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Foote A, Ishii K, Cullinane B, Tahara T, Goldsmith RH. Quantifying Microsecond Solution-Phase Conformational Dynamics of a DNA Hairpin at the Single-Molecule Level. ACS PHYSICAL CHEMISTRY AU 2024; 4:408-419. [PMID: 39069982 PMCID: PMC11274281 DOI: 10.1021/acsphyschemau.3c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 07/30/2024]
Abstract
Quantifying the rapid conformational dynamics of biological systems is fundamental to understanding the mechanism. However, biomolecules are complex, often containing static and dynamic heterogeneity, thus motivating the use of single-molecule methods, particularly those that can operate in solution. In this study, we measure microsecond conformational dynamics of solution-phase DNA hairpins at the single-molecule level using an anti-Brownian electrokinetic (ABEL) trap. Different conformational states were distinguished by their fluorescence lifetimes, and kinetic parameters describing transitions between these states were determined using two-dimensional fluorescence lifetime correlation (2DFLCS) analysis. Rather than combining fluorescence signals from the entire data set ensemble, long observation times of individual molecules allowed ABEL-2DFLCS to be performed on each molecule independently, yielding the underlying distribution of the system's kinetic parameters. ABEL-2DFLCS on the DNA hairpins resolved an underlying heterogeneity of fluorescence lifetimes and provided signatures of two-state exponential dynamics with rapid (
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Affiliation(s)
- Alexander
K. Foote
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Kunihiko Ishii
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Brendan Cullinane
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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2
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Michalski J, Kalwarczyk T, Kwapiszewska K, Enderlein J, Poniewierski A, Karpińska A, Kucharska K, Hołyst R. Rotational and translational diffusion of biomolecules in complex liquids and HeLa cells. SOFT MATTER 2024; 20:5810-5821. [PMID: 38995242 DOI: 10.1039/d4sm00422a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Diffusive motion accompanies many physical and biological processes. The Stokes-Sutherland-Einstein relation for the translational diffusion coefficient, DT, agrees with experiments done in simple fluids but fails for complex fluids. Moreover, the interdependence between DT and rotational diffusion coefficient, DR, also deviates in complex fluids from the classical relation of DT/DR = 4r2/3 known in simple fluids. Makuch et al. Soft Matter, 2020, 16, 114-124 presented a generalization of the classical translational and rotational diffusion theory for complex fluids. In this work, we empirically verify this model based on simultaneous translational and rotational diffusion measurements. We use fluorescently stained cowpea chlorotic mottle virus (CCMV) particles as monodisperse probes and aqueous polyethylene glycol (PEG) solutions as a model complex fluid. The theory and experimental data obtained from fluorescence correlation spectroscopy (FCS) measurements agreed. Finally, we used the same model and analyzed the diffusion of Yo-Pro-1 stained large ribosomal subunits (LSU) in the cytoplasm and nucleus of living HeLa cells.
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Affiliation(s)
- Jarosław Michalski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Karina Kwapiszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Andrzej Poniewierski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Aneta Karpińska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Karolina Kucharska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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3
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Murdoch TJ, Quienne B, Pinaud J, Caillol S, Martín-Fabiani I. Understanding associative polymer self-assembly with shrinking gate fluorescence correlation spectroscopy. NANOSCALE 2024; 16:12660-12669. [PMID: 38888295 DOI: 10.1039/d4nr00737a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The self-assembly of polymers is integral to their role in liquid formulations. In this study, we combine a dye whose lifetime is sensitive to the nanoviscosity of its local environment with shrinking gate fluorescence correlation spectroscopy (sgFCS) to study the self-assembly of a model telechelic polymer, hydrophobically modified ethoxylated urethane (HEUR). Fluorescence lifetime measurements show a monotonic increase in average lifetime with increasing HEUR concentration driven by a small fraction of dye (<1%) with long lifetimes strongly bound to HEUR. Despite this small fraction, sgFCS isolates the diffusional dynamics of the bound fraction with no a priori assumptions as to the distribution of lifetimes. Sensitivity is greatly enhanced compared to standard FCS, revealing micellar aggregates forming between 0.2 and 1 wt% followed by formation of a percolated network. This sgFCS approach, which we apply for the first time to polymers in this work, is readily extendable to any dye that changes lifetime on binding.
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Affiliation(s)
- Timothy J Murdoch
- Department of Materials, Loughborough University, LE11 1RJ Loughborough, UK.
| | | | - Julien Pinaud
- ICGM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
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4
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Obloy LM, Jockusch S, Tarnovsky AN. Shortwave infrared polymethine dyes for bioimaging: ultrafast relaxation dynamics and excited-state decay pathways. Phys Chem Chem Phys 2024. [PMID: 38895857 DOI: 10.1039/d4cp01411a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Excited-state relaxation in two prototypical shortwave infrared (SWIR) polymethine dyes developed for bioimaging, heptamethine chromenylium Chrom7 and flavylium Flav7, is studied by means of femtosecond transient absorption with broadband ultraviolet-to-SWIR probing complemented by steady-state and time-resolved fluorescence and phosphorescence measurements. The relaxation processes of the dyes in dichloromethane are resolved with sub-100 fs temporal resolution using SWIR, near-IR, and visible photoexcitation. Different population members of the ground-state inhomogeneous ensemble are found to equilibrate via skeletal deformation changes with time constants of 90 fs and either 230 fs (Chrom7) and 350 fs (Flav7) followed by slower evolution matching the 1-ps timescale of diffusive solvation dynamics. Molecules excited into high-lying singlet electronic states (Sn) by visible excitation repopulate with time constants of 400 fs (Chrom7) and 450 fs (Flav7) the corresponding first excited singlet S1 states, which decay within several hundreds of picoseconds in dichloromethane and chloroform solvents. Vibrational relaxation in S1 for both Chrom7 and Flav7 in dichloromethane occurs with time constants of 350 and 800 fs for excess of vibrational energy of ∼1000 and 10 000 cm-1 deposited by near-IR and visible excitation, respectively. Two competing non-radiative processes are present in S1: temperature-independent internal conversion, and thermally-activated twisting about a carbon-carbon bond of the conjugated chain, which is substantial at room temperature but essentially nonreactive, producing traces of isomer product. Intersystem crossing in S1, and thus the triplet quantum yield, is minor. The importance of absorption bands from the excited S1 state in applications requiring high-intensity excitation conditions is discussed.
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Affiliation(s)
- Laura M Obloy
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - Steffen Jockusch
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - Alexander N Tarnovsky
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
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5
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Deguchi T, Ries J. Simple and robust 3D MINFLUX excitation with a variable phase plate. LIGHT, SCIENCE & APPLICATIONS 2024; 13:134. [PMID: 38849346 PMCID: PMC11161593 DOI: 10.1038/s41377-024-01487-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024]
Abstract
MINFLUX has achieved extraordinary resolution in superresolution imaging and single fluorophore tracking. It is based on localizing single fluorophores by rapid probing with a patterned beam that features a local intensity minimum. Current implementations, however, are complex and expensive and are limited in speed and robustness. Here, we show that a combination of an electro-optical modulator with a segmented birefringent element such as a spatial light modulator produces a variable phase plate for which the phase can be scanned on the MHz timescale. Bisected or top-hat phase patterns generate high-contrast compact excitation point-spread functions for MINFLUX localization in the x, y, and z-direction, respectively, which can be scanned across a fluorophore within a microsecond, switched within 60 microseconds and alternated among different excitation wavelengths. We discuss how to compensate for non-optimal performance of the components and present a robust 3D and multi-color MINFLUX excitation module, which we envision as an integral component of a high-performance and cost-effective open-source MINFLUX.
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Affiliation(s)
- Takahiro Deguchi
- European Molecular Biology Laboratory, Cell Biology and Biophysics, Heidelberg, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics, Heidelberg, Germany.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Vienna, Austria.
- University of Vienna, Faculty of Physics, Vienna, Austria.
