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Mukherjee S, Thomas C, Wilson R, Simmerman E, Hung ST, Jimenez R. Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances. Phys Chem Chem Phys 2022; 24:14310-14323. [DOI: 10.1039/d2cp00889k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states...
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53
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Mennella V, Liu Z. Nanometer-Scale Molecular Mapping by Super-resolution Fluorescence Microscopy. Methods Mol Biol 2022; 2440:305-326. [PMID: 35218547 DOI: 10.1007/978-1-0716-2051-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The structural organization of macromolecules and their association in assemblies and organelles is key to understand cellular function. Super-resolution fluorescence microscopy has expanded our toolbox for examining such nanometer-scale cellular structures, by enabling positional mapping of proteins in situ. Here, we detail the workflow to build nanometer-scale maps focusing on two complementary super-resolution modalities: structured illumination microscopy (SIM) and stochastic optical reconstruction microscopy (STORM).
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Affiliation(s)
- Vito Mennella
- MRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK.
| | - Zhen Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
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Cherayil BJ. Particle dynamics in viscoelastic media: Effects of non-thermal white noise on barrier crossing rates. J Chem Phys 2021; 155:244903. [PMID: 34972363 DOI: 10.1063/5.0071206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The growing interest in the dynamics of self-driven particle motion has brought increased attention to the effects of non-thermal noise on condensed phase diffusion. Thanks to data recently collected by Ferrer et al. on activated dynamics in the presence of memory [Phys. Rev. Lett. 126, 108001 (2021)], some of these effects can now be characterized quantitatively. In the present paper, the data collected by Ferrer et al. are used to calculate the extent to which non-thermal white noise alters the time taken by single micron-sized silica particles in a viscoelastic medium to cross the barrier separating the two wells of an optically created bistable potential. The calculation-based on a generalized version of Kramers's flux-over-population approach-indicates that the added noise causes the barrier crossing rate (compared to the noise-free case) to first increase as a function of the noise strength and then to plateau to a constant value. The precise degree of rate enhancement may depend on how the data from the experiments conducted by Ferrer et al. are used in the flux-over-population approach. As claimed by Ferrer et al., this approach predicts barrier crossing times for the original silica-fluid system that agree almost perfectly with their experimental counterparts. However, this near-perfect agreement between theory and experiment is only achieved if the theoretical crossing times are obtained from the most probable values of a crossing time distribution constructed from the distributions of various parameters in Kramers's rate expression. If the mean values of these parameters are used in the expression instead, as would be commonly done, the theoretical crossing times are found to be as much as 1.5 times higher than the experimental values. However, these times turn out to be consistent with an alternative model of viscoelastic barrier crossing based on a mean first passage time formalism, which also uses mean parameter values in its rate expression. The rate enhancements predicted for barrier crossing under non-thermal noise are based on these mean parameter values and are open to experimental verification.
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Affiliation(s)
- Binny J Cherayil
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
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55
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Olejniczak A, Rich R, Gryczynski Z, Cichy B. Non-excitonic defect-assisted radiative transitions are responsible for new D-type blinking in ternary quantum dots. NANOSCALE HORIZONS 2021; 7:63-76. [PMID: 34792059 DOI: 10.1039/d1nh00424g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This work addresses the issue of dark states formation in QDs by cooperative excitonic and intrinsic defect-assisted radiative transitions. Here we refer to the observed blinking as D-type to distinguish it from purely excitonic types. It is shown experimentally that defect-assisted radiative relaxations in a single I-III-VI QD result in atypical blinking characteristics that cannot be explained on the basis of charged exciton models. In addition to the excitonic channel, it has been proposed that defect-assisted kinetics can also form blinking patterns. Two conditions for the formation of dark states have been identified which are related to correlation and competition when considering photons emitted from bright defects. Two transition schemes have therefore been proposed. The first transition scheme includes time-correlated trapping of more than one electron at a single trap centre. This is used to simulate variations in the defect's charge state and switching between radiative/nonradiative transitions. The latter scheme, on the other hand, involves uncorrelated trapping and radiative relaxations from two different types of defects (competition). Both schemes are seen to play an equal role in radiative processes in I-III-VI QDs. Considered together, the proposed models can reflect the experimental data with very good accuracy, providing a better understanding of the underlying physics. An important implication of these schemes is that dark states formation doesn't have to be limited to mechanisms that involve charged excitons, and it may also be observed for independent defect assisted kinetics. This is especially valid for highly defected or multinary QDs.
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Affiliation(s)
- Adam Olejniczak
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wrocław, Poland.
| | - Ryan Rich
- Department of Mathematics, Computer Science and Physics, Texas Wesleyan University, 1201 Wesleyan Street, Fort Worth, TX 76105, USA
| | - Zygmunt Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129, USA
| | - Bartłomiej Cichy
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wrocław, Poland.
