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Zhao X, Du J, Sun W, Fan J, Peng X. Regulating Charge Transfer in Cyanine Dyes: A Universal Methodology for Enhancing Cancer Phototherapeutic Efficacy. Acc Chem Res 2024; 57:2582-2593. [PMID: 39152945 DOI: 10.1021/acs.accounts.4c00399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
Abstract
ConspectusDue to the advantages of spatiotemporal selectivity and inherent noninvasiveness, cancer phototherapy, which includes both photodynamic therapy (PDT) and photothermal therapy (PTT), has garnered significant attention in recent years as a promising cancer treatment. Despite the commendable progress in this field, persistent challenges remain. In PDT, limitations in dyes manifest as low intersystem crossing (ISC) efficiency and oxygen-dependent photoactivity, resulting in unsatisfactory performance, particularly under hypoxic conditions. Similarly, PTT encounters consistent insufficiencies in the photothermal conversion efficiency (PCE) of dyes. Additionally, the suboptimal phototherapeutic efficacy often exhibits a limited immune response. These factors collectively impose significant constraints on phototherapy in oncological applications, leading to limited tumor inhibition, tumor recurrence, and even metastasis.Unlike strategies that rely on external assistance with complicated systems, manipulating excited-state deactivation pathways in biocompatible dyes offers a universal way to systematically address these challenges. Our group has devoted considerable effort to achieving this goal. In this Account, we present and discuss our journey in optimizing excited-state energy-release pathways through regulating molecular charge transfer based on cyanine dyes, which are renowned for their exceptional photophysical properties and harmonious biocompatibility. The investigation begins with the introduction of amino groups in the meso position of a heptamethine cyanine dye, where the intramolecular charge transfer (ICT) effect causes a significant enlargement of the Stokes shift. Subsequently, ICT induced by introducing functional electron-deficient groups in cyanines is found to decrease the overlap of electron distribution or narrow the energy gaps of molecular frontier orbitals. Such modifications result in a reduction of the energy gaps between singlet and triplet states or an improvement in internal conversion, ultimately promoting phototherapy efficacy in both primary and distant tumors. Furthermore, with the intensification of the charge transfer effect aided by light, photoinduced intramolecular electron transfer occurs in some cyanines, leading to complete charge separation in the excited state. This process enhances the transition to the ground or triplet states, improving tumor phototherapy and inhibiting metastasis by increasing the PCE or the yield of reactive oxygen species, respectively. Shifting focus from intramolecular to intermolecular interactions, we successfully constructed and explored cyanines based on intermolecular charge transfer. These dyes, with excited-state dynamics mimicking natural photosynthesis, generate radicals and facilitate oxygen-independent hypoxic tumor PDT. Finally, we outlined the existing challenges and future directions for optimizing phototherapeutic efficacy by regulating molecular charge transfer. This Account provides molecular-level insights into improving phototherapeutic performance, offering valuable perspectives, and inspiring the development of functional dyes in other application fields.
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Affiliation(s)
- Xueze Zhao
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jianjun Du
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
- Ningbo Institute of Dalian University of Technology, No. 26 Yucai Road, 315016 Ningbo, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, School of Chemical Engineering, Dalian University of Technology, No. 2 Linggong Road, 116024 Dalian, China
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2
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Chu J, Ejaz A, Lin KM, Joseph MR, Coraor AE, Drummond DA, Squires AH. Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels. NATURE NANOTECHNOLOGY 2024; 19:1150-1157. [PMID: 38750166 PMCID: PMC11329371 DOI: 10.1038/s41565-024-01672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
Multiplexed, real-time fluorescence detection at the single-molecule level can reveal the stoichiometry, dynamics and interactions of multiple molecular species in mixtures and other complex samples. However, fluorescence-based sensing is typically limited to the detection of just 3-4 colours at a time due to low signal-to-noise ratio, high spectral overlap and the need to maintain the chemical compatibility of dyes. Here we engineered a palette of several dozen composite fluorescent labels, called FRETfluors, for multiplexed spectroscopic measurements at the single-molecule level. FRETfluors are compact nanostructures constructed from three chemical components (DNA, Cy3 and Cy5) with tunable spectroscopic properties due to variations in geometry, fluorophore attachment chemistry and DNA sequence. We demonstrate FRETfluor labelling and detection for low-concentration (<100 fM) mixtures of mRNA, dsDNA and proteins using an anti-Brownian electrokinetic trap. In addition to identifying the unique spectroscopic signature of each FRETfluor, this trap differentiates FRETfluors attached to a target from unbound FRETfluors, enabling wash-free sensing. Although usually considered an undesirable complication of fluorescence, here the inherent sensitivity of fluorophores to the local physicochemical environment provides a new design axis complementary to changing the FRET efficiency. As a result, the number of distinguishable FRETfluor labels can be combinatorically increased while chemical compatibility is maintained, expanding prospects for spectroscopic multiplexing at the single-molecule level using a minimal set of chemical building blocks.
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Affiliation(s)
- Jiachong Chu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Ayesha Ejaz
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
- Interdisicplinary Scientist Training Program, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Madeline R Joseph
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Aria E Coraor
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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3
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Chowdhury P, Lu ZY, Su SP, Liu MH, Lin CY, Wang MW, Luo YC, Lee YJ, Chiang HK, Chan YH. Ultrabright Dibenzofluoran-Based Polymer Dots with NIR-IIa Emission Maxima and Unusual Large Stokes Shifts for 3D Rotational Stereo Imaging. Adv Healthc Mater 2024; 13:e2400606. [PMID: 38683681 DOI: 10.1002/adhm.202400606] [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: 02/17/2024] [Revised: 04/23/2024] [Indexed: 05/02/2024]
Abstract
Emerging organic molecules with emissions in the second near-infrared (NIR-II) region are garnering significant attention. Unfortunately, achieving accountable organic emission intensity over the NIR-IIa (1300 nm) region faces challenges due to the intrinsic energy gap law. Up to the current stage, all reported organic NIR-IIa emitters belong to polymethine-based dyes with small Stokes shifts (<50 nm) and low quantum yield (QY; ≤0.015%). However, such polymethines have proved to cause self-absorption with constrained emission brightness, limiting advanced development in deep-tissue imaging. Here a new NIR-IIa scaffold based on rigid and highly conjugated dibenzofluoran core terminated by amino-containing moieties that reveal emission peaks of 1230-1305 nm is designed. The QY is at least 10 times higher than all synthesized or reported NIR-IIa polymethines with extraordinarily large Stokes shifts of 370-446 nm. DBF-BJ is further prepared as a polymer dot to demonstrate its in vivo 3D stereo imaging of mouse vasculature with a 1400 nm long-pass filter.
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Affiliation(s)
- Partha Chowdhury
- Department of Applied Chemistry/Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Zhao-Yu Lu
- Department of Applied Chemistry/Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Shih-Po Su
- Institute of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Meng-Huan Liu
- Department of Applied Chemistry/Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Chun-Yi Lin
- Department of Applied Chemistry/Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Man-Wen Wang
- Department of Applied Chemistry/Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Yi-Chi Luo
- Department of Applied Chemistry/Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Yi-Jang Lee
- Department of Biomedical Imaging and Radiological Sciences, School of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Huihua Kenny Chiang
- Institute of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Yang-Hsiang Chan
- Department of Applied Chemistry/Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu, 30050, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
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4
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Song Y, Liang C. H-bond engineering as a general strategy for inhibiting twisted intramolecular charge transfer in donor-acceptor fluorescent probes: Reshaping the pre-twisting method. Talanta 2024; 272:125770. [PMID: 38340393 DOI: 10.1016/j.talanta.2024.125770] [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: 12/24/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Twisted intramolecular charge transfer (TICT) is a fluorescence quenching mechanism that occurs in donor-acceptor (D‒A) molecules. Chemical engineering research into TICT regulation over the past 50 years has primarily focused on manipulating steric factors by introducing alkyl groups at the D-A junction (pre-twisting). Herein, we report a significant advance in TICT-based probes through the introducing of H-bond as an efficient strategy for suppressing TICT. Accordingly, ortho-Cl installation in the N-phenylpyrazine-2-carboxamide (PPC) platform can achieve complete reversal from the quenching mode to the light-up mode. This specific H-bonding (N-H⋯Cl) effectively blocks N-C(Ar) bond rotation, leading to fluorescence-ON. This suggested that TICT inhibition may be involved. Therefore, in a sharp contrast to the general nature of the pre-twisting method in rotor molecules, which involves incorporating steric hindrance at either the donor or acceptor moiety to enhance intramolecular rotation (promotion TICT), the ortho-H bonding strategy completely freezes D‒A bond twisting (suppression TICT), resulting in improved fluorescent intensity. Furthermore, the fluorophores were evaluated for Hg2+ detection and in vivo bio-imaging. Notably, Hg-complexation induced another fluorescence inversion (OFF-ON) by imposing spatial constraints on twisting freedom in 3,4-Cl-PPC. Taken together, this work provides a valid and generalizable tactic for the development of high-performance sensing fluorophores through inhibition of TICT.
