Citation: PAN Wenhui, LI Wen, QU Jinghan, YE Yipei, QU Junle, YANG Zhigang. Research Progress on Organic Fluorescent Probes for Single Molecule Localization Microscopy[J]. Chinese Journal of Applied Chemistry, ;2019, 36(3): 269-281. doi: 10.11944/j.issn.1000-0518.2019.03.180249 shu

Research Progress on Organic Fluorescent Probes for Single Molecule Localization Microscopy

Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China

Corresponding author: YANG Zhigang, zhgyang@szu.edu.cn
Received Date: 24 July 2018
Revised Date: 5 September 2018
Accepted Date: 12 October 2018

Fund Project: the Shenzhen Basic Research Project JCYJ20170818100931714the National Natural Science Foundation of China 61875131the National Natural Science Foundation of China 61525503the National Natural Science Foundation of China 81727804the National Basic Research Program of China 2015CB352005the National Natural Science Foundation of China 61620106016Supported by the National Basic Research Program of China(No.2015CB352005), the National Natural Science Foundation of China(No.61525503, No.61875131, No.61620106016, No.81727804), the Shenzhen Basic Research Project(No.JCYJ20170818100931714)

Figures(14)

In the field of biology and biomedical science, it is of significance to image microscopic targets inside cells with high precision to afford accurate information for diagnosis. Since the emergence of optical microscope, it has been used as a powerful tool to provide precise results, achieving the visualization of tiny objects. However, due to the optical diffraction limit(~200 nm), it is difficult to distinguish the objects less than 200 nm in size, in particular, a lot of significant biological targets with size less than 200 nm in cells, which blocks further advancement of biology science. Recently, with the development of fluorescent probes, imaging system and reconstruction algorithm, superresolution imaging microscopy is emerging as an advanced technique capable of overcoming the limit of optical diffraction, which shows potentials in the study of tiny targets below optical diffraction limit. Among superresolution imaging nanoscopies, single molecule localization microscopies(SMLM), such as photo activation localization microscopy(PALM) and stochastically optical reconstruction microscopy(STORM), show typical advantages over other strategies. Smart fluorescent probes play key roles in PALM/STORM microscopy, of which the photophysical properties typically determine the imaging resolution. Therefore, it is of significance to develop fluorescent probes with excellent optical properties to achieve ultrafine structure imaging of interest inside single cell. In this work, we will mainly focus on recent progress on organic probes for single molecule localization microscopy, including working principles, selection criteria, designing strategies of fluorescent probe and their biological applications. Furthermore, we will also cover on the discussion of the shortcomings remaining to be solved in the future and figure out the possible advancement of SMLM to facilitate the researchers who are interested in or initially step into the area of super-resolution imaging microscopy with theoretical assistance.
1. [1]
  Abbe E. Beitrage zur Theorie des Mikroskops und der Mikroskopischen Wahrnehmung[J]. Arch Mikroskop Anat, 1873,9(1):413-420. doi: 10.1007/BF02956173
2. [2]
  Klein T, Proppert S, Sauer M. Eight Years of Single Molecule Localization Microscopy[J]. Histochem Cell Biol, 2014,141(6):561-575. doi: 10.1007/s00418-014-1184-3
3. [3]
  Hell S W, Wichmann J. Breaking the Diffraction Resolution Limit by Stimulated Emission:Stimulated Emission Depletion Microscopy[J]. Opt Lett, 1994,19(11):780-782. doi: 10.1364/OL.19.000780
4. [4]
  Rittweger E, Han K Y, Irvine S E. STED Microscopy Reveals Crystal Colourcentres with Nanometric Resolution[J]. Nat Photonics, 2009,3(3):144-147. doi: 10.1038/nphoton.2009.2
5. [5]