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Wang B, Xiong M, Susanto J, Li X, Leung WY, Xu K. Transforming Rhodamine Dyes for (d)STORM Super-Resolution Microscopy via 1,3-Disubstituted Imidazolium Substitution. Angew Chem Int Ed Engl 2021; 61:e202113612. [PMID: 34919772 DOI: 10.1002/anie.202113612] [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: 10/07/2021] [Indexed: 11/06/2022]
Abstract
We introduce a strategy to optimize the photoswitching behavior of rhodamines for (d)STORM super-resolution microscopy. By replacing the benzene ring in the rhodamine core with a permanently charged 1,3-disubstituted imidazolium, the resultant dyes are markedly sensitized toward photoswitching, and exhibit outstanding (d)STORM performance with fast on-off switching, long-lasting blinking, and bright single-molecule emission. We thus attain excellent (d)STORM images under green excitation that are on par with the "ideal" red-excited dyes, including for difficult structures as the mammalian actin cytoskeleton, and demonstrate high-quality two-color three-dimensional (d)STORM.
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Affiliation(s)
- Bowen Wang
- University of California Berkeley, Chemistry, UNITED STATES
| | - Michael Xiong
- University of California Berkeley, Chemistry, UNITED STATES
| | | | - Xue Li
- Biotium Inc., n/a, UNITED STATES
| | | | - Ke Xu
- University of California Berkeley, Department of Chemistry, 478 Stanley Hall, 94720, Berkeley, UNITED STATES
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57
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Colaruotolo LA, Peters E, Corradini MG. Novel luminescent techniques in aid of food quality, product development, and food processing. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2021.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Aleksejenko N, Heller J. Super-resolution imaging to reveal the nanostructure of tripartite synapses. Neuronal Signal 2021; 5:NS20210003. [PMID: 34737894 PMCID: PMC8536832 DOI: 10.1042/ns20210003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Even though neurons are the main drivers of information processing in the brain and spinal cord, other cell types are important to mediate adequate flow of information. These include electrically passive glial cells such as microglia and astrocytes, which recently emerged as active partners facilitating proper signal transduction. In disease, these cells undergo pathophysiological changes that propel disease progression and change synaptic connections and signal transmission. In the healthy brain, astrocytic processes contact pre- and postsynaptic structures. These processes can be nanoscopic, and therefore only electron microscopy has been able to reveal their structure and morphology. However, electron microscopy is not suitable in revealing dynamic changes, and it is labour- and time-intensive. The dawn of super-resolution microscopy, techniques that 'break' the diffraction limit of conventional light microscopy, over the last decades has enabled researchers to reveal the nanoscopic synaptic environment. In this review, we highlight and discuss recent advances in our understanding of the nano-world of the so-called tripartite synapses, the relationship between pre- and postsynapse as well as astrocytic processes. Overall, novel super-resolution microscopy methods are needed to fully illuminate the intimate relationship between glia and neuronal cells that underlies signal transduction in the brain and that might be affected in diseases such as Alzheimer's disease and epilepsy.
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Affiliation(s)
- Natalija Aleksejenko
- School of Biotechnology and National Institute for Cellular Biotechnology (NICB), Dublin City University, Glasnevin, Ireland
| | - Janosch P. Heller
- School of Biotechnology and National Institute for Cellular Biotechnology (NICB), Dublin City University, Glasnevin, Ireland
- Queen Square Institute of Neurology, University College London, London, United Kingdom
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59
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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60
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Shida JF, Spieglan E, Adams BW, Angelico E, Domurat-Sousa K, Elagin A, Frisch HJ, La Riviere P, Squires AH. Low-Dose High-Resolution TOF-PET Using Ionization-activated Multi-State Low-Z Detector Media. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH. SECTION A, ACCELERATORS, SPECTROMETERS, DETECTORS AND ASSOCIATED EQUIPMENT 2021; 1017:165801. [PMID: 34690392 PMCID: PMC8530277 DOI: 10.1016/j.nima.2021.165801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We propose PET scanners using low atomic number media that undergo a persistent local change of state along the paths of the Compton recoil electrons. Measurement of the individual scattering locations and angles, deposited energies, and recoil electron directions allows using the kinematical constraints of the 2-body Compton scattering process to perform a statistical time-ordering of the scatterings, with a high probability of precisely identifying where the gamma first interacted in the detector. In these cases the Line-of-Response is measured with high resolution, determined by the underlying physics processes and not the detector segmentation. There are multiple such media that act through different mechanisms. As an example in which the change of state is quantum-mechanical through a change in molecular configuration, rather than thermodynamic, as in a bubble chamber, we present simulations of a two-state photoswitchable organic dye, a 'Switchillator', that is activated to a fluorescent-capable state by the ionization of the recoil electrons. The activated state is persistent, and can be optically excited multiple times to image individual activated molecules. Energy resolution is provided by counting the activated molecules. Location along the LOR is implemented by large-area time-of-flight MCP-PMT photodetectors with single photon time resolution in the tens of ps and sub-mm spatial resolution. Simulations indicate a large reduction of dose.