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Affiliation(s)
- Yang Song
- College of Biology and Food, Shangqiu Normal University, Shangqiu, Henan, 476000, China; Henan Provincial Engineering Research Center for Development and Application of Characteristic Microorganism Resources, Shangqiu Normal University, Shangqiu, Henan, 476000, China.
| | - Chuan Liang
- Mental Health Education Center, Shangqiu Medical College, Shangqiu, Henan, 476000, China
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5
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Berndt D, Glaap D, Jennings T, Dose C, Werz DB, Reckert DNH. Water-Soluble Fluorescent Polymer Dyes with Tunable Emission Spectra for Flow Cytometry Applications. Angew Chem Int Ed Engl 2024; 63:e202402616. [PMID: 38488317 DOI: 10.1002/anie.202402616] [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: 02/05/2024] [Indexed: 04/04/2024]
Abstract
The application of spectrally unique, bright, and water-soluble fluorescent dyes is indispensable for the analysis of biological systems. Multiparameter flow cytometry is a powerful tool for characterization of mixed cell populations. To discriminate the different cell populations, they are typically stained by a set of fluorescent reagents, e.g., antibody-fluorophore conjugates. The number of parameters which can be studied simultaneously strongly depends on the availability of reagents which can be differentiated by their spectral properties. In this study a series of fluorescent polymer dyes was developed, that can be excited with a single violet laser (405 nm) but distinguished by their unique emission spectra. The polyfluorene-based polymers can be used on their own, or in combination with covalently bound small-molecule dyes to generate energy transfer constructs to red-shift the emission wavelength based on Förster resonance energy transfer (FRET). The polymer dyes were utilized in a biological flow cytometry assay by conjugating several of them to antibodies, demonstrating their effectiveness as reagents. This report represents the first systematic investigation of structure-property relationships for this type of fluorescent dyes.
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Affiliation(s)
- Daniel Berndt
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
- DFG Cluster of Excellence livMatS @FIT and Albert-Ludwigs-Universität Freiburg, Institut für Organische Chemie, Albertstraße 21, 79104, Freiburg, Germany
| | - Dorina Glaap
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Travis Jennings
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Christian Dose
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Daniel B Werz
- DFG Cluster of Excellence livMatS @FIT and Albert-Ludwigs-Universität Freiburg, Institut für Organische Chemie, Albertstraße 21, 79104, Freiburg, Germany
| | - Dirk N H Reckert
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
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Jiang G, Liu H, Liu H, Ke G, Ren TB, Xiong B, Zhang XB, Yuan L. Chemical Approaches to Optimize the Properties of Organic Fluorophores for Imaging and Sensing. Angew Chem Int Ed Engl 2024; 63:e202315217. [PMID: 38081782 DOI: 10.1002/anie.202315217] [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: 10/09/2023] [Indexed: 12/30/2023]
Abstract
Organic fluorophores are indispensable tools in cells, tissue and in vivo imaging, and have enabled much progress in the wide range of biological and biomedical fields. However, many available dyes suffer from insufficient performances, such as short absorption and emission wavelength, low brightness, poor stability, small Stokes shift, and unsuitable permeability, restricting their application in advanced imaging technology and complex imaging. Over the past two decades, many efforts have been made to improve these performances of fluorophores. Starting with the luminescence principle of fluorophores, this review clarifies the mechanisms of the insufficient performance for traditional fluorophores to a certain extent, systematically summarizes the modified approaches of optimizing properties, highlights the typical applications of the improved fluorophores in imaging and sensing, and indicates existing problems and challenges in this area. This progress not only proves the significance of improving fluorophores properties, but also provide a theoretical guidance for the development of high-performance fluorophores.
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Affiliation(s)
- Gangwei Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Han Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Hong Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Tian-Bing Ren
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Bin Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
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Fan F, Povedailo VA, Lysenko IL, Seviarynchyk TP, Sharko OL, Mazunin IO, Shmanai VV. Fluorescent Properties of Cyanine Dyes As a Matter of the Environment. J Fluoresc 2024; 34:925-933. [PMID: 37421567 DOI: 10.1007/s10895-023-03321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/16/2023] [Indexed: 07/10/2023]
Abstract
In non-viscous aqueous solutions, the cyanine fluorescent dyes Cy3 and Cy5 have rather low fluorescence efficiency (the fluorescence quantum yields of Cy3 and Cy5 are 0.04 and 0.3, respectively [1, 2]) and short excited state lifetimes due to their structural features. In this work, we investigated the effect of solubility and rotational degrees of freedom on the fluorescence efficiency of Cy3 and Cy5 in several ways. We compared the fluorescence efficiencies of two cyanine dyes sCy3 and sCy5 with the introduction of a sulfonyl substituent in the aromatic ring as well as covalently bound to T10 oligonucleotides. The results show that because of the different lengths of the polymethine chains between the aromatic rings of the dyes, cis-trans-isomerization has a much greater effect on the Cy3 molecule than on the Cy5 molecule, while the effect of aggregation is also significant.
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Affiliation(s)
- Fan Fan
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus
| | - Vladimir A Povedailo
- B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Nezavisimost' Ave., 220072, Minsk, Belarus
| | - Ivan L Lysenko
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus
| | - Tatsiana P Seviarynchyk
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus
| | - Olga L Sharko
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus
| | - Ilya O Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus.
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Chacko N, Motiei M, Suryakant JS, Firer M, Ankri R. Au nanodyes as enhanced contrast agents in wide field near infrared fluorescence lifetime imaging. DISCOVER NANO 2024; 19:18. [PMID: 38270794 PMCID: PMC10810770 DOI: 10.1186/s11671-024-03958-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
The near-infrared (NIR) range of the electromagnetic (EM) spectrum offers a nearly transparent window for imaging tissue. Despite the significant potential of NIR fluorescence-based imaging, its establishment in basic research and clinical applications remains limited due to the scarcity of fluorescent molecules with absorption and emission properties in the NIR region, especially those suitable for biological applications. In this study, we present a novel approach by combining the widely used IRdye 800NHS fluorophore with gold nanospheres (GNSs) and gold nanorods (GNRs) to create Au nanodyes, with improved quantum yield (QY) and distinct lifetimes. These nanodyes exhibit varying photophysical properties due to the differences in the separation distance between the dye and the gold nanoparticles (GNP). Leveraging a rapid and highly sensitive wide-field fluorescence lifetime imaging (FLI) macroscopic set up, along with phasor based analysis, we introduce multiplexing capabilities for the Au nanodyes. Our approach showcases the ability to differentiate between NIR dyes with very similar, short lifetimes within a single image, using the combination of Au nanodyes and wide-field FLI. Furthermore, we demonstrate the uptake of Au nanodyes by mineral-oil induced plasmacytomas (MOPC315.bm) cells, indicating their potential for in vitro and in vivo applications.
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Affiliation(s)
- Neelima Chacko
- Department of Physics, Faculty of Natural Science, Ariel University, 40700, Ariel, Israel
| | - Menachem Motiei
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Jadhav Suchita Suryakant
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, 40700, Ariel, Israel
| | - Michael Firer
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, 40700, Ariel, Israel
| | - Rinat Ankri
- Department of Physics, Faculty of Natural Science, Ariel University, 40700, Ariel, Israel.
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Martin A, Rivera-Fuentes P. A general strategy to develop fluorogenic polymethine dyes for bioimaging. Nat Chem 2024; 16:28-35. [PMID: 38012391 PMCID: PMC10774129 DOI: 10.1038/s41557-023-01367-y] [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: 02/06/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence imaging is an invaluable tool to study biological processes and further progress depends on the development of advanced fluorogenic probes that reach intracellular targets and label them with high specificity. Excellent fluorogenic rhodamine dyes have been reported, but they often require long and low-yielding syntheses, and are spectrally limited to the visible range. Here we present a general strategy to transform polymethine compounds into fluorogenic dyes using an intramolecular ring-closure approach. We illustrate the generality of this method by creating both spontaneously blinking and no-wash, turn-on polymethine dyes with emissions across the visible and near-infrared spectrum. These probes are compatible with self-labelling proteins and small-molecule targeting ligands, and can be combined with rhodamine-based dyes for multicolour and fluorescence lifetime multiplexing imaging. This strategy provides access to bright, fluorogenic dyes that emit at wavelengths that are more red-shifted compared with those of existing rhodamine-based dyes.