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6
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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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7
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Lu H, Wang Y, Hill SK, Jiang H, Ke Y, Huang S, Zheng D, Perrier S, Song Q. Supra-Cyanines: Ultrabright Cyanine-Based Fluorescent Supramolecular Materials in Solution and in the Solid State. Angew Chem Int Ed Engl 2023; 62:e202311224. [PMID: 37840434 DOI: 10.1002/anie.202311224] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023]
Abstract
Fluorescent materials with high brightness play a crucial role in the advancement of various technologies such as bioimaging, photonics, and OLEDs. While significant efforts are dedicated to designing new organic dyes with improved performance, enhancing the brightness of existing dyes holds equal importance. In this study, we present a simple supramolecular strategy to develop ultrabright cyanine-based fluorescent materials by addressing long-standing challenges associated with cyanine dyes, including undesired cis-trans photoisomerization and aggregation-caused quenching. Supra-cyanines are obtained by incorporating cyanine moieties in a cyclic peptide-based supramolecular scaffold, and exhibit high fluorescence quantum yields (up to 50 %) in both solution and in the solid state. These findings offer a versatile approach for constructing highly emissive cyanine-based supramolecular materials.
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Affiliation(s)
- Haicheng Lu
- Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuqian Wang
- Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Sophie K Hill
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Hanqiu Jiang
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, China
- Spallation Neutron Source Science Center, Dongguan, 523803, China
| | - Yubin Ke
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, China
- Spallation Neutron Source Science Center, Dongguan, 523803, China
| | - Shaohui Huang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101499, China
| | - Dunjin Zheng
- LightEdge Technologies Limited, Zhongshan, 528451, China
| | - Sébastien Perrier
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Qiao Song
- Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, 518055, China
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8
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Ploetz E, Ambrose B, Barth A, Börner R, Erichson F, Kapanidis AN, Kim HD, Levitus M, Lohman TM, Mazumder A, Rueda DS, Steffen FD, Cordes T, Magennis SW, Lerner E. A new twist on PIFE: photoisomerisation-related fluorescence enhancement. Methods Appl Fluoresc 2023; 12:012001. [PMID: 37726007 PMCID: PMC10570931 DOI: 10.1088/2050-6120/acfb58] [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: 02/27/2023] [Revised: 07/24/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023]
Abstract
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate ofcis/transphotoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule. In this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turning PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Benjamin Ambrose
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, United Kingdom
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Richard Börner
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Felix Erichson
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, United Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, United States of America
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, AZ,85287, United States of America
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States of America
| | - Abhishek Mazumder
- CSIR-Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, United Kingdom
| | - Fabio D Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Großhadernerstr. 2-4, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Eitan Lerner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
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9
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Demirbay B, Baryshnikov G, Haraldsson M, Piguet J, Ågren H, Widengren J. Photo-physical characterization of high triplet yield brominated fluoresceins by transient state (TRAST) spectroscopy. Methods Appl Fluoresc 2023; 11:045011. [PMID: 37726005 DOI: 10.1088/2050-6120/acfb59] [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] [Received: 05/12/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023]
Abstract
Photo-induced dark transient states of fluorophores can pose a problem in fluorescence spectroscopy. However, their typically long lifetimes also make them highly environment sensitive, suggesting fluorophores with prominent dark-state formation yields to be used as microenvironmental sensors in bio-molecular spectroscopy and imaging. In this work, we analyzed the singlet-triplet transitions of fluorescein and three synthesized carboxy-fluorescein derivatives, with one, two or four bromines linked to the anthracence backbone. Using transient state (TRAST) spectroscopy, we found a prominent internal heavy atom (IHA) enhancement of the intersystem crossing (ISC) rates upon bromination, inferred by density functional theory calculations to take place via a higher triplet state, followed by relaxation to the lowest triplet state. A corresponding external heavy atom (EHA) enhancement was found upon adding potassium iodide (KI). Notably, increased KI concentrations still resulted in lowered triplet state buildup in the brominated fluorophores, due to relatively lower enhancements in ISC, than in the triplet decay. Together with an antioxidative effect on the fluorophores, adding KI thus generated a fluorescence enhancement of the brominated fluorophores. By TRAST measurements, analyzing the average fluorescence intensity of fluorescent molecules subject to a systematically varied excitation modulation, dark state transitions within very high triplet yield (>90%) fluorophores can be directly analyzed under biologically relevant conditions. These measurements, not possible by other techniques such as fluorescence correlation spectroscopy, opens for bio-sensing applications based on high triplet yield fluorophores, and for characterization of high triplet yield photodynamic therapy agents, and how they are influenced by IHA and EHA effects.
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Affiliation(s)
- Baris Demirbay
- Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Department of Applied Physics, Albanova University Center, SE-106 91, Stockholm, Sweden
| | - Glib Baryshnikov
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174, Norrköping, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Joachim Piguet
- Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Department of Applied Physics, Albanova University Center, SE-106 91, Stockholm, Sweden
| | - Hans Ågren
- Department of Physics and Astronomy, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Jerker Widengren
- Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Department of Applied Physics, Albanova University Center, SE-106 91, Stockholm, Sweden
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10
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Sandberg E, Piguet J, Kostiv U, Baryshnikov G, Liu H, Widengren J. Photoisomerization of Heptamethine Cyanine Dyes Results in Red-Emissive Species: Implications for Near-IR, Single-Molecule, and Super-Resolution Fluorescence Spectroscopy and Imaging. J Phys Chem B 2023; 127:3208-3222. [PMID: 37011608 PMCID: PMC10108366 DOI: 10.1021/acs.jpcb.2c08016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Photoisomerization kinetics of the near-infrared (NIR) fluorophore Sulfo-Cyanine7 (SCy7) was studied by a combination of fluorescence correlation spectroscopy (FCS) and transient state (TRAST) excitation modulation spectroscopy. A photoisomerized state with redshifted emission was identified, with kinetics consistent with a three-state photoisomerization model. Combining TRAST excitation modulation with spectrofluorimetry (spectral-TRAST) further confirmed an excitation-induced redshift in the emission spectrum of SCy7. We show how this red-emissive photoisomerized state contributes to the blinking kinetics in different emission bands of NIR cyanine dyes, and how it can influence single-molecule, super-resolution, as well as Förster resonance energy transfer (FRET) and multicolor readouts. Since this state can also be populated at moderate excitation intensities, it can also more broadly influence fluorescence readouts, also readouts not relying on high excitation conditions. However, this additional red-emissive state and its photodynamics, as identified and characterized in this work, can also be used as a strategy to push the emission of NIR cyanine dyes further into the NIR and to enhance photosensitization of nanoparticles with absorption spectra further into the NIR. Finally, we show that the photoisomerization kinetics of SCy7 and the formation of its redshifted photoisomer depend strongly on local environmental conditions, such as viscosity, polarity, and steric constraints, which suggests the use of SCy7 and other NIR cyanine dyes as environmental sensors. Such environmental information can be monitored by TRAST, in the NIR, with low autofluorescence and scattering conditions and on a broad range of samples and experimental conditions.
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Affiliation(s)
- Elin Sandberg
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
| | - Joachim Piguet
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
| | - Uliana Kostiv
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
| | - Glib Baryshnikov
- Dept. Science and Technology, Linköping University, Campus Norrköping, 601 74 Norrköping, Sweden
| | - Haichun Liu
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
| | - Jerker Widengren
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
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11
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Kitamura A, Tornmalm J, Demirbay B, Piguet J, Kinjo M, Widengren J. Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells. Nucleic Acids Res 2023; 51:e27. [PMID: 36651281 PMCID: PMC10018373 DOI: 10.1093/nar/gkac1255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 11/23/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to in vitro conditions. Evidence of how GGGGCC repeats form into G-quadruplexes in vivo is sparse. We devised a readout strategy, exploiting the sensitivity of trans-cis isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent trans isomer and a non-fluorescent cis isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.
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Affiliation(s)
| | | | - Baris Demirbay
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Joachim Piguet
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
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12
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Barclay MS, Chowdhury AU, Biaggne A, Huff JS, Wright ND, Davis PH, Li L, Knowlton WB, Yurke B, Pensack RD, Turner DB. Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye. J Chem Phys 2023; 158:035101. [PMID: 36681650 DOI: 10.1063/5.0131795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5). A line shape analysis of the 2D spectra reveals a strong excitation-emission correlation present in only the dsDNA-Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA-Cy5 complex. These insights will support future studies on DNA's structural heterogeneity.