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Affiliation(s)
- J F Shida
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - E Spieglan
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - B W Adams
- Quantum Optics Applied Research, Naperville, IL 60564
| | - E Angelico
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - K Domurat-Sousa
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - A Elagin
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - H J Frisch
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - P La Riviere
- Department of Radiology, The University of Chicago, Billings Hospital, P220, 5841 South Maryland Avenue, MC2026, Chicago, IL 60637
| | - A H Squires
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637
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61
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Jing Y, Zhang C, Yu B, Lin D, Qu J. Super-Resolution Microscopy: Shedding New Light on In Vivo Imaging. Front Chem 2021; 9:746900. [PMID: 34595156 PMCID: PMC8476955 DOI: 10.3389/fchem.2021.746900] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/26/2021] [Indexed: 12/28/2022] Open
Abstract
Over the past two decades, super-resolution microscopy (SRM), which offered a significant improvement in resolution over conventional light microscopy, has become a powerful tool to visualize biological activities in both fixed and living cells. However, completely understanding biological processes requires studying cells in a physiological context at high spatiotemporal resolution. Recently, SRM has showcased its ability to observe the detailed structures and dynamics in living species. Here we summarized recent technical advancements in SRM that have been successfully applied to in vivo imaging. Then, improvements in the labeling strategies are discussed together with the spectroscopic and chemical demands of the fluorophores. Finally, we broadly reviewed the current applications for super-resolution techniques in living species and highlighted some inherent challenges faced in this emerging field. We hope that this review could serve as an ideal reference for researchers as well as beginners in the relevant field of in vivo super resolution imaging.
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Affiliation(s)
| | | | | | - Danying Lin
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
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62
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Wang J, Zhang Y. Adaptive optics in super-resolution microscopy. BIOPHYSICS REPORTS 2021; 7:267-279. [PMID: 37287764 PMCID: PMC10233472 DOI: 10.52601/bpr.2021.210015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/23/2021] [Indexed: 06/09/2023] Open
Abstract
Fluorescence microscopy has become a routine tool in biology for interrogating life activities with minimal perturbation. While the resolution of fluorescence microscopy is in theory governed only by the diffraction of light, the resolution obtainable in practice is also constrained by the presence of optical aberrations. The past two decades have witnessed the advent of super-resolution microscopy that overcomes the diffraction barrier, enabling numerous biological investigations at the nanoscale. Adaptive optics, a technique borrowed from astronomical imaging, has been applied to correct for optical aberrations in essentially every microscopy modality, especially in super-resolution microscopy in the last decade, to restore optimal image quality and resolution. In this review, we briefly introduce the fundamental concepts of adaptive optics and the operating principles of the major super-resolution imaging techniques. We highlight some recent implementations and advances in adaptive optics for active and dynamic aberration correction in super-resolution microscopy.
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Affiliation(s)
- Jingyu Wang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK
| | - Yongdeng Zhang
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
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63
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Valli J, Sanderson J. Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology. Curr Protoc 2021; 1:e224. [PMID: 34436832 DOI: 10.1002/cpz1.224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
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64
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Xiang L, Chen K, Xu K. Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy. ACS NANO 2021; 15:12483-12496. [PMID: 34304562 PMCID: PMC8789943 DOI: 10.1021/acsnano.1c04708] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.
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65
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Chen J, Chen Y. Parametric comparison between sparsity-based and deep learning-based image reconstruction of super-resolution fluorescence microscopy. BIOMEDICAL OPTICS EXPRESS 2021; 12:5246-5260. [PMID: 34513254 PMCID: PMC8407828 DOI: 10.1364/boe.427989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Sparsity-based and deep learning-based image reconstruction algorithms are two promising approaches to accelerate the image acquisition process for localization-based super-resolution microscopy, by allowing a higher density of fluorescing emitters to be imaged in a single frame. Despite the surging popularity, a comprehensive parametric study guiding the practical applications of sparsity-based and deep learning-based image reconstruction algorithms is yet to be conducted. In this study, we examined the performance of sparsity- and deep learning-based algorithms in reconstructing super-resolution images using simulated fluorescent microscopy images. The simulated images were synthesized with varying levels of sparsity and connectivity. We found the deep learning-based VDSR recovers image faster, with a higher recall rate and localization accuracy. The sparsity-based SPIDER recovers more zero pixels truthfully. We also compared the two algorithms using images acquired from a real super-resolution experiment, yielding results agreeing with the results from the evaluation using simulated images. We concluded that VDSR is preferable when accurate emitter localization is needed while SPIDER is more suitable when evaluation of the number of emitters is critical.