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Affiliation(s)
- Annabell Martin
- Department of Chemistry, University of Zurich, Zurich, Switzerland
- École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, Lausanne, Switzerland
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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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Archipowa N, Wittmann L, Köckenberger J, Ertl FJ, Gleixner J, Keller M, Heinrich MR, Kutta RJ. Characterization of Fluorescent Dyes Frequently Used for Bioimaging: Photophysics and Photocatalytical Reactions with Proteins. J Phys Chem B 2023; 127:9532-9542. [PMID: 37903729 DOI: 10.1021/acs.jpcb.3c04484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Derivatives of the rhodamine-based dye 5-TAMRA (5-carboxy-tetramethylrhodamine) and the indocarbocyanine-type Cy3B (cyclized derivative of the cyanine dye Cy3), both representing important fluorophores frequently used for the labeling of biomolecules (proteins, nucleic acids) and bioactive compounds, such as receptor ligands, were photophysically investigated in aqueous solution, i.e., in neat phosphate-buffered saline (PBS) and in PBS supplemented with 1 wt % bovine serum albumin (BSA). The dyes exhibit comparable absorption (λabs,max: 550-569 nm) and emission wavelengths (λem,max: 580-582 nm), and similar S1 lifetimes (2.27-2.75 ns), and their excited state deactivation proceeds mainly via the lowest excited singlet state (triplet quantum yield ca. 1%). However, the probes show marked differences with respect to their fluorescence quantum yield and photostability. While 5-TAMRA shows a lower quantum yield (37-39%) than the Cy3B derivative (ca. 57%), its photostability is considerably higher compared to Cy3B. Generally, the impact of the protein on the photophysics is low. However, on prolonged illumination, both fluorescent dyes undergo a photocatalytic reaction with tryptophan residues of BSA mediated by sensitized singlet oxygen resulting in a tryptophan photoproduct with an absorption maximum around 330 nm. The overall results of this work will assist in choosing the right dye for the labeling of bioactive compounds, and the study demonstrates that experiments performed with 5-TAMRA or Cy3B-labeled compounds in a biological environment may be influenced by photochemical modification of experimentally relevant proteins at aromatic amino acid residues.
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Affiliation(s)
- Nataliya Archipowa
- Institute of Biophysics and Physical Biochemistry, Faculty of Biology and Preclinical Medicine, University of Regensburg, D-93053 Regensburg, Germany
| | - Lukas Wittmann
- Institute of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Johannes Köckenberger
- Department of Chemistry and Pharmacy, Molecular and Clinical Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Fabian J Ertl
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Jakob Gleixner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Molecular and Clinical Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Roger Jan Kutta
- Institute of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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12
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He C, Wu CY, Li W, Xu K. Multidimensional Super-Resolution Microscopy Unveils Nanoscale Surface Aggregates in the Aging of FUS Condensates. J Am Chem Soc 2023; 145:24240-24248. [PMID: 37782826 PMCID: PMC10691933 DOI: 10.1021/jacs.3c08674] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remains unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here, we uncover nanoscale heterogeneities in FUS condensates and elucidate their evolution over aging. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SMdM), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems at the nanoscale.
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Affiliation(s)
- Changdong He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Chun Ying Wu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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13
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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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14
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He C, Wu CY, Li W, Xu K. Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548239. [PMID: 37503034 PMCID: PMC10369965 DOI: 10.1101/2023.07.12.548239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remain unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here we uncover nanoscale heterogeneities in the aging process of FUS condensates. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SM d M), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating nanoscale structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems.
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15
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Wei R, Dong Y, Wang X, Li J, Lei Z, Hu Z, Chen J, Sun H, Chen H, Luo X, Qian X, Yang Y. Rigid and Photostable Shortwave Infrared Dye Absorbing/Emitting beyond 1200 nm for High-Contrast Multiplexed Imaging. J Am Chem Soc 2023. [PMID: 37216464 DOI: 10.1021/jacs.3c00594] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The shortwave infrared (SWIR) spectral region beyond 1200 nm offers optimal tissue penetration depth and has broad potential in diagnosis, therapy, and surgery. Here, we devised a novel class of fluorochromic scaffold, i.e., a tetra-benzannulated xanthenoid (EC7). EC7 absorbs/emits maximally at 1204/1290 nm in CH2Cl2 and exhibits an unparalleled molar absorptivity of 3.91 × 105 cm-1 M-1 and high transparency to light at 400-900 nm. It also exhibited high resistance toward both photobleaching and symmetry breaking due to its unique structural rigidity. It is feasible for in vivo bioimaging and particularly suitable to couple with the shorter-wavelength analogues for high-contrast multiplexing. High-contrast dual-channel intraoperative imaging of the hepatobiliary system and three-channel in vivo imaging of the intestine, the stomach, and the vasculature were showcased. EC7 is a benchmark fluorochrome for facile biomedical exploitation of the SWIR region beyond 1200 nm.
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Affiliation(s)
- Ruwei Wei
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yan Dong
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jin Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zuhai Lei
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Zhangheng Road 826, Shanghai 201203, China
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Hao Chen
- Molecular Imaging Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiao Luo
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Youjun Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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16
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Zhang Y, Yang C, Peng S, Ling J, Chen P, Ma Y, Wang W, Chen Z, Chen C. General Strategy To Improve the Photon Budget of Thiol-Conjugated Cyanine Dyes. J Am Chem Soc 2023; 145:4187-4198. [PMID: 36756850 DOI: 10.1021/jacs.2c12635] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Maleimide-cysteine chemistry has been a routine practice for the site-specific labeling of fluorophores to proteins since the 1950s. This approach, however, cannot bring out the best photon budget of fluorophores. Here, we systematically measured the Cyanine3/5 dye conjugates via maleimide-thiol and amide linkages by counting the total emitted photons at the single-molecule level. While brightness and signal-to-noise ratios do not change significantly, dyes with thioether linkages exhibit more severe photobleaching than amide linkers. We then screened modern arylation-type bioconjugation strategies to alleviate this damage. Labeling thiols with phenyloxadiazole (POD) methyl sulfone, p-chloronitrobenzene, and fluorobenzene probes gave rise to electron-deficient aryl thioethers, effectively increasing the total emitted photons by 1.5-3 fold. Among the linkers, POD maintains labeling efficiency and specificity that are comparable to maleimide. Such an increase has proved to be universal among bulk and single-molecule assays, with or without triplet-state quenchers and oxygen scavengers, and on conformationally unrestricted or restricted cyanines. We demonstrated that cyanine-POD conjugates are general and superior fluorophores for thiol labeling in single-molecule FRET measurements of biomolecular conformational dynamics and in two-color STED nanoscopy using site-selectively labeled nanobodies. This work sheds light on the photobleaching mechanism of cyanines under single-molecule imaging while highlighting the interplay between the protein microenvironment, bioconjugation chemistry, and fluorophore photochemistry.
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Affiliation(s)
- Yuan Zhang
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Chen Yang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Sijia Peng
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Jing Ling
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng Chen
- PKU-Nanjing Institute of Translational Medicine, Nanjing 211800, China
| | - Yumiao Ma
- BSJ Institute, Beijing 100084, China
- Hangzhou Yanqu Information Technology Co., Ltd., Xihu District, Hangzhou City, Zhejiang Province 310003, China
| | - Wenjuan Wang
- School of Life Sciences, Technology Center for Protein Sciences, Tsinghua University, Beijing 100084, China
| | - Zhixing Chen
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- PKU-Nanjing Institute of Translational Medicine, Nanjing 211800, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
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17
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Barotov U, Arachchi DHT, Klein MD, Zhang J, Šverko T, Bawendi MG. Near-Unity Superradiant Emission from Delocalized Frenkel Excitons in a Two-Dimensional Supramolecular Assembly. ADVANCED OPTICAL MATERIALS 2023; 11:2201471. [PMID: 36846517 PMCID: PMC9957265 DOI: 10.1002/adom.202201471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Indexed: 06/18/2023]
Abstract
We demonstrate three general effective strategies to mitigate non-radiative losses in the superradiant emission from supramolecular assemblies. We focus on J-aggregates of 5,5',6,6'-tetrachloro-1,1'-diethyl-3,3'-di(4-sulfobutyl)-benzimidazolocarbocyanine (TDBC) and elucidate the nature of their nonradiative processes. We show that self-annealing at room temperature, photo-brightening, and the purification of the dye monomers all lead to substantial increases in emission quantum yields (QYs) and a concomitant lengthening of the emission lifetime, with purification of the monomers having the largest effect. We use structural and optical measurements to support a microscopic model that emphasizes the deleterious effects of a small number of impurity and defect sites that serve as non-radiative recombination centers. This understanding has yielded a room temperature molecular fluorophore in solution with an unprecedented combination of fast emissive lifetime and high QY. We obtain superradiant emission from J-aggregates of TDBC in solution at room temperature with a QY of 82% coupled with an emissive lifetime of 174 ps. This combination of high QY and fast lifetime at room temperature makes supramolecular assemblies of purified TDBC a model system for the study of fundamental superradiance phenomena. High QY J-aggregates are uniquely suited for the development of applications that require high speed and high brightness fluorophores such as devices for high speed optical communication.