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Affiliation(s)
- Matthew S Barclay
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Azhad U Chowdhury
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Austin Biaggne
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Jonathan S Huff
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Nicholas D Wright
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul H Davis
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Lan Li
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Bernard Yurke
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Ryan D Pensack
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
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13
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Sandberg E, Piguet J, Liu H, Widengren J. Combined Fluorescence Fluctuation and Spectrofluorometric Measurements Reveal a Red-Shifted, Near-IR Emissive Photo-Isomerized Form of Cyanine 5. Int J Mol Sci 2023; 24:ijms24031990. [PMID: 36768309 PMCID: PMC9916991 DOI: 10.3390/ijms24031990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
Cyanine fluorophores are extensively used in fluorescence spectroscopy and imaging. Upon continuous excitation, especially at excitation conditions used in single-molecule and super-resolution experiments, photo-isomerized states of cyanines easily reach population probabilities of around 50%. Still, effects of photo-isomerization are largely ignored in such experiments. Here, we studied the photo-isomerization of the pentamethine cyanine 5 (Cy5) by two similar, yet complementary means to follow fluorophore blinking dynamics: fluorescence correlation spectroscopy (FCS) and transient-state (TRAST) excitation-modulation spectroscopy. Additionally, we combined TRAST and spectrofluorimetry (spectral-TRAST), whereby the emission spectra of Cy5 were recorded upon different rectangular pulse-train excitations. We also developed a framework for analyzing transitions between multiple emissive states in FCS and TRAST experiments, how the brightness of the different states is weighted, and what initial conditions that apply. Our FCS, TRAST, and spectral-TRAST experiments showed significant differences in dark-state relaxation amplitudes for different spectral detection ranges, which we attribute to an additional red-shifted, emissive photo-isomerized state of Cy5, not previously considered in FCS and single-molecule experiments. The photo-isomerization kinetics of this state indicate that it is formed under moderate excitation conditions, and its population and emission may thus deserve also more general consideration in fluorescence imaging and spectroscopy experiments.
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14
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Kikuchi K, Adair LD, Lin J, New EJ, Kaur A. Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202204745. [PMID: 36177530 PMCID: PMC10100239 DOI: 10.1002/anie.202204745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.
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Affiliation(s)
- Kai Kikuchi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liam D Adair
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jiarun Lin
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J New
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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15
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Werner A. RNA double strand hybridization measured at the single molecule level. Anal Biochem 2023; 660:114959. [PMID: 36341770 DOI: 10.1016/j.ab.2022.114959] [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: 09/19/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022]
Abstract
RNA double strand hybridization is a hallmark for gene expression regulation. In this function, single stranded regulatory RNA forms Watson-Crick base pairs with complementary messenger RNA. In the presented work the dissociation constants of complementary equally sized RNA single strands were measured at the single molecule level applying fluorescence correlation spectroscopy (FCS). Dissociation constants of 3.2 nM, 1.4 nM and 1.0 nM were determined for 26 bp, 41 bp and 54 bp dsRNA, respectively. The translational diffusion coefficients of RNA, measured at infinite dilution, could be accurately predicted applying the model D = 4.58 × 10-10 N-0.39 m2s-1.
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Affiliation(s)
- Arne Werner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, Faculty of Mathematics, Computer Science and Natural Science; Hamburg University, Germany.
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16
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Sefer A, Kallis E, Eilert T, Röcker C, Kolesnikova O, Neuhaus D, Eustermann S, Michaelis J. Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level. Nat Commun 2022; 13:6569. [PMID: 36323657 PMCID: PMC9630430 DOI: 10.1038/s41467-022-34148-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1's multi-domain organization. Here, we directly probe this process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1's N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state.
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Affiliation(s)
- Anna Sefer
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Eleni Kallis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Tobias Eilert
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Boehringer Ingelheim, CoC CMC Statistics & Data Science, Birkendorfer Str. 65, 88400, Biberach, Germany
| | - Carlheinz Röcker
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Olga Kolesnikova
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Sebastian Eustermann
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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17
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Sequence-dependence of Cy3 and Cy5 dyes in 3' terminally-labeled single-stranded DNA. Sci Rep 2022; 12:14803. [PMID: 36045146 PMCID: PMC9428881 DOI: 10.1038/s41598-022-19069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Fluorescence is an ideal tool to see and manipulate nucleic acids, and engage in their rich and complex biophysical properties. Labeling is the preferred approach to track and quantify fluorescence with nucleic acids and cyanine dyes are emblematic in this context. The fluorescent properties of cyanine dyes are known to be sequence-dependent, with purines in the immediate vicinity increasing the fluorescence intensity of Cy3 and Cy5 dyes, and the ability of nucleobases to modulate the photophysical properties of common fluorophores may influence fluorescence measurements in critical assays such as FISH, qPCR or high-throughput sequencing. In this paper, we comprehensively map the sequence-dependence of Cy3 and Cy5 dyes in 3ʹ-fluorescently labeled single-stranded DNA by preparing the complete permutation library of the 5 consecutive nucleotides immediately adjacent to the dye, or 1024 sequences. G-rich motifs dominate the high fluorescence range, while C-rich motifs lead to significant quenching, an observation consistent with 5ʹ-labeled systems. We also uncover GCGC patterns in the extreme top range of fluorescence, a feature specific to 3ʹ-Cy3 and Cy5 oligonucleotides. This study represents the final piece in linking nucleotide identity to fluorescence changes for Cy3, Cy5 and fluorescein in all 3ʹ, 5ʹ, single-stranded and double-stranded DNA formats.
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18
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Helmerich DA, Beliu G, Taban D, Meub M, Streit M, Kuhlemann A, Doose S, Sauer M. Photoswitching fingerprint analysis bypasses the 10-nm resolution barrier. Nat Methods 2022; 19:986-994. [PMID: 35915194 PMCID: PMC9349044 DOI: 10.1038/s41592-022-01548-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/13/2022] [Indexed: 12/20/2022]
Abstract
Advances in super-resolution microscopy have demonstrated single-molecule localization precisions of a few nanometers. However, translation of such high localization precisions into sub-10-nm spatial resolution in biological samples remains challenging. Here we show that resonance energy transfer between fluorophores separated by less than 10 nm results in accelerated fluorescence blinking and consequently lower localization probabilities impeding sub-10-nm fluorescence imaging. We demonstrate that time-resolved fluorescence detection in combination with photoswitching fingerprint analysis can be used to determine the number and distance even of spatially unresolvable fluorophores in the sub-10-nm range. In combination with genetic code expansion with unnatural amino acids and bioorthogonal click labeling with small fluorophores, photoswitching fingerprint analysis can be used advantageously to reveal information about the number of fluorophores present and their distances in the sub-10-nm range in cells.
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Affiliation(s)
- Dominic A Helmerich
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Danush Taban
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Marcel Streit
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Alexander Kuhlemann
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany.
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.
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19
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Li J, Dong Y, Wei R, Jiang G, Yao C, Lv M, Wu Y, Gardner SH, Zhang F, Lucero MY, Huang J, Chen H, Ge G, Chan J, Chen J, Sun H, Luo X, Qian X, Yang Y. Stable, Bright, and Long-Fluorescence-Lifetime Dyes for Deep-Near-Infrared Bioimaging. J Am Chem Soc 2022; 144:14351-14362. [PMID: 35905456 DOI: 10.1021/jacs.2c05826] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Near-infrared (NIR) fluorophores absorbing maximally in the region beyond 800 nm, i.e., deep-NIR spectral region, are actively sought for biomedical applications. Ideal dyes are bright, nontoxic, photostable, biocompatible, and easily derivatized to introduce functionalities (e.g., for bioconjugation or aqueous solubility). The rational design of such fluorophores remains a major challenge. Silicon-substituted rhodamines have been successful for bioimaging applications in the red spectral region. The longer-wavelength silicon-substituted congeners for the deep-NIR spectral region are unknown to date. We successfully prepared four silicon-substituted bis-benzannulated rhodamine dyes (ESi5a-ESi5d), with an efficient five-step cascade on a gram-scale. Because of the extensive overlapping of their HOMO-LUMO orbitals, ESi5a-ESi5d are highly absorbing (λabs ≈ 865 nm and ε > 105 cm-1 M-1). By restraining both the rotational freedom via annulation and the vibrational freedom via silicon-imparted strain, the fluorochromic scaffold of ESi5 is highly rigid, resulting in an unusually long fluorescence lifetime (τ > 700 ps in CH2Cl2) and a high fluorescence quantum yield (ϕ = 0.14 in CH2Cl2). Their half-lives toward photobleaching are 2 orders of magnitude longer than the current standard (ICG in serum). They are stable in the presence of biorelevant concentration of nucleophiles or reactive oxygen species. They are minimally toxic and readily metabolized. Upon tail vein injection of ESi5a (as an example), the vasculature of a nude mouse was imaged with a high signal-to-background ratio. ESi5 dyes have broad potentials for bioimaging in the deep-NIR spectral region.