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Affiliation(s)
- Junjie Chen
- Department of Mechanical Engineering, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA
- Center for Cell Dynamics, Johns Hopkins University, 855 N Wolfe Street, Baltimore, MD 21205, USA
| | - Yun Chen
- Department of Mechanical Engineering, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA
- Center for Cell Dynamics, Johns Hopkins University, 855 N Wolfe Street, Baltimore, MD 21205, USA
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66
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Hara D, Uno SN, Motoki T, Kazuta Y, Norimine Y, Suganuma M, Fujiyama S, Shimaoka Y, Yamashita K, Okada M, Nishikawa Y, Amino H, Iwanaga S. Silinanyl Rhodamines and Silinanyl Fluoresceins for Super-Resolution Microscopy. J Phys Chem B 2021; 125:8703-8711. [PMID: 34328341 DOI: 10.1021/acs.jpcb.1c03193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-molecule localization microscopy (SMLM) enables the visualization of biomolecules at unprecedented resolution and requires control of the fluorescent blinking (ON/OFF) states of fluorophores to detect single-molecule fluorescence without overlapping of the signals. Although SMLM probes based on the intramolecular spirocyclization of Si-xanthene fluorophores have been developed, fluorophores with lower ON/OFF ratios are required for SMLM visualization of high-density structures. Here, we describe a silinane structure that lowers the ON/OFF ratio of Si-xanthene fluorophores. On the basis of Mulliken population analysis, we replaced the dimethylsilane moiety in Si-rhodamine with a silinane moiety to increase the partial charge at the 9-position of the carbon atom in the Si-xanthene ring and to promote the ring-closure reaction. Evaluation of fluorescence properties in a solution and in single-molecule imaging indicated that introducing the silinane sufficiently stabilized the nonfluorescent spirocyclic forms, thus decreasing the fluorescence ON/OFF ratio. This novel substitution was applied to Si-rhodamines with various amine structures and to an Si-fluorescein to expand the color palette. We demonstrated SMLM observation of microtubules in fixed HeLa cells using the developed fluorophores in two color channels. The results demonstrated the feasibility of extending the design strategies of SMLM probes based on Si-xanthenes through modification of the substituents on the Si atom.
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Affiliation(s)
- Daiki Hara
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Shin-Nosuke Uno
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Takafumi Motoki
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, Ibaraki 300-2635, Japan
| | - Yuji Kazuta
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, Ibaraki 300-2635, Japan
| | - Yoshihiko Norimine
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, Ibaraki 300-2635, Japan
| | - Masatoshi Suganuma
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Shingo Fujiyama
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Yuki Shimaoka
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Kazuto Yamashita
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Masaya Okada
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Youichi Nishikawa
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Hiroyuki Amino
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, Ibaraki 300-2635, Japan
| | - Shigeki Iwanaga
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
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67
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Aristova D, Kosach V, Chernii S, Slominsky Y, Balanda A, Filonenko V, Yarmoluk S, Rotaru A, Özkan HG, Mokhir A, Kovalska V. Monomethine cyanine probes for visualization of cellular RNA by fluorescence microscopy. Methods Appl Fluoresc 2021; 9. [PMID: 34198271 DOI: 10.1088/2050-6120/ac10ad] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022]
Abstract
We have studied spectral-luminescent properties of the monomethine cyanine dyes both in their free states and in the presence of either double-stranded deoxyribonucleic acids (dsDNAs) or single-stranded ribonucleic acids (RNAs). The dyes possess low fluorescence intensity in an unbound state, which is increased up to 479 times in the presence of the nucleic acids. In the presence of RNAs, the fluorescence intensity increase was stronger than that observed in the presence of dsDNA. Next, we have performed staining of live and fixed cells by all prepared dyes. The dyes proved to be cell and nuclear membrane permeant. They are photostable and brightly stain RNA-containing organelles in both live and fixed cells. The colocalization confirmed the specific nucleoli staining with anti-Ki-67 antibodies. The RNA digestion experiment has confirmed the selectivity of the dyes toward intracellular RNA. Based on the obtained results, we can conclude that the investigated monomethine cyanine dyes are useful fluorescent probes for the visualization of intracellular RNA and RNA-containing organelles such as nucleoli by using fluorescence microscopy.