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Affiliation(s)
- Ulugbek Barotov
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Dimuthu H. Thanippuli Arachchi
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Megan D. Klein
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Juanye Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Tara Šverko
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Moungi G. Bawendi
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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18
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Green CM, Spangler J, Susumu K, Stenger DA, Medintz IL, Díaz SA. Quantum Dot-Based Molecular Beacons for Quantitative Detection of Nucleic Acids with CRISPR/Cas(N) Nucleases. ACS NANO 2022; 16:20693-20704. [PMID: 36378103 DOI: 10.1021/acsnano.2c07749] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Strategies utilizing the CRISPR/Cas nucleases Cas13 and Cas12 have shown great promise in the development of highly sensitive and rapid diagnostic assays for the detection of pathogenic nucleic acids. The most common approaches utilizing fluorophore-quencher molecular beacons require strand amplification strategies or highly sensitive optical setups to overcome the limitations of the readout. Here, we demonstrate a flexible strategy for assembling highly luminescent and colorimetric quantum dot-nucleic acid hairpin (QD-HP) molecular beacons for use in CRISPR/Cas diagnostics. This strategy utilizes a chimeric peptide-peptide nucleic acid (peptide-PNA) to conjugate fluorescently labeled DNA or RNA hairpins to ZnS-coated QDs. QDs are particularly promising alternatives for molecular beacons due to their greater brightness, strong UV absorbance with large emission offset, exceptional photostability, and potential for multiplexing due to their sharp emission peaks. Using Förster resonance energy transfer (FRET), we have developed ratiometric reporters capable of pM target detection (without nucleotide amplification) for both target DNA and RNA, and we further demonstrated their capabilities for multiplexing and camera-phone detection. The flexibility of this system is imparted by the dual functionality of the QD as both a FRET donor and a central nanoscaffold for arranging nucleic acids and fluorescent acceptors on its surface. This method also provides a generalized approach that could be applied for use in other CRISPR/Cas nuclease systems.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Joseph Spangler
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
- Jacobs Corporation, Hanover, Maryland21076, United States
| | - David A Stenger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, 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
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
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19
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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20
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Choi AA, Park HH, Chen K, Yan R, Li W, Xu K. Displacement Statistics of Unhindered Single Molecules Show no Enhanced Diffusion in Enzymatic Reactions. J Am Chem Soc 2022; 144:4839-4844. [PMID: 35258969 PMCID: PMC8975259 DOI: 10.1021/jacs.1c12328] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent studies have sparked debate over whether catalytic reactions enhance the diffusion coefficients D of enzymes. Through high statistics of the transient (600 μs) displacements of unhindered single molecules freely diffusing in common buffers, we here quantify D for four enzymes under catalytic turnovers. We thus formulate how ∼ ±1% precisions may be achieved for D, and show no changes in diffusivity for catalase, urease, aldolase, and alkaline phosphatase under the application of wide concentration ranges of substrates. Our single-molecule approach thus overcomes potential limitations and artifacts underscored by recent studies to show no enhanced diffusion in enzymatic reactions.
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Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ha H. Park
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kun Chen
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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21
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
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22
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Caveat fluorophore: an insiders' guide to small-molecule fluorescent labels. Nat Methods 2022; 19:149-158. [PMID: 34949811 DOI: 10.1038/s41592-021-01338-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 11/01/2021] [Indexed: 01/20/2023]
Abstract
The last three decades have brought a revolution in fluorescence microscopy. The development of new microscopes, fluorescent labels and analysis techniques has pushed the frontiers of biological imaging forward, moving from fixed to live cells, from diffraction-limited to super-resolution imaging and from simple cell culture systems to experiments in vivo. The large and ever-evolving collection of tools can be daunting for biologists, who must invest substantial time and effort in adopting new technologies to answer their specific questions. This is particularly relevant when working with small-molecule fluorescent labels, where users must navigate the jargon, idiosyncrasies and caveats of chemistry. Here, we present an overview of chemical dyes used in biology and provide frank advice from a chemist's perspective.
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23
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Friedman HC, Cosco ED, Atallah TL, Jia S, Sletten EM, Caram JR. Establishing design principles for emissive organic SWIR chromophores from energy gap laws. Chem 2021; 7:3359-3376. [PMID: 34901520 PMCID: PMC8664240 DOI: 10.1016/j.chempr.2021.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rational design of bright near and shortwave infrared (NIR: 700-1000 SWIR: 1000- 2000 nm) emitters remains an open question with applications spanning imaging and photonics. Combining experiment and theory, we derive an energy gap quantum yield master equation (EQME), describing the fundamental limits in SWIR quantum yields (ϕ F ) for organic chromophores. Evaluating the photophysics of 21 polymethine NIR/SWIR chromophores to parameterize the EQME, we explain the precipitous decline of ϕ F past 900 nm through decreasing radiative rates and increasing nonradiative losses via high frequency vibrations relating to the energy gap. Using the EQME we develop an energy gap independent ϕ F NIR/SWIR chromophore comparison metric. We show electron donating character on polymethine heterocycles results in relative increases in radiative efficiency obscured by a simultaneous redshift. Finally, the EQME yields rational chromophore design insights shown by how deuteration (backed by our experimental results) or molecular aggregation increases SWIR ϕ F .
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Affiliation(s)
- Hannah C Friedman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Emily D Cosco
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305 USA
| | - Timothy L Atallah
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
- Department of Chemistry and Biochemistry, Denison University, 500 West Loop, Granville, Ohio 43023
| | - Shang Jia
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
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24
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Wang C, Chi W, Qiao Q, Tan D, Xu Z, Liu X. Twisted intramolecular charge transfer (TICT) and twists beyond TICT: from mechanisms to rational designs of bright and sensitive fluorophores. Chem Soc Rev 2021; 50:12656-12678. [PMID: 34633008 DOI: 10.1039/d1cs00239b] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The twisted intramolecular charge transfer (TICT) mechanism has guided the development of numerous bright and sensitive fluorophores. This review briefly overviews the history of establishing the TICT mechanism, and systematically summarizes the molecular design strategies in modulating the TICT tendency of various organic fluorophores towards different applications, along with key milestone studies and representative examples. Additionally, we also succinctly review the twisted intramolecular charge shuttle (TICS) and twists during photoinduced electron transfer (PET), and compare their similarities and differences with TICT, with emphasis on understanding the structure-property relationships between the twisted geometries and how they can directly affect the fluorescence of the molecules. Such structure-property relationships presented herein will greatly aid the rational development of fluorophores that involve molecular twisting in the excited state.
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Affiliation(s)
- Chao Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China. .,Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore.
| | - Weijie Chi
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore.
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Davin Tan
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore.
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore.
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25
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Zhao X, Yao Q, Long S, Chi W, Yang Y, Tan D, Liu X, Huang H, Sun W, Du J, Fan J, Peng X. An Approach to Developing Cyanines with Simultaneous Intersystem Crossing Enhancement and Excited-State Lifetime Elongation for Photodynamic Antitumor Metastasis. J Am Chem Soc 2021; 143:12345-12354. [PMID: 34323480 DOI: 10.1021/jacs.1c06275] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heavy-atom-based photosensitizers usually exhibit shortened triplet-state lifetimes, which is not ideal for hypoxic tumor photodynamic therapy. Although several heavy-atom-free photosensitizers possess long triplet-state lifetimes, the clinical applicability is limited by their short excitation wavelengths, poor photon capture abilities, and intrinsically hydrophobic structures. Herein we developed a novel NIR heavy-atom-free photosensitizer design strategy by introducing sterically bulky and electron-rich moieties at the meso position of the pentamethine cyanine (Cy5) skeleton, which simultaneously enhanced intersystem crossing (ISC) and prolonged excited-state lifetime. We found that the 1O2 generation ability is directly correlated to the electron-donating ability of the meso substituent in cyanine, and the excited-state lifetime was simultaneously much elongated when the substituents were anthracene derivatives substituted at the 9-position. Our star compound, ANOMe-Cy5, exhibits intense NIR absorption, the highest 1O2 quantum yield (4.48-fold higher than Cy5), the longest triplet-state lifetime (9.80-fold longer than Cy5), and lossless emission intensity (nearly no change compared with Cy5). Such excellent photophysical properties coupled with its inherently cationic and hydrophilic nature enable the photosensitizer to realize photoablation of solid tumor and antitumor lung metastasis. This study highlights the design of a new generation of NIR photosensitizers for imaging-guided photodynamic cancer treatment.