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Affiliation(s)
- Jin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Shanghai Key Laboratory of Chemical Biology, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yan Dong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Shanghai Key Laboratory of Chemical Biology, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ruwei Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Shanghai Key Laboratory of Chemical Biology, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Guanyu Jiang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Cheng Yao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Shanghai Key Laboratory of Chemical Biology, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Meng Lv
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yuyang Wu
- Molecular Imaging Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Sarah H Gardner
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Feng Zhang
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Melissa Y Lucero
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Jian Huang
- Pharmacology and Toxicology Division, Shanghai Institute of Food and Drug Control, 1111 Halei Road, Shanghai, 201203, China
| | - Hao Chen
- Molecular Imaging Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Jefferson Chan
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiao Luo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Shanghai Key Laboratory of Chemical Biology, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Shanghai Key Laboratory of Chemical Biology, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Youjun Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Shanghai Key Laboratory of Chemical Biology, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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20
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Li R, Wang D, Li X, Zhang Z, Li W. A visible-light-responsive DiSCn(3)-type fluorescent probe for the rapid, sensitive, and specific detection of tin(II) ions in aqueous solution. JOURNAL OF CHEMICAL RESEARCH 2022. [DOI: 10.1177/17475198221089833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Visible-light-excited fluorescent probes with excellent water solubility are of significant research importance in the biomedical field. In this work, a series of visible-light-responsive carbocyanine fluorescent compounds [DiSCn(3)] are synthesized from 2-methylbenzothiazole and are employed as fluorescent probes for detecting tin(II) ions. Upon addition of tin(II) ions to an aqueous solution of compounds DiSCn(3)-3 and 4, both exhibit considerable changes in their absorption and fluorescent intensity, respectively. These spectral changes may correspond to the binding between tin(II) ions and the sulfur atom in the benzothiazole unit to form a metal complex. This indicates that DiSCn(3)-3 and 4 can be used as promising fluorescent chemical sensors for detecting tin(II) ions in aqueous solution via visible-light excitation.
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Affiliation(s)
- Ruiji Li
- School of Pharmacy, Jining Medical University, Rizhao, P.R. China
| | - Dong Wang
- School of Pharmacy, Jining Medical University, Rizhao, P.R. China
| | - Xiaoyun Li
- School of Pharmacy, Jining Medical University, Rizhao, P.R. China
| | - Zehui Zhang
- School of Pharmacy, Jining Medical University, Rizhao, P.R. China
| | - Wei Li
- School of Pharmacy, Jining Medical University, Rizhao, P.R. China
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21
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Sakhapov D, Gregor I, Karedla N, Enderlein J. Measuring Photophysical Transition Rates with Fluorescence Correlation Spectroscopy and Antibunching. J Phys Chem Lett 2022; 13:4823-4830. [PMID: 35616286 DOI: 10.1021/acs.jpclett.2c00896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We present a new method that combines fluorescence correlation spectroscopy (FCS) on the microsecond time scale with fluorescence antibunching measurements on the nanosecond time scale for measuring photophysical rate constants of fluorescent molecules. The antibunching measurements allow us to quantify the average excitation rate of fluorescent molecules within the confocal detection volume of the FCS measurement setup. Knowledge of this value allows us then to quantify, in an absolute manner, the intersystem crossing rate and triplet state lifetime from the microsecond temporal decay of the FCS curves. We present a theoretical analysis of the method and estimate the maximum bias caused by the averaging of all quantities (excitation rate and photophysical rates) over the confocal detection volume, and we show that this bias is smaller than 5% in most cases. We apply the method for measuring the photophysical rate constants of the widely used dyes Rhodamine 110 and ATTO 655.
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Affiliation(s)
- Damir Sakhapov
- III. Institute of Physics - Biophysics, Georg-August-University, 37077 Göttingen, Germany
| | - Ingo Gregor
- III. Institute of Physics - Biophysics, Georg-August-University, 37077 Göttingen, Germany
| | - Narain Karedla
- The Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, U.K
| | - 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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22
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Study of cholesterol phase effect on the dynamics of DOPC and DPPC small vesicle membranes using single-molecule fluorescence correlation spectroscopy. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Du Z, Piguet J, Baryshnikov G, Tornmalm J, Demirbay B, Ågren H, Widengren J. Imaging Fluorescence Blinking of a Mitochondrial Localization Probe: Cellular Localization Probes Turned into Multifunctional Sensors. J Phys Chem B 2022; 126:3048-3058. [PMID: 35417173 PMCID: PMC9059120 DOI: 10.1021/acs.jpcb.2c01271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Indexed: 11/29/2022]
Abstract
Mitochondrial membranes and their microenvironments directly influence and reflect cellular metabolic states but are difficult to probe on site in live cells. Here, we demonstrate a strategy, showing how the widely used mitochondrial membrane localization fluorophore 10-nonyl acridine orange (NAO) can be transformed into a multifunctional probe of membrane microenvironments by monitoring its blinking kinetics. By transient state (TRAST) studies of NAO in small unilamellar vesicles (SUVs), together with computational simulations, we found that NAO exhibits prominent reversible singlet-triplet state transitions and can act as a light-induced Lewis acid forming a red-emissive doublet radical. The resulting blinking kinetics are highly environment-sensitive, specifically reflecting local membrane oxygen concentrations, redox conditions, membrane charge, fluidity, and lipid compositions. Here, not only cardiolipin concentration but also the cardiolipin acyl chain composition was found to strongly influence the NAO blinking kinetics. The blinking kinetics also reflect hydroxyl ion-dependent transitions to and from the fluorophore doublet radical, closely coupled to the proton-transfer events in the membranes, local pH, and two- and three-dimensional buffering properties on and above the membranes. Following the SUV studies, we show by TRAST imaging that the fluorescence blinking properties of NAO can be imaged in live cells in a spatially resolved manner. Generally, the demonstrated blinking imaging strategy can transform existing fluorophore markers into multiparametric sensors reflecting conditions of large biological relevance, which are difficult to retrieve by other means. This opens additional possibilities for fundamental membrane studies in lipid vesicles and live cells.
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Affiliation(s)
- Zhixue Du
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
| | - Joachim Piguet
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
| | - Glib Baryshnikov
- Laboratory
of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174 Norrköping, Sweden
| | - Johan Tornmalm
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
| | - Baris Demirbay
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
| | - Hans Ågren
- Department
of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
| | - Jerker Widengren
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
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24
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Barth A, Opanasyuk O, Peulen TO, Felekyan S, Kalinin S, Sanabria H, Seidel CAM. Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines. J Chem Phys 2022; 156:141501. [PMID: 35428384 PMCID: PMC9014241 DOI: 10.1063/5.0089134] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/31/2023] Open
Abstract
Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a tethered donor and acceptor dye pair are a powerful tool to investigate the structure and dynamics of labeled molecules. However, capturing and quantifying conformational dynamics in intensity-based smFRET experiments remains challenging when the dynamics occur on the sub-millisecond timescale. The method of multiparameter fluorescence detection addresses this challenge by simultaneously registering fluorescence intensities and lifetimes of the donor and acceptor. Together, two FRET observables, the donor fluorescence lifetime τD and the intensity-based FRET efficiency E, inform on the width of the FRET efficiency distribution as a characteristic fingerprint for conformational dynamics. We present a general framework for analyzing dynamics that relates average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms. We present parametric relations of these observables for interpreting the location of FRET populations in E-τD diagrams, called FRET-lines. To facilitate the analysis of complex exchange equilibria, FRET-lines serve as reference curves for a graphical interpretation of experimental data to (i) identify conformational states, (ii) resolve their dynamic connectivity, (iii) compare different kinetic models, and (iv) infer polymer properties of unfolded or intrinsically disordered proteins. For a simplified graphical analysis of complex kinetic networks, we derive a moment-based representation of the experimental data that decouples the motion of the fluorescence labels from the conformational dynamics of the biomolecule. Importantly, FRET-lines facilitate exploring complex dynamic models via easily computed experimental observables. We provide extensive computational tools to facilitate applying FRET-lines.
