of cholesterol-enriched lipid domains and their molecular constituents. The challenges introduced by super-resolution optical microscopy are discussed, as well as possible scenarios for future developments in the field, including virtual ("no staining") staining.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)-National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina.
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34
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Rubio-Sánchez R, Fabrini G, Cicuta P, Di Michele L. Amphiphilic DNA nanostructures for bottom-up synthetic biology. Chem Commun (Camb) 2021; 57:12725-12740. [PMID: 34750602 PMCID: PMC8631003 DOI: 10.1039/d1cc04311k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022]
Abstract
DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Giacomo Fabrini
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
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35
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Pan V, Wang W, Heaven I, Bai T, Cheng Y, Chen C, Ke Y, Wei B. Monochromatic Fluorescent Barcodes Hierarchically Assembled from Modular DNA Origami Nanorods. ACS NANO 2021; 15:15892-15901. [PMID: 34570467 DOI: 10.1021/acsnano.1c03796] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
With the rapid advancement of fluorescence microscopy, there is a growing interest in the multiplexed detection and identification of various bioanalytes (e.g., nucleic acids and proteins) for efficient sample processing and analysis. We introduce in this work a simple and robust method to provide combinations for micrometer-scale fluorescent DNA barcodes of hierarchically assembled DNA origami superstructures for multiplexed molecular probing. In addition to optically resolvable dots, we placed fluorescent loci on adjacent origami within the diffraction limit of each other, rendering them as unresolvable bars of measurable lengths. We created a basic set of barcodes and trained a machine learning algorithm to process and identify individual barcodes from raw images with high accuracy. Moreover, we demonstrated that the number of combinations can be increased exponentially by generating longer barcodes, by controlling the number of incorporated fluorophores to create multiple levels of fluorescence intensity, and by employing super-resolution imaging. To showcase the readiness of the barcodes for applications, we used our barcodes to capture and identify target nucleic acid sequences and for simultaneous multiplexed characterization of binding kinetics of several orthogonal complementary nucleic acids.
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Affiliation(s)
- Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
- Department of Biomedical Engineering, Peking University, Beijing 100871, China
| | - Wen Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Ian Heaven
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30322, United States
| | - Tanxi Bai
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yongxin Cheng
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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36
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Kollimada S, Senger F, Vignaud T, Théry M, Blanchoin L, Kurzawa L. The biochemical composition of the actomyosin network sets the magnitude of cellular traction forces. Mol Biol Cell 2021; 32:1737-1748. [PMID: 34410837 PMCID: PMC8684728 DOI: 10.1091/mbc.e21-03-0109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The regulation of cellular force production relies on the complex interplay between a well-conserved set of proteins of the cytoskeleton: actin, myosin, and α-actinin. Despite our deep knowledge of the role of these proteins in force production at the molecular scale, our understanding of the biochemical regulation of the magnitude of traction forces generated at the entire-cell level has been limited, notably by the technical challenge of measuring traction forces and the endogenous biochemical composition in the same cell. In this study, we developed an alternative Traction-Force Microscopy (TFM) assay, which used a combination of hydrogel micropatterning to define cell adhesion and shape and an intermediate fixation/immunolabeling step to characterize strain energies and the endogenous protein contents in single epithelial cells. Our results demonstrated that both the signal intensity and the area of the Focal Adhesion (FA)–associated protein vinculin showed a strong positive correlation with strain energy in mature FAs. Individual contents from actin filament and phospho-myosin displayed broader deviation in their linear relationship to strain energies. Instead, our quantitative analyzes demonstrated that their relative amount exhibited an optimum ratio of phospho-myosin to actin, allowing maximum force production by cells. By contrast, although no correlation was identified between individual α-actinin content and strain energy, the ratio of α-actinin to actin filaments was inversely related to strain energy. Hence, our results suggest that, in the cellular model studied, traction-force magnitude is dictated by the relative numbers of molecular motors and cross-linkers per actin filament, rather than the amounts of an individual component in the cytoskeletal network. This assay offers new perspectives to study in more detail the complex interplay between the endogenous biochemical composition of individual cells and the force they produce.