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Affiliation(s)
- Xueze Zhao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Qichao Yao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Saran Long
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Weijie Chi
- Fluorescence Research Group, Singapore University of Technology and Design, 487372, Singapore
| | - Yuxin Yang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Davin Tan
- Fluorescence Research Group, Singapore University of Technology and Design, 487372, Singapore
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 487372, Singapore
| | - Haiqiao Huang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.,Ningbo Institute of Dalian University of Technology, Dalian University of Technology, Ningbo 315016, China
| | - Jianjun Du
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.,Ningbo Institute of Dalian University of Technology, Dalian University of Technology, Ningbo 315016, China
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.,Ningbo Institute of Dalian University of Technology, Dalian University of Technology, Ningbo 315016, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.,Shenzhen Research Institute, Dalian University of Technology, Shenzhen 518057, China
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26
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Yang Z, Xu H, Wang J, Chen W, Zhao M. Single-Molecule Fluorescence Techniques for Membrane Protein Dynamics Analysis. APPLIED SPECTROSCOPY 2021; 75:491-505. [PMID: 33825543 DOI: 10.1177/00037028211009973] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorescence-based single-molecule techniques, mainly including fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence resonance energy transfer (smFRET), are able to analyze the conformational dynamics and diversity of biological macromolecules. They have been applied to analysis of the dynamics of membrane proteins, such as membrane receptors and membrane transport proteins, due to their superior ability in resolving spatio-temporal heterogeneity and the demand of trace amounts of analytes. In this review, we first introduced the basic principle involved in FCS and smFRET. Then we summarized the labeling and immobilization strategies of membrane protein molecules, the confocal-based and TIRF-based instrumental configuration, and the data processing methods. The applications to membrane protein dynamics analysis are described in detail with the focus on how to select suitable fluorophores, labeling sites, experimental setup, and analysis methods. In the last part, the remaining challenges to be addressed and further development in this field are also briefly discussed.
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Affiliation(s)
- Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Haiqi Xu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
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27
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Glazier R, Shinde P, Ogasawara H, Salaita K. Spectroscopic Analysis of a Library of DNA Tension Probes for Mapping Cellular Forces at Fluid Interfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:2145-2164. [PMID: 33417432 DOI: 10.1021/acsami.0c09774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Oligonucleotide-based probes offer the highest spatial resolution, force sensitivity, and molecular specificity for cellular tension sensing and have been developed to measure a variety of molecular forces mediated by individual receptors in T cells, platelets, fibroblasts, B-cells, and immortalized cancer cell lines. These fluorophore-oligonucleotide conjugate probes are designed with a stem-loop structure that engages cell receptors and reversibly unfolds due to mechanical strain. With the growth of recent work bridging molecular mechanobiology and biomaterials, there is a need for a detailed spectroscopic analysis of DNA tension probes that are used for cellular imaging. In this manuscript, we conducted an analysis of 19 DNA hairpin-based tension probe variants using molecular dynamics simulations, absorption spectroscopy, and fluorescence imaging (epifluorescence and fluorescence lifetime imaging microscopy). We find that tension probes are highly sensitive to their molecular design, including donor and acceptor proximity and pairing, DNA stem-loop structure, and conjugation chemistry. We demonstrate the impact of these design features using a supported lipid bilayer model of podosome-like adhesions. Finally, we discuss the requirements for tension imaging in various biophysical contexts and offer a series of experimental recommendations, thus providing a guide for the design and application of DNA hairpin-based molecular tension probes.
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Affiliation(s)
- Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Pushkar Shinde
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hiroaki Ogasawara
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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28
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Andronov L, Vonesch JL, Klaholz BP. Practical Aspects of Super-Resolution Imaging and Segmentation of Macromolecular Complexes by dSTORM. Methods Mol Biol 2021; 2247:271-286. [PMID: 33301123 DOI: 10.1007/978-1-0716-1126-5_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Super-resolution fluorescence microscopy allows imaging macromolecular complexes down to the nanoscopic scale and thus is a great tool to combine and integrate cellular imaging in the native cellular environment with structural analysis by X-ray crystallography or high-resolution cryo electron microscopy or tomography. Here we describe practical aspects of SMLM imaging by dSTORM, from the initial sample preparation using mounting media, antibodies and fluorescent markers, the experimental setup for data acquisition including multi-color colocalization and 3D data acquisition, and finally tips and clues on advanced data processing that includes image reconstruction and data segmentation using 2D or 3D clustering methods. This approach opens the path toward multi-resolution integration in cellular structural biology.
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Affiliation(s)
- Leonid Andronov
- Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, Illkirch, France
| | - Jean-Luc Vonesch
- Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, Illkirch, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, Illkirch, France.
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29
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Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020; 25:molecules25225369. [PMID: 33212871 PMCID: PMC7698394 DOI: 10.3390/molecules25225369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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30
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Stainer S, Reisetbauer S, Ahiable JEA, Ebner L, Zhu R, Reindl D, Körmöczi GF, Ebner A. Single molecule distribution of RhD binding epitopes on ultraflat erythrocyte ghosts. NANOSCALE 2020; 12:22097-22106. [PMID: 33118583 DOI: 10.1039/d0nr04393a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Rh blood group system plays a key role in transfusion and organ transplant medicine. The complex transmembrane Rh polypeptides RhD and RhCE carry numerous antigens, including the extremely immunogenic D antigen. The Rh polypeptides form multimolecular Rh complexes with certain transmembrane and skeletal proteins, with so far only incompletely understood physiological functions. Determination of the energy landscape of individual Rh binding epitopes towards their specific interaction partners as well as their localization across the red blood cell (RBC) membrane requires single molecule approaches including large area high resolution recognition imaging. Atomic force microscopy based molecular recognition force spectroscopy in combination with single molecule recognition imaging fulfills these requirements. For unbiased single molecule results, nano-mechanical influences due to cell elasticity have to be eliminated. This is realized by generation of ultra flat erythrocyte ghosts on a solid support. We developed a protocol for the preparation of complete ultraflat erythrocyte ghosts and determined the molecular binding behaviour of different anti-D antibodies towards their binding epitopes on RhD positive and negative erythrocytes. Performing optimized topography and recognition imaging at 16 Mpixel resolution allowed localisation of individual RhD molecules at the single molecule level across an entire RBC. A map of Rh antigens across integer ultraflat RBC ghosts was generated with nanometer resolution. Here we show a homogeneous distribution on rim and dimple regions with comparable receptor densities. Furthermore, differences in the energy landscape between specific monoclonal antibodies were determined at the single molecule level.
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Affiliation(s)
- Sarah Stainer
- Molecular Biosensing group, Institute of Biophysics, Johannes Kepler University Linz, Austria.
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31
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Juvekar V, Lim CS, Lee DJ, Park SJ, Song GO, Kang H, Kim HM. An azo dye for photodynamic therapy that is activated selectively by two-photon excitation. Chem Sci 2020; 12:427-434. [PMID: 34163605 PMCID: PMC8178981 DOI: 10.1039/d0sc05686c] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Two-photon photodynamic therapy (TP-PDT) is a promising approach for the treatment of cancer because of its better penetration depth and superior spatial selectivity. Here, we describe an azo group containing cyclized-cyanine derivatives (ACC1 and ACC2) as a two-photon activated, type I based photosensitizer (PS). These small-molecule and heavy atom-free organic dyes showed marked reactive oxygen species (ROS)-generating ability under physiological conditions, as well as fast loading ability into the cells and negligible dark toxicity. Live cell analyses with one- and two-photon microscopy revealed that these dyes showed higher ROS generation ability upon two-photon excitation than upon one-photon excitation via the type I process. The PSs have superior PDT properties compared to conventional Visudyne and 5-ALA under mild conditions. These characteristics allowed for precise PDT at the target region in mimic tumor spheroids, demonstrating that the developed TP PS could be useful in efficient PDT applications and in designing various PSs. Azo containing dyes as a two-photon selective and type I based photosensitizers (PSs) were developed that exhibit excellent photodynamic therapy properties under mild condition.![]()
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Affiliation(s)
- Vinayak Juvekar
- Department of Chemistry, Department of Energy Systems Research, Ajou University Suwon 443-749 South Korea
| | - Chang Su Lim
- Department of Chemistry, Department of Energy Systems Research, Ajou University Suwon 443-749 South Korea
| | - Dong Joon Lee
- Department of Energy Systems Research, Ajou University Suwon 443-749 South Korea
| | - Sang Jun Park
- Department of Energy Systems Research, Ajou University Suwon 443-749 South Korea
| | - Gyeong Ok Song
- Department of Energy Systems Research, Ajou University Suwon 443-749 South Korea
| | - Hyuk Kang
- Department of Chemistry, Department of Energy Systems Research, Ajou University Suwon 443-749 South Korea
| | - Hwan Myung Kim
- Department of Chemistry, Department of Energy Systems Research, Ajou University Suwon 443-749 South Korea .,Department of Energy Systems Research, Ajou University Suwon 443-749 South Korea
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32
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Kang J, Lhee S, Lee JK, Zare RN, Nam HG. Restricted intramolecular rotation of fluorescent molecular rotors at the periphery of aqueous microdroplets in oil. Sci Rep 2020; 10:16859. [PMID: 33033365 PMCID: PMC7545199 DOI: 10.1038/s41598-020-73980-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/17/2020] [Indexed: 01/14/2023] Open
Abstract
Fluorescent molecular rotor dyes, including Cy3, Cy5, and Alexa Fluor 555, dissolved in micron-sized aqueous droplets (microdroplets) in oil were excited, and the fluorescence intensity was recorded as function of time. We observed lengthening of the fluorescence lifetime of these dyes at the water-oil periphery, which extended several microns inward. This behavior shows that intramolecular rotation is restricted at and near the microdroplet interface. Lengthened lifetimes were observed in water microdroplets but not in microdroplets composed of organic solvents. This lifetime change was relatively insensitive to added glycerol up to 60%, suggesting that solution viscosity is not the dominant mechanism. These restricted intramolecular rotations at and near the microdroplet periphery are consistent with the reduced entropy observed in chemical reactions in microdroplets compared to the same reaction conditions in bulk solution and helps us further understand why microdroplet chemistry differs so markedly from bulk-phase chemistry.