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Affiliation(s)
- Daria Aristova
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Viktoriia Kosach
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Svitlana Chernii
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Yuriy Slominsky
- Institute of Organic Chemistry NASU, 5 Murmans'ka St., 02094 Kyiv, Ukraine
| | - Anatoliy Balanda
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Valeriy Filonenko
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Sergiy Yarmoluk
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Alexandru Rotaru
- 'Petru Poni' Institute of Macromolecular Chemistry, Romanian Academy, Grigore Ghica Voda Alley 41A, 700487 Iasi, Romania
| | - Hülya Gizem Özkan
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Andriy Mokhir
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Vladyslava Kovalska
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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68
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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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69
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Lin LE, Miao K, Qian C, Wei L. High spatial-resolution imaging of label-free in vivo protein aggregates by VISTA. Analyst 2021; 146:4135-4145. [PMID: 33949430 PMCID: PMC8238904 DOI: 10.1039/d1an00060h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Amyloid aggregation, formed by aberrant proteins, is a pathological hallmark for neurodegenerative diseases, including Alzheimer's disease and Huntington's disease. High-resolution holistic mapping of the fine structures from these aggregates should facilitate our understanding of their pathological roles. Here, we achieved label-free high-resolution imaging of the polyQ and the amyloid-beta (Aβ) aggregates in cells and tissues utilizing a sample-expansion stimulated Raman strategy. We further focused on characterizing the Aβ plaques in 5XFAD mouse brain tissues. 3D volumetric imaging enabled visualization of the whole plaques, resolving both the fine protein filaments and the surrounding components. Coupling our expanded label-free Raman imaging with machine learning, we obtained specific segmentation of aggregate cores, peripheral filaments together with cell nuclei and blood vessels by pre-trained convolutional neural network models. Combining with 2-channel fluorescence imaging, we achieved a 6-color holistic view of the same sample. This ability for precise and multiplex high-resolution imaging of the protein aggregates and their micro-environment without the requirement of labeling would open new biomedical applications.
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Affiliation(s)
- Li-En Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
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70
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Lisovskaya A, Carmichael I, Harriman A. Pulse Radiolysis Investigation of Radicals Derived from Water-Soluble Cyanine Dyes: Implications for Super-resolution Microscopy. J Phys Chem A 2021; 125:5779-5793. [PMID: 34165985 DOI: 10.1021/acs.jpca.1c03776] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Light-induced blinking, an inherent feature of many forms of super-resolution microscopy, has been linked to transient reduction of the fluorescent cyanine dye used as an imaging agent. There is, however, only scant literature information related to one-electron reduced cyanine dyes, especially in an aqueous environment. Here, we examine a small series of cyanine dyes, possessing disparate π-conjugation lengths, under selective reducing or oxidizing conditions. The experiment allows recording of both differential absorption spectra and decay kinetics of the resultant one-electron reduced or oxidized transient species in water. Relative to the ground state, absorption transitions for the various radicals are weak and somewhat broadened but do allow correlation with the π-conjugation length. In all cases, absorption maxima lie to the blue of the main ground-state transition. Under anaerobic conditions, the transient species decay on the microsecond to millisecond time scale, with the mean lifetime depending on molecular structure, radiation dose, and dye concentration. The experimental absorption spectra recorded for the one-electron reduced radicals and the presumed dimer cation radical compare well to spectra obtained from time-dependent density functional theory calculations. The results allow conclusions to be drawn regarding the plausibility of the reduced species being responsible for light-induced blinking in direct stochastic optical reconstruction microscopy.
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Affiliation(s)
- Alexandra Lisovskaya
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Anthony Harriman
- Molecular Photonics Laboratory, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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71
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Matryba P, Łukasiewicz K, Pawłowska M, Tomczuk J, Gołąb J. Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging? Int J Mol Sci 2021; 22:ijms22136730. [PMID: 34201632 PMCID: PMC8268743 DOI: 10.3390/ijms22136730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.