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Affiliation(s)
- Somanna Kollimada
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Fabrice Senger
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Timothée Vignaud
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France.,Clinique de chirurgie digestive et endocrinienne, Hôtel Dieu, Nantes, 44093, France
| | - Manuel Théry
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France.,Institut de Recherche Saint Louis, U976 Human Immunology Pathophysiology Immunotherapy (HIPI), CytoMorpho Lab, University of Paris, INSERM, CEA, Paris, France
| | - Laurent Blanchoin
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France.,Institut de Recherche Saint Louis, U976 Human Immunology Pathophysiology Immunotherapy (HIPI), CytoMorpho Lab, University of Paris, INSERM, CEA, Paris, France
| | - Laëtitia Kurzawa
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
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37
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Swenson CS, Lackey HH, Reece EJ, Harris JM, Heemstra JM, Peterson EM. Evaluating the effect of ionic strength on PNA:DNA duplex formation kinetics. RSC Chem Biol 2021; 2:1249-1256. [PMID: 34458838 PMCID: PMC8341200 DOI: 10.1039/d1cb00025j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin-Watson-Crick base pairing provided by PNA, particularly at lower ionic strengths. However, our understanding of the relationship between the kinetics of PNA:DNA hybridization and ionic strength is incomplete. Here we measured the kinetics of association and dissociation of PNA with DNA across a range of ionic strengths and temperatures at single-molecule resolution using total internal reflection fluorescence imaging. Unlike DNA:DNA duplexes, PNA:DNA duplexes are more stable at lower ionic strength, and we demonstrate that this is due to a higher association rate. While the dissociation rate of PNA:DNA duplexes is largely insensitive to ionic strength, it is significantly lower than that of DNA:DNA duplexes having the same number and sequence of base pairing interactions. The temperature dependence of PNA:DNA kinetic rate constants indicate a significant enthalpy barrier to duplex dissociation, and to a lesser extent, duplex formation. This investigation into the kinetics of PNA:DNA hybridization provides a framework towards better understanding and design of PNA sequences for future applications.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University Atlanta GA 30322 USA
| | - Hershel H Lackey
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Eric J Reece
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | - Joel M Harris
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
| | | | - Eric M Peterson
- Department of Chemistry, University of Utah Salt Lake City UT 84112 USA
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38
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Tracking single particles for hours via continuous DNA-mediated fluorophore exchange. Nat Commun 2021; 12:4432. [PMID: 34290254 PMCID: PMC8295357 DOI: 10.1038/s41467-021-24223-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/07/2021] [Indexed: 01/13/2023] Open
Abstract
Monitoring biomolecules in single-particle tracking experiments is typically achieved by employing fixed organic dyes or fluorescent fusion proteins linked to a target of interest. However, photobleaching typically limits observation times to merely a few seconds, restricting downstream statistical analysis and observation of rare biological events. Here, we overcome this inherent limitation via continuous fluorophore exchange using DNA-PAINT, where fluorescently-labeled oligonucleotides reversibly bind to a single-stranded DNA handle attached to the target molecule. Such versatile and facile labeling allows uninterrupted monitoring of single molecules for extended durations. We demonstrate the power of our approach by observing DNA origami on membranes for tens of minutes, providing perspectives for investigating cellular processes on physiologically relevant timescales. The length of single-particle tracking experiments are limited due to photobleaching. Here the authors achieve long-term single-particle tracking with continuous fluorophore exchange in DNA-PAINT and use this to observe DNA origami on lipid bilayers for tens of minutes.