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Affiliation(s)
- Jooyoun Kang
- Center for Plant Aging Research, Institute for Basic Science, Daegu, 42988, Republic of Korea.,Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - SangMoon Lhee
- Center for Plant Aging Research, Institute for Basic Science, Daegu, 42988, Republic of Korea
| | - Jae Kyoo Lee
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science, Daegu, 42988, Republic of Korea. .,Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
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33
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Raducanu VS, Isaioglou I, Raducanu DV, Merzaban JS, Hamdan SM. Simplified detection of polyhistidine-tagged proteins in gels and membranes using a UV-excitable dye and a multiple chelator head pair. J Biol Chem 2020; 295:12214-12223. [PMID: 32647010 PMCID: PMC7443479 DOI: 10.1074/jbc.ra120.014132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/29/2020] [Indexed: 12/22/2022] Open
Abstract
The polyhistidine tag (His-tag) is one of the most popular protein tags used in the life sciences. Traditionally, the detection of His-tagged proteins relies on immunoblotting with anti-His antibodies. This approach is laborious for certain applications, such as protein purification, where time and simplicity are critical. The His-tag can also be directly detected by metal ion-loaded nickel-nitrilotriacetic acid-based chelator heads conjugated to fluorophores, which is a convenient alternative method to immunoblotting. Typically, such chelator heads are conjugated to either green or red fluorophores, the detection of which requires specialized excitation sources and detection systems. Here, we demonstrate that post-run staining is ideal for His-tag detection by metal ion-loaded and fluorescently labeled chelator heads in PAGE and blot membranes. Additionally, by comparing the performances of different chelator heads, we show how differences in microscopic affinity constants translate to macroscopic differences in the detection limits in environments with limited diffusion, such as PAGE. On the basis of these results, we devise a simple approach, called UVHis-PAGE, that uses metal ion-loaded and fluorescently labeled chelator heads to detect His-tagged proteins in PAGE and blot membranes. Our method uses a UV transilluminator as an excitation source, and the results can be visually inspected by the naked eye.
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Affiliation(s)
- Vlad-Stefan Raducanu
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ioannis Isaioglou
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Daniela-Violeta Raducanu
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jasmeen S Merzaban
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Samir M Hamdan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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34
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Lelle M, Otte M, Bonus M, Gohlke H, Benndorf K. Fluorophore-Labeled Cyclic Nucleotides as Potent Agonists of Cyclic Nucleotide-Regulated Ion Channels. Chembiochem 2020; 21:2311-2320. [PMID: 32227403 PMCID: PMC7497086 DOI: 10.1002/cbic.202000116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/26/2020] [Indexed: 12/22/2022]
Abstract
High-affinity fluorescent derivatives of cyclic adenosine and guanosine monophosphate are powerful tools for investigating their natural targets. Cyclic nucleotide-regulated ion channels belong to these targets and are vital for many signal transduction processes, such as vision and olfaction. The relation of ligand binding to activation gating is still challenging, and there is a need for fluorescent probes that enable the process to be broken down to the single-molecule level. This inspired us to prepare fluorophore-labeled cyclic nucleotides, which are composed of a bright dye and a nucleotide derivative with a thiophenol motif at position 8 that has already been shown to enable superior binding affinity. These bioconjugates were prepared by a novel cross-linking strategy that involves substitution of the nucleobase with a modified thiophenolate in good yield. Both fluorescent nucleotides are potent activators of different cyclic nucleotide-regulated ion channels with respect to the natural ligand and previously reported substances. Molecular docking of the probes excluding the fluorophore reveals that the high potency can be attributed to additional hydrophobic and cation-π interactions between the ligand and the protein. Moreover, the introduced substances have the potential to investigate related target proteins, such as cAMP- and cGMP-dependent protein kinases, exchange proteins directly activated by cAMP or phosphodiesterases.
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Affiliation(s)
- Marco Lelle
- Institute of Physiology IIUniversity Hospital JenaKollegiengasse 907743JenaGermany
| | - Maik Otte
- Institute of Physiology IIUniversity Hospital JenaKollegiengasse 907743JenaGermany
| | - Michele Bonus
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstrasse 140225DüsseldorfGermany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstrasse 140225DüsseldorfGermany
- John von Neumann Institute for Computing (NIC)Jülich Supercomputing Centre (JSC) andInstitute of Biological Information Processing (IBI-7: Structural Biochemistry)Forschungszentrum Jülich GmbHWilhelm-Johnen-Strasse52425JülichGermany
| | - Klaus Benndorf
- Institute of Physiology IIUniversity Hospital JenaKollegiengasse 907743JenaGermany
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35
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Allikalt A, Laasfeld T, Ilisson M, Kopanchuk S, Rinken A. Quantitative analysis of fluorescent ligand binding to dopamine D 3 receptors using live-cell microscopy. FEBS J 2020; 288:1514-1532. [PMID: 32783364 DOI: 10.1111/febs.15519] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 12/29/2022]
Abstract
Dopamine receptors are G protein-coupled receptors that have several essential functions in the central nervous system. A better understanding of the regulatory mechanisms of ligand binding to the receptor may open new possibilities to affect the downstream signal transduction pathways. The majority of the available ligand binding assays use either membrane preparations, cell suspensions, or genetically modified receptors, which may give at least partially incorrect understanding of ligand binding. In this study, we implemented an assay combining fluorescence and bright-field microscopy to measure ligand binding to dopamine D3 receptors in live mammalian cells. For membrane fluorescence intensity quantification from microscopy images, we developed a machine learning-based user-friendly software membrane tools and incorporated it into a data management software aparecium that has been previously developed in our workgroup. For the experiments, a fluorescent ligand NAPS-Cy3B was synthesized by conjugating a dopaminergic antagonist N-(p-aminophenethyl)spiperone with a fluorophore Cy3B. The subnanomolar affinity of NAPS-Cy3B makes it a suitable ligand for the characterization of D3 receptors in live HEK293 cells. Using a microplate compatible automated widefield fluorescence microscope, together with the membrane tools software, enables the detection and quantification of ligand binding with a high-throughput. The live cell assay is suitable for the characterization of fluorescent ligand binding and also in the competition experiments for the screening of novel unlabeled dopaminergic ligands. We propose that this simple yet more native-like approach is feasible in GPCR research, as it enables the detection of ligand binding in an environment containing more components involved in the signal transduction cascade.
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Affiliation(s)
- Anni Allikalt
- Institute of Chemistry, University of Tartu, Estonia.,Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nürnberg, Germany
| | | | | | | | - Ago Rinken
- Institute of Chemistry, University of Tartu, Estonia
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36
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Kitajima N, Takikawa K, Sekiya H, Satoh K, Asanuma D, Sakamoto H, Takahashi S, Hanaoka K, Urano Y, Namiki S, Iino M, Hirose K. Real-time in vivo imaging of extracellular ATP in the brain with a hybrid-type fluorescent sensor. eLife 2020; 9:e57544. [PMID: 32648544 PMCID: PMC7398694 DOI: 10.7554/elife.57544] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Adenosine 5' triphosphate (ATP) is a ubiquitous extracellular signaling messenger. Here, we describe a method for in-vivo imaging of extracellular ATP with high spatiotemporal resolution. We prepared a comprehensive set of cysteine-substitution mutants of ATP-binding protein, Bacillus FoF1-ATP synthase ε subunit, labeled with small-molecule fluorophores at the introduced cysteine residue. Screening revealed that the Cy3-labeled glutamine-105 mutant (Q105C-Cy3; designated ATPOS) shows a large fluorescence change in the presence of ATP, with submicromolar affinity, pH-independence, and high selectivity for ATP over ATP metabolites and other nucleotides. To enable in-vivo validation, we introduced BoNT/C-Hc for binding to neuronal plasma membrane and Alexa Fluor 488 for ratiometric measurement. The resulting ATPOS complex binds to neurons in cerebral cortex of living mice, and clearly visualized a concentrically propagating wave of extracellular ATP release in response to electrical stimulation. ATPOS should be useful to probe the extracellular ATP dynamics of diverse biological processes in vivo.