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Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
- The Doctoral School of the Medical University of Warsaw, Medical University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Correspondence:
| | - Kacper Łukasiewicz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Monika Pawłowska
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Tomczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
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72
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Bishop LDC, Misiura A, Landes CF. A new metric for relating macroscopic chromatograms to microscopic surface dynamics: the distribution function ratio (DFR). Analyst 2021; 146:4268-4279. [PMID: 34105529 DOI: 10.1039/d1an00370d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heterogeneous stationary phase chemistry causes chromatographic tailing that lowers separation efficiency and complicates optimizing mobile phase conditions. Model-free metrics are attractive for assessing optimal separation conditions due to the low quantity of information required, but often do not reveal underlying mechanisms that cause tailing, for example, heterogeneous retention modes. We report a new metric, which we call the Distribution Function Ratio (DFR), based on a graphical comparison between the chromatogram and Gaussian cumulative distribution functions, achieving correspondence to ground truth surface dynamics with a single chromatogram. Using a Monte Carlo framework, we show that the DFR can predict the prevalence of heterogeneous retention modes with high precision when the relative desorption rate between modes is known, as in during surface dynamics experiments. Ground truth comparisons reveal that the DFR outperforms both the asymmetry factor and skewness by yielding a one-to-one correspondence with heterogeneous retention mode prevalence over a broad range of experimentally realistic values. Perhaps of more value, we illustrate that the DFR, when combined with the asymmetry factor and skewness, can estimate microscopic surface dynamics, providing valuable insights into surface chemistry using existing chromatographic instrumentation. Connecting ensemble results to microscopic quantities through the lens of simulation establishes a new chemistry-driven route to measuring and advancing separations.
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Affiliation(s)
- Logan D C Bishop
- Department of Chemistry, Rice University, Houston, Texas 77251, USA.
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73
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Calovi S, Soria FN, Tønnesen J. Super-resolution STED microscopy in live brain tissue. Neurobiol Dis 2021; 156:105420. [PMID: 34102277 DOI: 10.1016/j.nbd.2021.105420] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
STED microscopy is one of several fluorescence microscopy techniques that permit imaging at higher spatial resolution than what the diffraction-limit of light dictates. STED imaging is unique among these super-resolution modalities in being a beam-scanning microscopy technique based on confocal or 2-photon imaging, which provides the advantage of superior optical sectioning in thick samples. Compared to the other super-resolution techniques that are based on widefield microscopy, this makes STED particularly suited for imaging inside live brain tissue, such as in slices or in vivo. Notably, the 50 nm resolution provided by STED microscopy enables analysis of neural morphologies that conventional confocal and 2-photon microscopy approaches cannot resolve, including all-important synaptic structures. Over the course of the last 20 years, STED microscopy has undergone extensive developments towards ever more versatile use, and has facilitated remarkable neurophysiological discoveries. The technique is still not widely adopted for live tissue imaging, even though one of its particular strengths is exactly in resolving the nanoscale dynamics of synaptic structures in brain tissue, as well as in addressing the complex morphologies of glial cells, and revealing the intricate structure of the brain extracellular space. Not least, live tissue STED microscopy has so far hardly been applied in settings of pathophysiology, though also here it shows great promise for providing new insights. This review outlines the technical advantages of STED microscopy for imaging in live brain tissue, and highlights key neurobiological findings brought about by the technique.
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Affiliation(s)
- Stefano Calovi
- Laboratory of Molecular Pharmacology, Institute of Experimental Medicine, Budapest, Hungary; János Szentágothai Doctoral School, Semmelweis University, Budapest, Hungary; Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Federico N Soria
- Achucarro Basque Center for Neuroscience, Leioa, Spain; Department of Neuroscience, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jan Tønnesen
- Achucarro Basque Center for Neuroscience, Leioa, Spain; Department of Neuroscience, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain.
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74
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Cheng X, Yin W. Probing Biosensing Interfaces With Single Molecule Localization Microscopy (SMLM). Front Chem 2021; 9:655324. [PMID: 33996750 PMCID: PMC8117217 DOI: 10.3389/fchem.2021.655324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/16/2021] [Indexed: 11/23/2022] Open
Abstract
Far field single molecule localization microscopy (SMLM) has been established as a powerful tool to study biological structures with resolution far below the diffraction limit of conventional light microscopy. In recent years, the applications of SMLM have reached beyond traditional cellular imaging. Nanostructured interfaces are enriched with information that determines their function, playing key roles in applications such as chemical catalysis and biological sensing. SMLM enables detailed study of interfaces at an individual molecular level, allowing measurements of reaction kinetics, and detection of rare events not accessible to ensemble measurements. This paper provides an update to the progress made to the use of SMLM in characterizing nanostructured biointerfaces, focusing on practical aspects, recent advances, and emerging opportunities from an analytical chemistry perspective.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory for Modern Optical Instrumentations, National Engineering Research Center of Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Wei Yin
- Core Facilities, School of Medicine, Zhejiang University, Hangzhou, China
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75
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Danielsen SPO, Beech HK, Wang S, El-Zaatari BM, Wang X, Sapir L, Ouchi T, Wang Z, Johnson PN, Hu Y, Lundberg DJ, Stoychev G, Craig SL, Johnson JA, Kalow JA, Olsen BD, Rubinstein M. Molecular Characterization of Polymer Networks. Chem Rev 2021; 121:5042-5092. [PMID: 33792299 DOI: 10.1021/acs.chemrev.0c01304] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polymer networks are complex systems consisting of molecular components. Whereas the properties of the individual components are typically well understood by most chemists, translating that chemical insight into polymer networks themselves is limited by the statistical and poorly defined nature of network structures. As a result, it is challenging, if not currently impossible, to extrapolate from the molecular behavior of components to the full range of performance and properties of the entire polymer network. Polymer networks therefore present an unrealized, important, and interdisciplinary opportunity to exert molecular-level, chemical control on material macroscopic properties. A barrier to sophisticated molecular approaches to polymer networks is that the techniques for characterizing the molecular structure of networks are often unfamiliar to many scientists. Here, we present a critical overview of the current characterization techniques available to understand the relation between the molecular properties and the resulting performance and behavior of polymer networks, in the absence of added fillers. We highlight the methods available to characterize the chemistry and molecular-level properties of individual polymer strands and junctions, the gelation process by which strands form networks, the structure of the resulting network, and the dynamics and mechanics of the final material. The purpose is not to serve as a detailed manual for conducting these measurements but rather to unify the underlying principles, point out remaining challenges, and provide a concise overview by which chemists can plan characterization strategies that suit their research objectives. Because polymer networks cannot often be sufficiently characterized with a single method, strategic combinations of multiple techniques are typically required for their molecular characterization.