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39
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Huang Q, Chen B, Shen J, Liu L, Li J, Shi J, Li Q, Zuo X, Wang L, Fan C, Li J. Encoding Fluorescence Anisotropic Barcodes with DNA Fameworks. J Am Chem Soc 2021; 143:10735-10742. [PMID: 34242004 DOI: 10.1021/jacs.1c04942] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence anisotropy (FA) holds great potential for multiplexed analysis and imaging of biomolecules since it can effectively discriminate fluorophores with overlapping emission spectra. Nevertheless, its susceptibility to environmental variation hampers its widespread applications in biology and biotechnology. In this study, we design FA DNA frameworks (FAFs) by scaffolding fluorophores in a fluorescent protein-like microenvironment. We find that the FA stability of the fluorophores is remarkably improved due to the sequestration effects of FAFs. The FA level of the fluorophores can be finely tuned when placed at different locations on an FAF, analogous to spectral shifts of protein-bound fluorophores. The high programmability of FAFs further enables the design of a spectrum of encoded FA barcodes for multiplexed sensing of nucleic acids and multiplexed labeling of live cells. This FAF system thus establishes a new paradigm for designing multiplexing FA probes for cellular imaging and other biological applications.
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Affiliation(s)
- Qiuling Huang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiajun Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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40
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van Wee R, Filius M, Joo C. Completing the canvas: advances and challenges for DNA-PAINT super-resolution imaging. Trends Biochem Sci 2021; 46:918-930. [PMID: 34247944 DOI: 10.1016/j.tibs.2021.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/16/2021] [Accepted: 05/31/2021] [Indexed: 01/02/2023]
Abstract
Single-molecule localization microscopy (SMLM) is a potent tool to examine biological systems with unprecedented resolution, enabling the investigation of increasingly smaller structures. At the forefront of these developments is DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT), which exploits the stochastic and transient binding of fluorescently labeled DNA probes. In its early stages the implementation of DNA-PAINT was burdened by low-throughput, excessive acquisition time, and difficult integration with live-cell imaging. However, recent advances are addressing these challenges and expanding the range of applications of DNA-PAINT. We review the current state of the art of DNA-PAINT in light of these advances and contemplate what further developments remain indispensable to realize live-cell imaging.
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Affiliation(s)
- Raman van Wee
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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41
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Fu S, Zhang T, Jiang H, Xu Y, Chen J, Zhang L, Su X. DNA nanotechnology enhanced single-molecule biosensing and imaging. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116267] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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Tomov ML, O'Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M. Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Commun Biol 2021; 4:786. [PMID: 34168275 PMCID: PMC8225800 DOI: 10.1038/s42003-021-02276-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/28/2021] [Indexed: 12/30/2022] Open
Abstract
Human induced pluripotent stem cell-derived (iPSC) neural cultures offer clinically relevant models of human diseases, including Amyotrophic Lateral Sclerosis, Alzheimer’s, and Autism Spectrum Disorder. In situ characterization of the spatial-temporal evolution of cell state in 3D culture and subsequent 2D dissociated culture models based on protein expression levels and localizations is essential to understanding neural cell differentiation, disease state phenotypes, and sample-to-sample variability. Here, we apply PRobe-based Imaging for Sequential Multiplexing (PRISM) to facilitate multiplexed imaging with facile, rapid exchange of imaging probes to analyze iPSC-derived cortical and motor neuron cultures that are relevant to psychiatric and neurodegenerative disease models, using over ten protein targets. Our approach permits analysis of cell differentiation, cell composition, and functional marker expression in complex stem-cell derived neural cultures. Furthermore, our approach is amenable to automation, offering in principle the ability to scale-up to dozens of protein targets and samples. Tomov et al. utilize DNA-PRISM to allow for multiplexed imaging of cultured cells using antibodies modified with oligonucleotide probes. The differentiation of iPSCs to cortical and motor neurons is characterized in model cultures, relevant for use in disease research and drug screening.