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Affiliation(s)
- Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Oleg Opanasyuk
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Thomas-Otavio Peulen
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, USA
| | - Claus A. M. Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
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25
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Assessing hypoxic damage to placental trophoblasts by measuring membrane viscosity of extracellular vesicles. Placenta 2022; 121:14-22. [PMID: 35245720 PMCID: PMC9010367 DOI: 10.1016/j.placenta.2022.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/06/2022] [Accepted: 02/22/2022] [Indexed: 11/22/2022]
Abstract
INTRODUCTION As highly sophisticated intercellular communication vehicles in biological systems, extracellular vesicles (EVs) have been investigated as both promising liquid biopsy-based disease biomarkers and drug delivery carriers. Despite tremendous progress in understanding their biological and physiological functions, mechanical characterization of these nanoscale entities remains challenging due to the limited availability of proper techniques. Especially, whether damage to parental cells can be reflected by the mechanical properties of their EVs remains unknown. METHODS In this study, we characterized membrane viscosities of different types of EVs collected from primary human trophoblasts (PHTs), including apoptotic bodies, microvesicles and small extracellular vesicles, using fluorescence lifetime imaging microscopy (FLIM). The biochemical origin of EV membrane viscosity was examined by analyzing their phospholipid composition, using mass spectrometry. RESULTS We found that different EV types derived from the same cell type exhibit different membrane viscosities. The measured membrane viscosity values are well supported by the lipidomic analysis of the phospholipid compositions. We further demonstrate that the membrane viscosity of microvesicles can faithfully reveal hypoxic injury of the human trophoblasts. More specifically, the membrane of PHT microvesicles released under hypoxic condition is less viscous than its counterpart under standard culture condition, which is supported by the reduction in the phosphatidylethanolamine-to-phosphatidylcholine ratio in PHT microvesicles. DISCUSSION Our study suggests that biophysical properties of released trophoblastic microvesicles can reflect cell health. Characterizing EV's membrane viscosity may pave the way for the development of new EV-based clinical applications.
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26
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Yang Y, Zhang F. Molecular fluorophores for in vivo bioimaging in the second near-infrared window. Eur J Nucl Med Mol Imaging 2022; 49:3226-3246. [PMID: 35088125 DOI: 10.1007/s00259-022-05688-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/11/2022] [Indexed: 12/23/2022]
Abstract
PURPOSE This systematic review aims to summarize the current developments of fluorescence and chemi/bioluminescence imaging based on the molecular fluorophores for in vivo imaging in the second near-infrared window. METHODS AND RESULTS By investigating most of the relevant references on the web of science and some journals, this review firstly begins with an overview of the background of fluorescence and chemi/bioluminescence imaging. Secondly, the chemical and optical properties of NIR-II dyes are discussed, such as water solubility, chemostability and photo-stability, and brightness. Thirdly, the bioimaging based on NIR-II fluorescence emission is outlined, including the in vivo imaging of polymethine dyes, donor - acceptor - donor (D - A - D) chromophores, and lanthanide complexes. Fourthly, we demonstrate the chemi/bioluminescence in vivo imaging in the second near-infrared window. Fifthly, the clinical application and translation of near-infrared fluorescence imaging are presented. Finally, the current challenges, feasible strategies and potential prospects of the fluorophores and in vivo bioimaging are discussed. CONCLUSIONS Based on the above literature research on the applications of molecular fluorescent and chemi/bioluminescent probes in the second near-infrared window in recent years, this review weighs the advantages and disadvantages of fluorescence and chemi/bioluminescence imaging, and NIR-II fluorophores based on polymethine dyes, D - A - D chromophores, and lanthanide complexes. Besides, this review also provides a very important guidance for expanding the imaging applications of molecular fluorophores in the second near-infrared window.
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Affiliation(s)
- Yanling Yang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Fan Zhang
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and iChem, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200433, China.
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27
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Eiring P, McLaughlin R, Matikonda SS, Han Z, Grabenhorst L, Helmerich DA, Meub M, Beliu G, Luciano M, Bandi V, Zijlstra N, Shi ZD, Tarasov SG, Swenson R, Tinnefeld P, Glembockyte V, Cordes T, Sauer M, Schnermann MJ. Targetable Conformationally Restricted Cyanines Enable Photon-Count-Limited Applications*. Angew Chem Int Ed Engl 2021; 60:26685-26693. [PMID: 34606673 PMCID: PMC8649030 DOI: 10.1002/anie.202109749] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/18/2021] [Indexed: 12/15/2022]
Abstract
Cyanine dyes are exceptionally useful probes for a range of fluorescence-based applications, but their photon output can be limited by trans-to-cis photoisomerization. We recently demonstrated that appending a ring system to the pentamethine cyanine ring system improves the quantum yield and extends the fluorescence lifetime. Here, we report an optimized synthesis of persulfonated variants that enable efficient labeling of nucleic acids and proteins. We demonstrate that a bifunctional sulfonated tertiary amide significantly improves the optical properties of the resulting bioconjugates. These new conformationally restricted cyanines are compared to the parent cyanine derivatives in a range of contexts. These include their use in the plasmonic hotspot of a DNA-nanoantenna, in single-molecule Förster-resonance energy transfer (FRET) applications, far-red fluorescence-lifetime imaging microscopy (FLIM), and single-molecule localization microscopy (SMLM). These efforts define contexts in which eliminating cyanine isomerization provides meaningful benefits to imaging performance.
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Affiliation(s)
- Patrick Eiring
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ryan McLaughlin
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Siddharth S Matikonda
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Zhongying Han
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Dominic A Helmerich
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Michael Luciano
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Venu Bandi
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Zhen-Dan Shi
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, NIH, Rockville, MD, 20850, USA
| | - Sergey G Tarasov
- Biophysics Resource in the Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Rolf Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, NIH, Rockville, MD, 20850, USA
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Martin J Schnermann
- Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
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28
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Eiring P, McLaughlin R, Matikonda SS, Han Z, Grabenhorst L, Helmerich DA, Meub M, Beliu G, Luciano M, Bandi V, Zijlstra N, Shi Z, Tarasov SG, Swenson R, Tinnefeld P, Glembockyte V, Cordes T, Sauer M, Schnermann MJ. Targetable Conformationally Restricted Cyanines Enable Photon‐Count‐Limited Applications**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Patrick Eiring
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Ryan McLaughlin
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Siddharth S. Matikonda
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Zhongying Han
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Germany
| | - Dominic A. Helmerich
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Michael Luciano
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Venu Bandi
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Niels Zijlstra
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Zhen‐Dan Shi
- Chemistry and Synthesis Center National Heart, Lung, and Blood Institute NIH Rockville MD 20850 USA
| | - Sergey G. Tarasov
- Biophysics Resource in the Center for Structural Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
| | - Rolf Swenson
- Chemistry and Synthesis Center National Heart, Lung, and Blood Institute NIH Rockville MD 20850 USA
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Germany
| | - Thorben Cordes
- Physical and Synthetic Biology Faculty of Biology Ludwig-Maximilians-Universität München Großhadernerstr. 2–4 82152 Planegg-Martinsried Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter Julius-Maximilians-Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Martin J. Schnermann
- Laboratory of Chemical Biology Center for Cancer Research National Cancer Institute Frederick MD 21702 USA
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29
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Pace NA, Hennelly SP, Goodwin PM. Immobilization of Cyanines in DNA Produces Systematic Increases in Fluorescence Intensity. J Phys Chem Lett 2021; 12:8963-8971. [PMID: 34506152 DOI: 10.1021/acs.jpclett.1c02022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cyanines are useful fluorophores for a myriad of biological labeling applications, but their interactions with biomolecules are unpredictable. Cyanine fluorescence intensity can be highly variable due to complex photoisomerization kinetics, which are exceedingly sensitive to the surrounding environment. This introduces large errors in Förster resonance energy transfer (FRET)-based experiments where fluorescence intensity is the output parameter. However, this environmental sensitivity is a strength from a biological sensing point of view if specific relationships between biomolecular structure and cyanine photophysics can be identified. We describe a set of DNA structures that modulate cyanine fluorescence intensity through the insertion of adenine or thymine bases. These structures simultaneously provide photophysical predictability and tunability. We characterize these structures using steady-state fluorescence measurements, fluorescence correlation spectroscopy (FCS), and time-resolved photoluminescence (TRPL). We find that the photoisomerization rate decreases over an order of magnitude across the adenine series, which is consistent with increasing immobilization of the cyanine moiety by the surrounding DNA structure.