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Grants
- 17H04029 Ministry of Education, Culture, Sports, Science, and Technology
- 17K08584 Ministry of Education, Culture, Sports, Science, and Technology
- JPMJPR17P1 Japan Science and Technology Agency
- 19K22247 Ministry of Education, Culture, Sports, Science, and Technology
- 25221304 Ministry of Education, Culture, Sports, Science, and Technology
- 18K14915 Ministry of Education, Culture, Sports, Science, and Technology
- 17H04764 Ministry of Education, Culture, Sports, Science, and Technology
- 18H04726 Ministry of Education, Culture, Sports, Science, and Technology
- 19K16251 Ministry of Education, Culture, Sports, Science, and Technology
- 18H04609 Ministry of Education, Culture, Sports, Science, and Technology
- 19H05414 Ministry of Education, Culture, Sports, Science, and Technology
- Takeda Science Foundation
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Affiliation(s)
- Nami Kitajima
- Department of Pharmacology, Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Kenji Takikawa
- Department of Pharmacology, Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Hiroshi Sekiya
- Department of Physiology, Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Kaname Satoh
- Department of Pharmacology, Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Daisuke Asanuma
- Department of Pharmacology, Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Hirokazu Sakamoto
- Department of Pharmacology, Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Shodai Takahashi
- Graduate School of Pharmaceutical Sciences, The University of TokyoTokyoJapan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of TokyoTokyoJapan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of TokyoTokyoJapan
- Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Shigeyuki Namiki
- Department of Pharmacology, Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Masamitsu Iino
- Department of Cellular and Molecular Pharmacology, Nihon University School of MedicineTokyoJapan
| | - Kenzo Hirose
- Department of Pharmacology, Graduate School of Medicine, The University of TokyoTokyoJapan
- International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of TokyoTokyoJapan
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37
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Sobek J, Schmidt M, Grossmann J, Rehrauer H, Schmidt L, Schlapbach R. Single-molecule chemistry. Part I: monitoring oxidation of G in oligonucleotides using CY3 fluorescence. Methods Appl Fluoresc 2020; 8:035010. [PMID: 32428873 DOI: 10.1088/2050-6120/ab947d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule hybridisation of CY3 dye labelled short oligonucleotides to surface immobilised probes was investigated in zero-mode waveguide nanostructures using a modified DNA sequencer. At longer measuring times, we observed changes of the initial hybridisation fluorescence pulse pattern which we attribute to products created by chemical reactions at the nucleobases. The origin is a charge separated state created by a photoinduced electron transfer from nucleobases to the dye followed by secondary reactions with oxygen and water, respectively. The positive charge can migrate through the hybrid resulting in base modifications at distant sites. Static fluorescence spectra were recorded in order to determine the properties of CY3 stacking to different base pairs, and compared to pulse intensities. A characteristic pulse pattern change was assigned to the oxidation of G to 8-oG besides the formation of a number of secondary products that are not yet identified. Further, we present a method to visualise the degree of chemical reactions to gain an overview of ongoing processes. Our study demonstrates that CY3 is able to oxidise nucleobases in ds DNA, and also in ss overhangs. An important finding is the correlation between nucleobase oxidation potential and fluorescence quenching which explains the intensity changes observed in single molecule measurements. The analysis of fluorescence traces provides the opportunity to track complete and coherent reaction sequences enabling to follow the fate of a single molecule over a long period of time, and to observe chemical reactions in real-time. This opens up the opportunity to analyse reaction pathways, to detect new products and short-lived intermediates, and to investigate rare events due to the large number of single molecules observed in parallel.
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Affiliation(s)
- Jens Sobek
- Functional Genomics Center Zurich, Eidgenössische Technische Hochschule (ETH) Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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38
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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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39
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Matikonda SS, Götz R, McLaughlin R, Sauer M, Schnermann MJ. Conformationally restrained pentamethine cyanines and use in reductive single molecule localization microscopy. Methods Enzymol 2020; 641:225-244. [PMID: 32713524 PMCID: PMC10759545 DOI: 10.1016/bs.mie.2020.04.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pentamethine cyanines are a class of far-red fluorophores that find extensive use in single-molecule localization microscopy (SMLM), as well as a broad range of other techniques. A drawback of this scaffold is its relatively low quantum yields, which is due to excited state deactivation via trans-to-cis chromophore isomerization. Here we describe a synthetic strategy to improve the photon output of these molecules. In the key synthetic transformation, a protected dialdehyde precursor undergoes a cascade reaction that forms a tetracyclic ring system. The resulting conformationally restrained analogs exhibit improved fluorescence quantum yield and extended fluorescence lifetimes. These properties, together with their ability to efficiently recover from hydride reduction, enable a uniquely simple form of single-molecule localization microscopy (SMLM).
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Affiliation(s)
- Siddharth S Matikonda
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Ralph Götz
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University Würzburg, Würzburg, Germany
| | - Ryan McLaughlin
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University Würzburg, Würzburg, Germany
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States.
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40
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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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41
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Ankri R, Basu A, Ulku AC, Bruschini C, Charbon E, Weiss S, Michalet X. Single-Photon, Time-Gated, Phasor-Based Fluorescence Lifetime Imaging through Highly Scattering Medium. ACS PHOTONICS 2020; 7:68-79. [PMID: 35936550 PMCID: PMC9355389 DOI: 10.1021/acsphotonics.9b00874] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Fluorescence lifetime imaging (FLI) is increasingly recognized as a powerful tool for biochemical and cellular investigations, including in vivo applications. Fluorescence lifetime is an intrinsic characteristic of any fluorescent dye which, to a large extent, does not depend on excitation intensity and signal level. In particular, it allows distinguishing dyes with similar emission spectra, offering additional multiplexing capabilities. However, in vivo FLI in the visible range is complicated by the contamination by (i) tissue autofluorescence, which decreases contrast, and by (ii) light scattering and absorption in tissues, which significantly reduce fluorescence intensity and modify the temporal profile of the signal. Here, we demonstrate how these issues can be accounted for and overcome, using a new time-gated single-photon avalanche diode array camera, SwissSPAD2, combined with phasor analysis to provide a simple and fast visual method for lifetime imaging. In particular, we show how phasor dispersion increases with increasing scattering and/or decreasing fluorescence intensity. Next, we show that as long as the fluorescence signal of interest is larger than the phantom autofluorescence, the presence of a distinct lifetime can be clearly identified with appropriate background correction. We use these results to demonstrate the detection of A459 cells expressing the fluorescent protein mCyRFP1 through highly scattering and autofluorescent phantom layers. These results showcase the possibility to perform FLI in challenging conditions, using standard, bright, visible fluorophore or fluorescence proteins.
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Affiliation(s)
- Rinat Ankri
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
- Corresponding Authors:.
| | - Arkaprabha Basu
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Arin Can Ulku
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Claudio Bruschini
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Edoardo Charbon
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
- Corresponding Authors:.
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42
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Qian K, Qu C, Ma X, Chen H, Kandawa-Schulz M, Song W, Miao W, Wang Y, Cheng Z. Tuning the near infrared II emitting wavelength of small molecule dyes by single atom alteration. Chem Commun (Camb) 2019; 56:523-526. [PMID: 31821402 DOI: 10.1039/c9cc08434g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A series of small molecule dyes demonstrate the feasibility of manipulating Near Infrared II emission by simply altering the donors' heteroatoms, which involved both electronegativity and intramolecular steric effects. Furthermore, these dyes show high resolution and stability for in vivo imaging after being complexed with human serum albumin.
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Affiliation(s)
- Kun Qian
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China. and Molecular Imaging Program at Stanford (MIPS), Bio-X Program, and Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, California, 94305-5344, USA.
| | - Chunrong Qu
- Molecular Imaging Program at Stanford (MIPS), Bio-X Program, and Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, California, 94305-5344, USA.
| | - Xiangyu Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Hao Chen
- Molecular Imaging Program at Stanford (MIPS), Bio-X Program, and Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, California, 94305-5344, USA.
| | | | - Wei Song
- Department of Chemistry and Biochemistry, University of Namibia, Windhoek, Namibia
| | - Weimin Miao
- Jiangsu Meizhong Medical Technology Co., Ltd, Nantong, China
| | - Yihong Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Zhen Cheng
- Molecular Imaging Program at Stanford (MIPS), Bio-X Program, and Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, California, 94305-5344, USA.