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Affiliation(s)
- Martin L Tomov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Alison O'Neil
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Hamdah S Abbasi
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beth A Cimini
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lee L Rubin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Mark Bathe
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
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43
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Schlichthaerle T, Lindner C, Jungmann R. Super-resolved visualization of single DNA-based tension sensors in cell adhesion. Nat Commun 2021; 12:2510. [PMID: 33947854 PMCID: PMC8097079 DOI: 10.1038/s41467-021-22606-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/18/2021] [Indexed: 01/07/2023] Open
Abstract
Cell-extracellular matrix sensing plays a crucial role in cellular behavior and leads to the formation of a macromolecular protein complex called the focal adhesion. Despite their importance in cellular decision making, relatively little is known about cell-matrix interactions and the intracellular transduction of an initial ligand-receptor binding event on the single-molecule level. Here, we combine cRGD-ligand-decorated DNA tension sensors with DNA-PAINT super-resolution microscopy to study the mechanical engagement of single integrin receptors and the downstream influence on actin bundling. We uncover that integrin receptor clustering is governed by a non-random organization with complexes spaced at 20–30 nm distances. The DNA-based tension sensor and analysis framework provide powerful tools to study a multitude of receptor-ligand interactions where forces are involved in ligand-receptor binding. Relatively little is known about cell-matrix interactions and the intracellular transduction of an initial ligand-receptor binding event on the single-molecule level. Here authors combine ligand-decorated DNA tension sensors with DNA-PAINT super-resolution microscopy to study the mechanical engagement of single integrin receptors and the downstream influence on actin bundling.
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Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Caroline Lindner
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany. .,Max Planck Institute of Biochemistry, Martinsried, Germany.
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44
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Hugelier S, Van den Eynde R, Vandenberg W, Dedecker P. Fluorophore unmixing based on bleaching and recovery kinetics using MCR-ALS. Talanta 2021; 226:122117. [PMID: 33676672 DOI: 10.1016/j.talanta.2021.122117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 02/03/2023]
Abstract
Fluorescence microscopy is a key technology in the life sciences, though its performance is constrained by the number of labels that can be recorded. We propose to use the kinetics of fluorophore photodestruction and subsequent fluorescence recovery to distinguish multiple spectrally-overlapping emitters in fixed cells, thus enhancing the information that can be obtained from a single measurement. We show that the data can be directly processed using multivariate curve resolution - alternating least squares (MCR-ALS) to deliver distinct images for each fluorophore in their local environment, and apply this methodology to membrane imaging using DiBAC4(3) and concanavalin A - Alexa Fluor 488 as the fluorophores. We find that the DiBAC4(3) displays two distinct degradation/recovery kinetics that correspond to two different label distributions, allowing us to simultaneously distinguish three different fluorescence distributions from two spectrally overlapping fluorophores. We expect that our approach will scale to other dynamically-binding dyes, leading to similarly increased multiplexing capability.
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Affiliation(s)
- S Hugelier
- Laboratory for Nanobiology, KU Leuven, B-3001 Leuven, Belgium.
| | - R Van den Eynde
- Laboratory for Nanobiology, KU Leuven, B-3001 Leuven, Belgium
| | - W Vandenberg
- Laboratory for Nanobiology, KU Leuven, B-3001 Leuven, Belgium; Univ. Lille, CNRS, Laboratoire de Spectroscopie pour Les Interactions, La Réactivité et L'Environnement (LASIRE), F-59000 Lille, France
| | - P Dedecker
- Laboratory for Nanobiology, KU Leuven, B-3001 Leuven, Belgium
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45
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Dickinson GD, Mortuza GM, Clay W, Piantanida L, Green CM, Watson C, Hayden EJ, Andersen T, Kuang W, Graugnard E, Zadegan R, Hughes WL. An alternative approach to nucleic acid memory. Nat Commun 2021; 12:2371. [PMID: 33888693 PMCID: PMC8062470 DOI: 10.1038/s41467-021-22277-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/04/2021] [Indexed: 11/08/2022] Open
Abstract
DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency. Previous studies have used artificially synthesized DNA to store data and automated next-generation sequencing to read it back. Here, we report digital Nucleic Acid Memory (dNAM) for applications that require a limited amount of data to have high information density, redundancy, and copy number. In dNAM, data is encoded by selecting combinations of single-stranded DNA with (1) or without (0) docking-site domains. When self-assembled with scaffold DNA, staple strands form DNA origami breadboards. Information encoded into the breadboards is read by monitoring the binding of fluorescent imager probes using DNA-PAINT super-resolution microscopy. To enhance data retention, a multi-layer error correction scheme that combines fountain and bi-level parity codes is used. As a prototype, fifteen origami encoded with 'Data is in our DNA!\n' are analyzed. Each origami encodes unique data-droplet, index, orientation, and error-correction information. The error-correction algorithms fully recover the message when individual docking sites, or entire origami, are missing. Unlike other approaches to DNA-based data storage, reading dNAM does not require sequencing. As such, it offers an additional path to explore the advantages and disadvantages of DNA as an emerging memory material.