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Affiliation(s)
- Natalie A Pace
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Scott P Hennelly
- Bioenergy and Biome Sciences Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Peter M Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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30
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Sparrenberg LT, Greiner B, Mathis HP. The Mean Single Molecule Rate (mSMR) in the Analysis of Fluorescence Fluctuations: Measurements on DNA Mixtures of Defined Composition. J Fluoresc 2021; 31:1883-1894. [PMID: 34529200 PMCID: PMC8547212 DOI: 10.1007/s10895-021-02803-3] [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: 03/22/2021] [Accepted: 08/11/2021] [Indexed: 12/03/2022]
Abstract
We present a method for the evaluation of fluorescence fluctuations on the basis of Mandel’s Q parameter, using sampling time-dependent factorial cumulants. By relating the Q parameter to the sampling time, we obtain the mean single molecule rate (mSMR), an easy to interpret expression that provides both brightness and diffusion information. The model is suitable for the widely used confocal setups with single photon excitation and a single detection channel. We present a way to correct the mSMR for afterpulsing, dead time and background noise. To account for photokinetic effects at short sampling times, we expand the model by a simple on/off isomerization term, which is similar to the well-known triplet model. The functionality of the mSMR is shown using Monte Carlo simulations. The correction mechanisms and the experimental applicability of the model are then demonstrated by DNA measurements of defined composition. By systematically analyzing DNA mixtures, we can show that at large sampling times, the mSMR correctly describes the single molecule brightness rates and the diffusive properties of DNA molecules. At short sampling times, the photokinetic effects of isomerization are accurately described by the mSMR model. Since additionally the mSMR can easily be corrected for measurement artefacts such as detector dead time, afterpulsing and background noise, this is a valuable advantage over the standard method of fluorescence correlation spectroscopy.
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Affiliation(s)
- Lorenz T Sparrenberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany. .,Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany.
| | - Benjamin Greiner
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany
| | - Harald P Mathis
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany
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31
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Xu J, Fan S, Xu L, Maruyama A, Fujitsuka M, Kawai K. Control of Triplet Blinking Using Cyclooctatetraene to Access the Dynamics of Biomolecules at the Single‐Molecule Level. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jie Xu
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Shuya Fan
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Lei Xu
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology Tokyo Institute of Technology 4259 B-57 Nagatsuta, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
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32
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Xu J, Fan S, Xu L, Maruyama A, Fujitsuka M, Kawai K. Control of Triplet Blinking Using Cyclooctatetraene to Access the Dynamics of Biomolecules at the Single‐Molecule Level. Angew Chem Int Ed Engl 2021; 60:12941-12948. [DOI: 10.1002/anie.202101606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/25/2021] [Indexed: 01/04/2023]
Affiliation(s)
- Jie Xu
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Shuya Fan
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Lei Xu
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology Tokyo Institute of Technology 4259 B-57 Nagatsuta, Midori-ku Yokohama Kanagawa 226-8501 Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN) Osaka University Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
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33
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Nasir I, Bentley EP, Deniz AA. Ratiometric Single-Molecule FRET Measurements to Probe Conformational Subpopulations of Intrinsically Disordered Proteins. ACTA ACUST UNITED AC 2021; 12:e80. [PMID: 32159932 PMCID: PMC7508418 DOI: 10.1002/cpch.80] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past few decades, numerous examples have demonstrated that intrinsic disorder in proteins lies at the heart of many vital processes, including transcriptional regulation, stress response, cellular signaling, and most recently protein liquid-liquid phase separation. The so-called intrinsically disordered proteins (IDPs) involved in these processes have presented a challenge to the classic protein "structure-function paradigm," as their functions do not necessarily involve well-defined structures. Understanding the mechanisms of IDP function is likewise challenging because traditional structure determination methods often fail with such proteins or provide little information about the diverse array of structures that can be related to different functions of a single IDP. Single-molecule fluorescence methods can overcome this ensemble-average masking, allowing the resolution of subpopulations and dynamics and thus providing invaluable insights into IDPs and their function. In this protocol, we describe a ratiometric single-molecule Förster resonance energy transfer (smFRET) routine that permits the investigation of IDP conformational subpopulations and dynamics. We note that this is a basic protocol, and we provide brief information and references for more complex analysis schemes available for in-depth characterization. This protocol covers optical setup preparation and protein handling and provides insights into experimental design and outcomes, together with background information about theory and a brief discussion of troubleshooting. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Ratiometric smFRET detection and analysis of IDPs Support Protocol 1: Fluorophore labeling of a protein through maleimide chemistry Support Protocol 2: Sample chamber preparation Support Protocol 3: Determination of direct excitation of acceptor by donor excitation and leakage of donor emission to acceptor emission channel.
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Affiliation(s)
- Irem Nasir
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.,Department of Biology and Biological Engineering, Division of Chemical Biology, Chalmers Institute of Technology, Gothenburg, Sweden
| | - Emily P Bentley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
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34
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Lei Z, Zhang F. Molecular Engineering of NIR‐II Fluorophores for Improved Biomedical Detection. Angew Chem Int Ed Engl 2021; 60:16294-16308. [DOI: 10.1002/anie.202007040] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Zuhai Lei
- Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and iChEM Fudan University Shanghai 200433 P. R. China
- School of Pharmacy Fudan University Shanghai 200433 P. R. China
| | - Fan Zhang
- Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and iChEM Fudan University Shanghai 200433 P. R. China
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35
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Lei Z, Zhang F. Molecular Engineering of NIR‐II Fluorophores for Improved Biomedical Detection. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202007040] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Zuhai Lei
- Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and iChEM Fudan University Shanghai 200433 P. R. China
- School of Pharmacy Fudan University Shanghai 200433 P. R. China
| | - Fan Zhang
- Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and iChEM Fudan University Shanghai 200433 P. R. China
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36
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Hackl S, Ng XW, Lu D, Wohland T, Becker CFW. Cytoskeleton-dependent clustering of membrane-bound prion protein on the cell surface. J Biol Chem 2021; 296:100359. [PMID: 33539927 PMCID: PMC7988330 DOI: 10.1016/j.jbc.2021.100359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/23/2022] Open
Abstract
Prion diseases are a group of neurodegenerative disorders that infect animals and humans with proteinaceous particles called prions. Prions consist of scrapie prion protein (PrPSc), a misfolded version of the cellular prion protein (PrPC). During disease progression, PrPSc replicates by interacting with PrPC and inducing its conversion to PrPSc. Attachment of PrPC to cellular membranes via a glycosylphosphatidylinositol (GPI) anchor is critical for the conversion of PrPC into PrPSc. However, the mechanisms governing PrPC conversion and replication on the membrane remain largely unclear. Here, a site-selectively modified PrP variant equipped with a fluorescent GPI anchor mimic (PrP-GPI) was employed to directly observe PrP at the cellular membrane in neuronal SH-SY5Y cells. PrP-GPI exhibits a cholesterol-dependent membrane accumulation and a cytoskeleton-dependent mobility. More specifically, inhibition of actin polymerization reduced the diffusion of PrP-GPI indicating protein clustering, which resembles the initial step of PrP aggregation and conversion into its pathogenic isoform. An intact actin cytoskeleton might therefore prevent conversion of PrPC into PrPSc and offer new therapeutic angles.