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Affiliation(s)
- Scott P O Danielsen
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Haley K Beech
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shu Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Bassil M El-Zaatari
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Xiaodi Wang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | | | | | - Zi Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Patricia N Johnson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yixin Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David J Lundberg
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Georgi Stoychev
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Stephen L Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julia A Kalow
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael Rubinstein
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Departments of Biomedical Engineering and Physics, Duke University, Durham, North Carolina 27708, United States.,World Primer Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
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76
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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77
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Toropov N, Vollmer F. Whispering-gallery microlasers for cell tagging and barcoding: the prospects for in vivo biosensing. LIGHT, SCIENCE & APPLICATIONS 2021; 10:77. [PMID: 33854030 PMCID: PMC8046988 DOI: 10.1038/s41377-021-00517-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Researchers in the field of whispering-gallery-mode (WGM) microresonators have proposed biointegrated low-threshold WGM lasers, to enable large-scale parallel single-cell tracking and barcoding. Although the reported devices have so far been primarily investigated in model applications, most recent results represent important steps towards the development of in vivo tags and sensors that utilize the unique and narrow spectral features of miniature WGM lasers.
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Affiliation(s)
- Nikita Toropov
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.
| | - Frank Vollmer
- Department of Physics and Astronomy, Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.
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78
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Lee D, Qian C, Wang H, Li L, Miao K, Du J, Shcherbakova DM, Verkhusha VV, Wang LV, Wei L. Toward photoswitchable electronic pre-resonance stimulated Raman probes. J Chem Phys 2021; 154:135102. [PMID: 33832245 PMCID: PMC8019356 DOI: 10.1063/5.0043791] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Reversibly photoswitchable probes allow for a wide variety of optical imaging applications. In particular, photoswitchable fluorescent probes have significantly facilitated the development of super-resolution microscopy. Recently, stimulated Raman scattering (SRS) imaging, a sensitive and chemical-specific optical microscopy, has proven to be a powerful live-cell imaging strategy. Driven by the advances of newly developed Raman probes, in particular the pre-resonance enhanced narrow-band vibrational probes, electronic pre-resonance SRS (epr-SRS) has achieved super-multiplex imaging with sensitivity down to 250 nM and multiplexity up to 24 colors. However, despite the high demand, photoswitchable Raman probes have yet to be developed. Here, we propose a general strategy for devising photoswitchable epr-SRS probes. Toward this goal, we exploit the molecular electronic and vibrational coupling, in which we switch the electronic states of the molecules to four different states to turn their ground-state epr-SRS signals on and off. First, we showed that inducing transitions to both the electronic excited state and triplet state can effectively diminish the SRS peaks. Second, we revealed that the epr-SRS signals can be effectively switched off in red-absorbing organic molecules through light-facilitated transitions to a reduced state. Third, we identified that photoswitchable proteins with near-infrared photoswitchable absorbance, whose states are modulable with their electronic resonances detunable toward and away from the pump photon energy, can function as the photoswitchable epr-SRS probes with desirable sensitivity (<1 µM) and low photofatigue (>40 cycles). These photophysical characterizations and proof-of-concept demonstrations should advance the development of novel photoswitchable Raman probes and open up the unexplored Raman imaging capabilities.