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Affiliation(s)
- George D Dickinson
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
| | - Golam Md Mortuza
- Department of Computer Science, Boise State University, Boise, ID, USA
| | - William Clay
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
| | - Luca Piantanida
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
| | - Christopher M Green
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Chad Watson
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
| | - Eric J Hayden
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Tim Andersen
- Department of Computer Science, Boise State University, Boise, ID, USA
| | - Wan Kuang
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID, USA
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
| | - Reza Zadegan
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, NC, USA
| | - William L Hughes
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID, USA.
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46
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DNA hybridisation kinetics using single-molecule fluorescence imaging. Essays Biochem 2021; 65:27-36. [PMID: 33491734 PMCID: PMC8056036 DOI: 10.1042/ebc20200040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023]
Abstract
Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.
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47
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Hartland GV. Virtual Issue on Super-Resolution Far-Field Optical Microscopy. J Phys Chem B 2021; 124:1581-1584. [PMID: 32131600 DOI: 10.1021/acs.jpcb.0c01501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Local Protein Translation and RNA Processing of Synaptic Proteins in Autism Spectrum Disorder. Int J Mol Sci 2021; 22:ijms22062811. [PMID: 33802132 PMCID: PMC8001067 DOI: 10.3390/ijms22062811] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a heritable neurodevelopmental condition associated with impairments in social interaction, communication and repetitive behaviors. While the underlying disease mechanisms remain to be fully elucidated, dysfunction of neuronal plasticity and local translation control have emerged as key points of interest. Translation of mRNAs for critical synaptic proteins are negatively regulated by Fragile X mental retardation protein (FMRP), which is lost in the most common single-gene disorder associated with ASD. Numerous studies have shown that mRNA transport, RNA metabolism, and translation of synaptic proteins are important for neuronal health, synaptic plasticity, and learning and memory. Accordingly, dysfunction of these mechanisms may contribute to the abnormal brain function observed in individuals with autism spectrum disorder (ASD). In this review, we summarize recent studies about local translation and mRNA processing of synaptic proteins and discuss how perturbations of these processes may be related to the pathophysiology of ASD.
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49
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Platnich CM, Rizzuto FJ, Cosa G, Sleiman HF. Single-molecule methods in structural DNA nanotechnology. Chem Soc Rev 2021; 49:4220-4233. [PMID: 32538403 DOI: 10.1039/c9cs00776h] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single molecules can now be visualised with unprecedented precision. As the resolution of single-molecule experiments improves, so too does the breadth, quantity and quality of information that can be extracted using these methodologies. In the field of DNA nanotechnology, we use programmable interactions between nucleic acids to generate complex, multidimensional structures. We can use single-molecule techniques - ranging from electron and fluorescence microscopies to electrical and force spectroscopies - to report on the structure, morphology, robustness, sample heterogeneity and other properties of these DNA nanoconstructs. In this Tutorial Review, we will detail how complementarity between static and dynamic single-molecule techniques can provide a unified image of DNA nanoarchitectures. The single-molecule methods that we discuss provide unprecedented insight into chemical and structural behaviour, yielding not just an average outcome but reporting on the distribution of values, ultimately showing how bulk properties arise from the collective behaviour of individual structures. As the fields of both DNA nanotechnology and single-molecule characterisation intertwine, a feedback loop is generated between disciplines, providing new opportunities for the development and operation of DNA-based materials as sensors, delivery vehicles, machinery and structural scaffolds.
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Affiliation(s)
- Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
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50
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Affiliation(s)
- Keke Hu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Tho D. K. Nguyen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pieter E. Oomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
- ParaMedir B.V., 1e Energieweg 13, 9301 LK Roden, The Netherlands
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
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