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43
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Robust evaluation of intermolecular FRET using a large Stokes shift fluorophore as a donor. Biotechniques 2019; 65:211-218. [PMID: 30284937 DOI: 10.2144/btn-2018-0041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fluorescence (or Förster) resonance energy transfer (FRET) is a straightforward and sensitive technique to evaluate molecular interactions. However, most of the popular FRET pairs suffer cross-excitation of the acceptor, which could lead to false positives. To overcome this problem, we selected a large Stokes shift (LSS) fluorophore as a FRET donor. As a successful example, we employed a new FRET pair mAmetrine (an LSS yellow fluorescence protein)/DY-547 (a cyanine derivative) to substitute CFP/fluorescein that we previously employed to study molecular interactions between cyclic nucleotide-binding domains and cyclic nucleotides. The new FRET pair is practically free of cross-excitation of the acceptor. Namely, a change in the fluorescence spectral shape implies evidence of FRET without other control experiments.
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44
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Viirlaid E, Ilisson M, Kopanchuk S, Mäeorg U, Rinken A, Rinken T. Immunoassay for rapid on-site detection of glyphosate herbicide. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:507. [PMID: 31342281 DOI: 10.1007/s10661-019-7657-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Glyphosate is the most widespread herbicide and its global use is steadily increasing. Although glyphosate is considered to have low toxicity, its wide application has raised concerns about its effects on human health. The extensive use of glyphosate has risen a need of its continuous monitoring in drinking and surface waters to assure in accordance with the set standards. Within the present study, we have developed a novel assay for the on-site detection of glyphosate by combining flow-through technology with the high specificity of immunorecognition. The proposed biosensing system was based on the detection of fluorescence signal generated by the quantitative replacement of glyphosate in antigen-antibody complex with IgY-type anti-glyphosate antibodies on microbeads by synthetic 5-carboxytetramethylrhodamine (5-TAMRA) conjugated glyphosate. The working range of this assay was in low millimolar range and the time required for glyphosate detection around 0.5 h. The applicability of the immunoassay for glyphosate detection in surface water was tested and the biosensor results were validated with high-performance liquid chromatography.
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Affiliation(s)
- E Viirlaid
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia.
| | - M Ilisson
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - S Kopanchuk
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - U Mäeorg
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - A Rinken
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
| | - T Rinken
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411, Tartu, Estonia
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45
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Usama SM, Thompson T, Burgess K. Productive Manipulation of Cyanine Dye π-Networks. Angew Chem Int Ed Engl 2019; 58:8974-8976. [PMID: 31124257 DOI: 10.1002/anie.201902956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/02/2019] [Indexed: 11/08/2022]
Abstract
Polymethine bridges in cyanine dyes may be constrained by setting them into edge-fused ring systems, or extended by conjugation with carefully chosen heterocycles. Recent studies have shown that modifications like these can give significantly brighter dyes with red-shifted absorbance and emission maxima.
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Affiliation(s)
- Syed Muhammad Usama
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX, 77842, USA
| | - Tye Thompson
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX, 77842, USA
| | - Kevin Burgess
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX, 77842, USA
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46
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Usama SM, Thompson T, Burgess K. Produktive Modifikationen von Cyaninfarbstoff‐π‐Netzwerken. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Syed Muhammad Usama
- Department of Chemistry Texas A&M University Box 30012 College Station TX 77842 USA
| | - Tye Thompson
- Department of Chemistry Texas A&M University Box 30012 College Station TX 77842 USA
| | - Kevin Burgess
- Department of Chemistry Texas A&M University Box 30012 College Station TX 77842 USA
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47
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Luo X, Li J, Zhao J, Gu L, Qian X, Yang Y. A general approach to the design of high-performance near-infrared (NIR) D-π-A type fluorescent dyes. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.03.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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48
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Kinz-Thompson CD, Gonzalez RL. Increasing the Time Resolution of Single-Molecule Experiments with Bayesian Inference. Biophys J 2019; 114:289-300. [PMID: 29401427 DOI: 10.1016/j.bpj.2017.11.3741] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/19/2017] [Accepted: 11/21/2017] [Indexed: 01/19/2023] Open
Abstract
Many time-resolved single-molecule biophysics experiments seek to characterize the kinetics of biomolecular systems exhibiting dynamics that challenge the time resolution of the given technique. Here, we present a general, computational approach to this problem that employs Bayesian inference to learn the underlying dynamics of such systems, even when they are much faster than the time resolution of the experimental technique being used. By accurately and precisely inferring rate constants, our Bayesian inference for the analysis of subtemporal resolution dynamics approach effectively enables the experimenter to super-resolve the poorly resolved dynamics that are present in their data.
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Affiliation(s)
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, New York.
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49
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Blumhardt P, Stein J, Mücksch J, Stehr F, Bauer J, Jungmann R, Schwille P. Photo-Induced Depletion of Binding Sites in DNA-PAINT Microscopy. Molecules 2018; 23:molecules23123165. [PMID: 30513691 PMCID: PMC6321339 DOI: 10.3390/molecules23123165] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/25/2022] Open
Abstract
The limited photon budget of fluorescent dyes is the main limitation for localization precision in localization-based super-resolution microscopy. Points accumulation for imaging in nanoscale topography (PAINT)-based techniques use the reversible binding of fluorophores and can sample a single binding site multiple times, thus elegantly circumventing the photon budget limitation. With DNA-based PAINT (DNA-PAINT), resolutions down to a few nanometers have been reached on DNA-origami nanostructures. However, for long acquisition times, we find a photo-induced depletion of binding sites in DNA-PAINT microscopy that ultimately limits the quality of the rendered images. Here we systematically investigate the loss of binding sites in DNA-PAINT imaging and support the observations with measurements of DNA hybridization kinetics via surface-integrated fluorescence correlation spectroscopy (SI-FCS). We do not only show that the depletion of binding sites is clearly photo-induced, but also provide evidence that it is mainly caused by dye-induced generation of reactive oxygen species (ROS). We evaluate two possible strategies to reduce the depletion of binding sites: By addition of oxygen scavenging reagents, and by the positioning of the fluorescent dye at a larger distance from the binding site.
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Affiliation(s)
- Philipp Blumhardt
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Johannes Stein
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Jonas Mücksch
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Florian Stehr
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Julian Bauer
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Ralf Jungmann
- Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany.
| | - Petra Schwille
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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50
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Huth K, Glaeske M, Achazi K, Gordeev G, Kumar S, Arenal R, Sharma SK, Adeli M, Setaro A, Reich S, Haag R. Fluorescent Polymer-Single-Walled Carbon Nanotube Complexes with Charged and Noncharged Dendronized Perylene Bisimides for Bioimaging Studies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800796. [PMID: 29870583 DOI: 10.1002/smll.201800796] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/20/2018] [Indexed: 05/28/2023]
Abstract
Fluorescent nanomaterials are expected to revolutionize medical diagnostic, imaging, and therapeutic tools due to their superior optical and structural properties. Their inefficient water solubility, cell permeability, biodistribution, and high toxicity, however, limit the full potential of their application. To overcome these obstacles, a water-soluble, fluorescent, cytocompatible polymer-single-walled carbon nanotube (SWNT) complex is introduced for bioimaging applications. The supramolecular complex consists of an alkylated polymer conjugated with neutral hydroxylated or charged sulfated dendronized perylene bisimides (PBIs) and SWNTs as a general immobilization platform. The polymer backbone solubilizes the SWNTs, decorates them with fluorescent PBIs, and strongly improves their cytocompatibility by wrapping around the SWNT scaffold. In photophysical measurements and biological in vitro studies, sulfated complexes exhibit superior optical properties, cellular uptake, and intracellular staining over their hydroxylated analogs. A toxicity assay confirms the highly improved cytocompatibility of the polymer-wrapped SWNTs toward surfactant-solubilized SWNTs. In microscopy studies the complexes allow for the direct imaging of the SWNTs' cellular uptake via the PBI and SWNT emission using the 1st and 2nd optical window for bioimaging. These findings render the polymer-SWNT complexes with nanometer size, dual fluorescence, multiple charges, and high cytocompatibility as valuable systems for a broad range of fluorescence bioimaging studies.
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Affiliation(s)
- Katharina Huth
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Mareen Glaeske
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Katharina Achazi
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Georgy Gordeev
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Shiv Kumar
- Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Raúl Arenal
- Institute of Nanoscience of Aragon (INA), Advanced Microscopy Laboratory (LMA), University of Zaragoza, 50018, Zaragoza, Spain
- Foundation ARAID, 50018, Zaragoza, Spain
| | - Sunil K Sharma
- Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Mohsen Adeli
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
- Department of Chemistry, Faculty of Science, Lorestan University, Khorram Abad, 68151-44316, Iran
| | - Antonio Setaro
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Stephanie Reich
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
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