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Affiliation(s)
- Stefanie Hackl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Xue Wen Ng
- Departments of Biological Sciences and Chemistry and Centre for Bioimaging Sciences (CBIS), National University of Singapore (NUS), Singapore
| | - Danqin Lu
- Departments of Biological Sciences and Chemistry and Centre for Bioimaging Sciences (CBIS), National University of Singapore (NUS), Singapore; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry and Centre for Bioimaging Sciences (CBIS), National University of Singapore (NUS), Singapore
| | - Christian F W Becker
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
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37
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Advanced Fluorescence Imaging to Distinguish Between Intracellular Fractions of Antisense Oligonucleotides. Methods Mol Biol 2020; 2063:119-138. [PMID: 31667767 DOI: 10.1007/978-1-0716-0138-9_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Antisense oligonucleotides (AON) have been intensively studied as tools in molecular cell biology and as novel therapeutics in various diseases over the past two decades. Especially cellular uptake and endosomal release of AONs are topics of interest, as these are crucial steps in reaching the subcellular AON target sites and achieving biological activity. We used cell-penetrating peptides (CPPs) to enhance uptake and endosomal release of AONs, and monitored these two processes and the subsequent fate of the AONs by advanced fluorescence microscopy in living cells. In this chapter, we discuss the use of automated time-lapse confocal laser scanning microscopy (CLSM) to follow AON uptake and trafficking in time, fluorescence lifetime imaging microscopy (FLIM) to distinguish between free and AON-bound fluorophore, and fluorescence correlation spectroscopy (FCS) to measure subcellular AON concentrations and molecular associations. Additionally, we expand on the analysis of these microscopy data.
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38
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Hensbergen AW, de Kleer MA, Boutkan MS, van Willigen DM, van der Wijk FA, Welling MM, Wester HJ, Buckle T, van Leeuwen FW. Evaluation of asymmetric orthogonal cyanine fluorophores. DYES AND PIGMENTS 2020; 183:108712. [DOI: 10.1016/j.dyepig.2020.108712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
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39
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Helmerich DA, Beliu G, Sauer M. Multiple-Labeled Antibodies Behave Like Single Emitters in Photoswitching Buffer. ACS NANO 2020; 14:12629-12641. [PMID: 32804475 DOI: 10.1021/acsnano.0c06099] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The degree of labeling (DOL) of antibodies has so far been optimized for high brightness and specific and efficient binding. The influence of the DOL on the blinking performance of antibodies used in direct stochastic optical reconstruction microscopy (dSTORM) has so far attained limited attention. Here, we investigated the spectroscopic characteristics of IgG antibodies labeled at DOLs of 1.1-8.3 with Alexa Fluor 647 (Al647) at the ensemble and single-molecule level. Multiple-Al647-labeled antibodies showed weak and strong quenching interactions in aqueous buffer but could all be used for dSTORM imaging with spatial resolutions of ∼20 nm independent of the DOL. Single-molecule fluorescence trajectories and photon antibunching experiments revealed that individual multiple-Al647-labeled antibodies show complex photophysics in aqueous buffer but behave as single emitters in photoswitching buffer independent of the DOL. We developed a model that explains the observed blinking of multiple-labeled antibodies and can be used for the development of improved fluorescent probes for dSTORM experiments.
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Affiliation(s)
- Dominic A Helmerich
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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40
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Gidi Y, Payne L, Glembockyte V, Michie MS, Schnermann MJ, Cosa G. Unifying Mechanism for Thiol-Induced Photoswitching and Photostability of Cyanine Dyes. J Am Chem Soc 2020; 142:12681-12689. [PMID: 32594743 DOI: 10.1021/jacs.0c03786] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cyanines (Cy3, Cy5, Cy3B) are the most utilized dyes for single-molecule fluorescence and localization-based super-resolution imaging. These modalities exploit cyanines' versatile photochemical behavior with thiols. A mechanism reconciling seemingly divergent results and enabling control over cyanine photoreactivity is however missing. Utilizing single-molecule fluorescence on Cy5 and Cy5B, transient-absorption spectroscopy, and DFT modeling on a range of cyanine dyes, herein we show that photoinduced electron transfer (PeT) from a thiolate to Cy in their triplet excited state and then triplet-to-singlet intersystem crossing in the nascent geminate radical pair are crucial steps. Next, a bifurcation occurs, yielding either back electron transfer and regeneration of ground state Cy, required for photostabilization, or Cy-thiol adduct formation, necessary for super-resolution microscopy. Cy regeneration via photoinduced thiol elimination is favored by adduct absorption spectra broadening. Elimination is also shown to occur through an acid-catalyzed reaction. Overall, our work provides a roadmap for designing fluorophores, photoswitching agents, and triplet excited state quenchers for single-molecule and super-resolution imaging.
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Affiliation(s)
- Yasser Gidi
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Liam Payne
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Viktorija Glembockyte
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Megan S Michie
- Laboratory of Chemical Biology, NIH/NCI/CCR, 376 Boyles Street, Frederick, Maryland 21702, United States
| | - Martin J Schnermann
- Laboratory of Chemical Biology, NIH/NCI/CCR, 376 Boyles Street, Frederick, Maryland 21702, United States
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
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41
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Hart SM, Banal JL, Bathe M, Schlau-Cohen GS. Identification of Nonradiative Decay Pathways in Cy3. J Phys Chem Lett 2020; 11:5000-5007. [PMID: 32484350 DOI: 10.1021/acs.jpclett.0c01201] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Photoexcited fluorescent markers are extensively used in spectroscopy, imaging, and analysis of biological systems. The performance of fluorescent markers depends on high levels of emission, which are limited by competing nonradiative decay pathways. Small-molecule fluorescent dyes have been increasingly used as markers due to their high and stable emission. Despite their prevalence, the nonradiative decay pathways of these dyes have not been determined. Here, we investigate these pathways for a widely used indocarbocyanine dye, Cy3, using transient grating spectroscopy. We identify a nonradiative decay pathway via a previously unknown dark state formed within ∼1 ps of photoexcitation. Our experiments, in combination with electronic structure calculations, suggest that the generation of the dark state is mediated by picosecond vibrational mode coupling, likely via a conical intersection. We further identify the vibrational modes, and thus structural elements, responsible for the formation and dynamics of the dark state, providing insight into suppressing nonradiative decay pathways in fluorescent markers such as Cy3.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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42
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Knox SL, Steinauer A, Alpha-Cobb G, Trexler A, Rhoades E, Schepartz A. Quantification of protein delivery in live cells using fluorescence correlation spectroscopy. Methods Enzymol 2020; 641:477-505. [PMID: 32713536 DOI: 10.1016/bs.mie.2020.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a quantitative single-molecule method that measures the concentration and rate of diffusion of fluorophore-tagged molecules, both large and small, in vitro and within live cells, and even within discrete cellular compartments. FCS is exceptionally well-suited to directly quantify the efficiency of intracellular protein delivery-specifically, how well different "cell-penetrating" proteins and peptides guide proteinaceous materials into the cytosol and nuclei of live mammalian cells. This article provides an overview of the procedures necessary to execute robust FCS experiments and evaluate endosomal escape efficiencies: preparation of fluorophore-tagged proteins, incubation with mammalian cells and preparation of FCS samples, setup and execution of an FCS experiment, and a detailed discussion of and custom MATLAB® script for analyzing the resulting autocorrelation curves in the context of appropriate diffusion models.
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Affiliation(s)
- Susan L Knox
- Department of Chemistry, University of California, Berkeley, CA, United States
| | - Angela Steinauer
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Garrett Alpha-Cobb
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Adam Trexler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, CA, United States; Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States.
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43
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Adablah JE, Wang Y, Donohue M, Roper MG. Profiling Glucose-Stimulated and M3 Receptor-Activated Insulin Secretion Dynamics from Islets of Langerhans Using an Extended-Lifetime Fluorescence Dye. Anal Chem 2020; 92:8464-8471. [PMID: 32429660 PMCID: PMC7304439 DOI: 10.1021/acs.analchem.0c01226] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Pulsatile insulin
from pancreatic islets is crucial for glucose
homeostasis, but the mechanism behind coordinated pulsatility is still
under investigation. One hypothesis suggests that cholinergic stimulation
of islets by pancreatic ganglia resets these endocrine units, producing
synchronization. Previously, it was shown that intracellular Ca2+ oscillations within islets can be entrained by pulses of
a cholinergic agonist, carbachol (CCh). Although these proxy measurements
of Ca2+ provided insight into the synchronization mechanism,
measurement of insulin output would be more direct evidence. To this
end, a fluorescence anisotropy competitive immunoassay for online
insulin detection from single and grouped islets in a microfluidic
system was developed using a piezoelectric pressure-driven fluid delivery
system and a squaraine rotaxane fluorophore, SeTau-647, as the fluorescent
label for insulin. Due to SeTau-647 having a longer lifetime and higher
brightness compared to the previously used Cy5 fluorophore, a 45%
increase in the anisotropy range was observed with enhanced signal-to-noise
ratio (S/N) of the measurements. This new system was tested by measuring
glucose-stimulated insulin secretion from single and groups of murine
and human islets. Distinct islet entrainment of groups of murine islets
by pulses of CCh was also observed, providing further evidence for
the hypothesis that pulsatile output from the ganglia can synchronize
islet behavior. We expect that this relatively straightforward, homogeneous
assay can be widely used for examining not only insulin secretion
but other secreted factors from different tissues.