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Affiliation(s)
- Dongkwan Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Chenxi Qian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Lei Li
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, USA
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Daria M. Shcherbakova
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | - Lihong V. Wang
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, USA
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA,Author to whom correspondence should be addressed:
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79
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80
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A localized adaptor protein performs distinct functions at the Caulobacter cell poles. Proc Natl Acad Sci U S A 2021; 118:2024705118. [PMID: 33753507 PMCID: PMC8020655 DOI: 10.1073/pnas.2024705118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Asymmetric cell division yields two distinct daughter cells by mechanisms that underlie stem cell behavior and cellular diversity in all organisms. The bacterium Caulobacter crescentus is able to orchestrate this complex process with less than 4,000 genes. This article describes a strategy deployed by Caulobacter where a regulatory protein, PopA, is programed to perform distinct roles based on its subcellular address. We demonstrate that, depending on the availability of a second messenger molecule, PopA adopts either a monomer or dimer form. The two oligomeric forms interact with different partners at the two cell poles, playing a critical role in the degradation of a master transcription factor at one pole and flagellar assembly at the other pole. Asymmetric cell division generates two daughter cells with distinct characteristics and fates. Positioning different regulatory and signaling proteins at the opposing ends of the predivisional cell produces molecularly distinct daughter cells. Here, we report a strategy deployed by the asymmetrically dividing bacterium Caulobacter crescentus where a regulatory protein is programmed to perform distinct functions at the opposing cell poles. We find that the CtrA proteolysis adaptor protein PopA assumes distinct oligomeric states at the two cell poles through asymmetrically distributed c-di-GMP: dimeric at the stalked pole and monomeric at the swarmer pole. Different polar organizing proteins at each cell pole recruit PopA where it interacts with and mediates the function of two molecular machines: the ClpXP degradation machinery at the stalked pole and the flagellar basal body at the swarmer pole. We discovered a binding partner of PopA at the swarmer cell pole that together with PopA regulates the length of the flagella filament. Our work demonstrates how a second messenger provides spatiotemporal cues to change the physical behavior of an effector protein, thereby facilitating asymmetry.
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Kandy SK, Janmey PA, Radhakrishnan R. Membrane signalosome: where biophysics meets systems biology. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 25:34-41. [PMID: 33997528 PMCID: PMC8117111 DOI: 10.1016/j.coisb.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We opine on the recent advances in experiments and modeling of modular signaling complexes assembled on mammalian cell membranes (membrane signalosomes) in the context of several applications including intracellular trafficking, cell migration, and immune response. Characterizing the individual components of the membrane assemblies at the nanoscale, ranging from protein-lipid and protein-protein interactions, to membrane morphology, and the energetics of emergent assemblies at the subcellular to cellular scales pose significant challenges. Overcoming these challenges through the iterative coupling of multiscale modeling and experiment can be transformative in terms of addressing the gaps between structural biology and super-resolution microscopy, as it holds the key to the discovery of fundamental mechanisms behind the emergence of function in the membrane signalosome.
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Affiliation(s)
- Sreeja K Kandy
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
| | - Paul A Janmey
- Department of Physiology, University of Pennsylvania, Philadelphia, PA
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
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Zhou W, Fang X, Qiao Q, Jiang W, Zhang Y, Xu Z. Quantitative assessment of rhodamine spectra. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Choi NE, Lee JY, Park EC, Lee JH, Lee J. Recent Advances in Organelle-Targeted Fluorescent Probes. Molecules 2021; 26:E217. [PMID: 33406634 PMCID: PMC7795030 DOI: 10.3390/molecules26010217] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/27/2022] Open
Abstract
Recent advances in fluorescence imaging techniques and super-resolution microscopy have extended the applications of fluorescent probes in studying various cellular processes at the molecular level. Specifically, organelle-targeted probes have been commonly used to detect cellular metabolites and transient chemical messengers with high precision and have become invaluable tools to study biochemical pathways. Moreover, several recent studies reported various labeling strategies and novel chemical scaffolds to enhance target specificity and responsiveness. In this review, we will survey the most recent reports of organelle-targeted fluorescent probes and assess their general strategies and structural features on the basis of their target organelles. We will discuss the advantages of the currently used probes and the potential challenges in their application as well as future directions.
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Affiliation(s)
| | | | | | | | - Jiyoun Lee
- Department of Next-Generation Applied Science, and Global Medical Science, Sungshin University, Seoul 01133, Korea; (N.-E.C.); (J.-Y.L.); (E.-C.P.); (J.-H.L.)
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Abstract
Optical studies of single molecules have taught us much over the past three decades, but these individual quantum-mechanical objects continue to have promise as probes of nanoscale structure and dynamics in complex systems.
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Affiliation(s)
- W E Moerner
- Departments of Chemistry and of Applied Physics (courtesy), Stanford University, Stanford, California 94305-4401, United States
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