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Affiliation(s)
- Joel E Adablah
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Yao Wang
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Matthew Donohue
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Michael G Roper
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
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44
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Mazuski RJ, Díaz SA, Wood RE, Lloyd LT, Klein WP, Mathur D, Melinger JS, Engel GS, Medintz IL. Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency. J Phys Chem Lett 2020; 11:4163-4172. [PMID: 32391695 DOI: 10.1021/acs.jpclett.0c01020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
DNA scaffolds enable base-pair-specific positioning of fluorescent molecules, allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based molecular photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Förster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye molecules becomes comparable to their size (∼2 nm). Here we compare dye conjugation with single versus dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temperature (RT) under low-light conditions, end-labeled uncoupled dye molecules provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temperatures, the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become critical, and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.
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Affiliation(s)
- Richard J Mazuski
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ryan E Wood
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Lawson T Lloyd
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Divita Mathur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joseph S Melinger
- Electronic Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory S Engel
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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45
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Matikonda SS, Hammersley G, Kumari N, Grabenhorst L, Glembockyte V, Tinnefeld P, Ivanic J, Levitus M, Schnermann MJ. Impact of Cyanine Conformational Restraint in the Near-Infrared Range. J Org Chem 2020; 85:5907-5915. [PMID: 32275153 PMCID: PMC8459201 DOI: 10.1021/acs.joc.0c00236] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Appending conformationally restraining ring systems to the cyanine chromophore creates exceptionally bright fluorophores in the visible range. Here, we report the application of this strategy in the near-infrared range through the preparation of the first restrained heptamethine indocyanine. Time-resolved absorption spectroscopy and fluorescence correlation spectroscopy verify that, unlike the corresponding parent unrestrained variant, the restrained molecule is not subject to photoisomerization. Notably, however, the room-temperature emission efficiency and the fluorescence lifetime of the restrained cyanine are not extended relative to the parent cyanine, even in viscous solvents. Thus, in contrast to prior reports, the photoisomerization of heptamethine cyanines does not contribute significantly to the excited-state chemistry of these molecules. We also find that the fluorescence lifetime of the restrained heptamethine cyanine is temperature-insensitive and significantly extended at moderately elevated temperatures relative to the parent cyanine. Finally, computational studies have been used to evaluate the impact of the conformational restraint on atomic and orbital structure across the cyanine series. These studies clarify the role of photoisomerization in the heptamethine cyanine scaffold and demonstrate the dramatic effect of restraint on the temperature sensitivity of these dyes.
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Affiliation(s)
- Siddharth S Matikonda
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, Maryland 21702, United States
| | - Gabrielle Hammersley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, Maryland 21702, United States
| | - Nikita Kumari
- School of Molecular Sciences and The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
| | - Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, 81377, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, 81377, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, 81377, Germany
| | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Marcia Levitus
- School of Molecular Sciences and The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, Maryland 21702, United States
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46
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Melnychuk N, Egloff S, Runser A, Reisch A, Klymchenko AS. Light‐Harvesting Nanoparticle Probes for FRET‐Based Detection of Oligonucleotides with Single‐Molecule Sensitivity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913804] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nina Melnychuk
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Sylvie Egloff
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Anne Runser
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
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47
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Melnychuk N, Egloff S, Runser A, Reisch A, Klymchenko AS. Light‐Harvesting Nanoparticle Probes for FRET‐Based Detection of Oligonucleotides with Single‐Molecule Sensitivity. Angew Chem Int Ed Engl 2020; 59:6811-6818. [DOI: 10.1002/anie.201913804] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/30/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Nina Melnychuk
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Sylvie Egloff
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Anne Runser
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
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48
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Grabenhorst L, Trofymchuk K, Steiner F, Glembockyte V, Tinnefeld P. Fluorophore photostability and saturation in the hotspot of DNA origami nanoantennas. Methods Appl Fluoresc 2020; 8:024003. [DOI: 10.1088/2050-6120/ab6ac8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Tornmalm J, Piguet J, Chmyrov V, Widengren J. Imaging of intermittent lipid-receptor interactions reflects changes in live cell membranes upon agonist-receptor binding. Sci Rep 2019; 9:18133. [PMID: 31792325 PMCID: PMC6889430 DOI: 10.1038/s41598-019-54625-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/11/2019] [Indexed: 12/26/2022] Open
Abstract
Protein-lipid interactions in cellular membranes modulate central cellular functions, are often transient in character, but occur too intermittently to be readily observable. We introduce transient state imaging (TRAST), combining sensitive fluorescence detection of fluorophore markers with monitoring of their dark triplet state transitions, allowing imaging of such protein-lipid interactions. We first determined the dark state kinetics of the biomembrane fluorophore 7-nitrobenz-2-oxa-1,3-diazole-4-yl (NBD) in lipid vesicles, and how its triplet state is quenched by spin-labels in the same membranes. We then monitored collisional quenching of NBD-lipid derivatives by spin-labelled stearic acids in live cell plasma membranes, and of NBD-lipid derivatives by spin-labelled G-Protein Coupled Receptors (GPCRs). We could then resolve transient interactions between the GPCRs and different lipids, how these interactions changed upon GPCR activation, thereby demonstrating a widely applicable means to image and characterize transient molecular interactions in live cell membranes in general, not within reach via traditional fluorescence readouts.
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Affiliation(s)
- Johan Tornmalm
- Experimental Biomolecular Physics, KTH, 10691, Stockholm, Sweden
| | - Joachim Piguet
- Experimental Biomolecular Physics, KTH, 10691, Stockholm, Sweden.
| | | | - Jerker Widengren
- Experimental Biomolecular Physics, KTH, 10691, Stockholm, Sweden.
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50
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Kumari N, Ciuba MA, Levitus M. Photophysical properties of the hemicyanine Dy-630 and its potential as a single-molecule fluorescent probe for biophysical applications. Methods Appl Fluoresc 2019; 8:015004. [PMID: 31585443 DOI: 10.1088/2050-6120/ab4b0d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Protein-induced fluorescence enhancement (PIFE) is an increasingly used approach to investigate DNA-protein interactions at the single molecule level. The optimal probe for this type of application is highly photostable, has a high absorption extinction coefficient, and has a moderate fluorescence quantum yield that increases significantly when the dye is in close proximity to a large macromolecule such as a protein. So far, the green-absorbing symmetric cyanine known as Cy3 has been the probe of choice in this field because the magnitude of the increase observed upon protein binding (usually 2-4 -fold) is large enough to allow for the analysis of protein dynamics on the inherently noisy single-molecule signals. Here, we report the characterization of the photophysical properties of the red-absorbing hemicyanine dye Dy-630 in the context of its potential application as a single-molecule PIFE probe. The behavior of Dy-630 in solution is similar to that of Cy3; the fluorescence quantum yield and lifetime of Dy-630 increase with increasing viscosity, and decrease with increasing temperature indicating the existence of an activated nonradiative process that depopulates the singlet state of the dye. As in the case of Cy3, the results of transient spectroscopy experiments are consistent with the formation of a photoisomer that reverts to the ground state thermally in the microsecond timescale. Unfortunately, experiments with DNA samples paint a more complex scenario. As in the case of Cy3, the fluorescence quantum yield of Dy-630 increases significantly when the dye interacts with the DNA bases, but in the case of Dy-630 attachment to DNA results in an already long fluorescence lifetime that does not provide a significant window for the protein-induced enhancement observed with Cy3. Although we show that Dy-630 may not be well-suited for PIFE, our results shed light on the optimal design principles for probes for PIFE applications.
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