  Yang Z, Sharma A, Qi J. Super-Resolution Fluorescent Materials:An Insight into Design and Bioimaging Applications[J]. Chem Soc Rev, 2016,45(17):4651-4667. doi: 10.1039/C5CS00875A
6. [6]
  Bretschneider S, Eggeling C, Hell S W. Breaking the Diffraction Barrier in Fluorescence Microscopy by Optical Shelving[J]. Phys Rev Lett, 2007,98(21)218103. doi: 10.1103/PhysRevLett.98.218103
7. [7]
  Hofmann M, Eggeling C, Jakobs S. Breaking the Diffraction Barrier in Fluorescence Microscopy at Low Light Intensities by Using Reversibly Photoswitchable Proteins[J]. Proc Natl Acad Sci, 2005,102(49)17565. doi: 10.1073/pnas.0506010102
8. [8]
  Gustafsson M G L. Nonlinear Structured-Illumination Microscopy:Wide-Field Fluorescence Imaging with Theoretically Unlimited Resolution[J]. Proc Natl Acad Sci USA, 2005,102(37)13081. doi: 10.1073/pnas.0406877102
9. [9]
  Shroff H, Galbraith C G, Galbraith J A. Live-Cell Photoactivated Localization Microscopy of Nanoscale Adhesion Dynamics[J]. Nat Methods, 2008,5(5):417-423. doi: 10.1038/nmeth.1202
10. [10]
  Rust M J, Bates M, Zhuang X. Sub-Diffraction-Limit Imaging by Stochastic Optical Reconstruction Microscopy(STORM)[J]. Nat Methods, 2006,3(10):793-796. doi: 10.1038/nmeth929
11. [11]
  Sharonov A, Hochstrasser R M. Wide-Field Subdiffraction Imaging by Accumulated Binding of Diffusing Probes[J]. Proc Natl Acad Sci USA, 2006,103(50):18911-18916. doi: 10.1073/pnas.0609643104
12. [12]
  Heilemann M, van de Linde S, Schüttpelz M. Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes[J]. Angew Chem Int Ed, 2008,47(33):6172-6176. doi: 10.1002/anie.v47:33
13. [13]
  Dempsey G T, Vaughan J C, Chen K H. Evaluation of Fuorophores for Optimal Performance in Localization-Based Super-Resolution Imaging[J]. Nat Methods, 2011,8(12):1027-1040. doi: 10.1038/nmeth.1768
14. [14]
  Heilemann M, Margeat E, Kasper R. Carbocyanine Dyes as Efficient Reversible Single-Molecule Optical Switch[J]. J Am Chem Soc, 2005,127(11):3801-3806. doi: 10.1021/ja044686x
15. [15]
  Bates M, Blosser T R, Zhuang X. Short-Range Spectroscopic Ruler Based on a Single-Molecule Optical Switch[J]. Phys Rev Lett, 2005,94(10)108101. doi: 10.1103/PhysRevLett.94.108101
16. [16]
  Dempsey G T, Bates M, Kowtoniuk W E. Photoswitching Mechanism of Cyanine Dyes[J]. J Am Chem Soc, 2009,131(51):18192-18193. doi: 10.1021/ja904588g
17. [17]
  Vaughan J C, Dempsey G T, Sun E. Phosphine Quenching of Cyanine Dyes as a Versatile Tool for Fluorescence Microscopy[J]. J Am Chem Soc, 2013,135(4):1197-1200. doi: 10.1021/ja3105279
18. [18]
  Heilemann M, van de Linde S, Mukherjee A. Super-Resolution Imaging with Small Organic Fluorophores[J]. Angew Chem Int Ed, 2009,48(37):6903-6908. doi: 10.1002/anie.v48:37
19. [19]
  van de Linde S, Sauer M. How to Switch a Fluorophore:From Undesired Blinking to Controlled Photoswitching[J]. Chem Soc Rev, 2014,43(4):1076-1087. doi: 10.1039/C3CS60195A
20. [20]
  Kottke T, van de Linde S, Sauer M. Identification of the Product of Photoswitching of an Oxazine Fluorophore Using Fourier Transform Infrared Difference Spectroscopy[J]. J Phys Chem Lett, 2010,1(21):3156-3159. doi: 10.1021/jz101300t
21. [21]
  Vaughan J C, Jia S, Zhuang X. Ultrabright Photoactivatable Fluorophores Created by Reductive Caging[J]. Nat Methods, 2012,9(12):1181-1184. doi: 10.1038/nmeth.2214
22. [22]
  Bates M, Huang B, Dempsey G T. Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes[J]. Science, 2007,317(5845):1749-1753. doi: 10.1126/science.1146598
23. [23]
  Huang B, Jones S A, Brandenburg B. Whole-Cell 3D STORM Reveals Interactions Between Cellular Structures with Nanometer-Scale Resolution[J]. Nat Methods, 2008,5(12):1047-1052. doi: 10.1038/nmeth.1274
24. [24]
  Bates M, Dempsey G T, Chen K H. Multicolor Super-Resolution Fluorescence Imaging via Multi-parameter Fluorophore Detection[J]. Chem Phys Chem, 2012,13(1):99-107.
25. [25]
  van de Linde S, Endesfelder U, Mukherjee A. Multicolor Photoswitching Microscopy for Subdiffraction-Resolution Fluorescence Imaging[J]. Photobio Sci, 2009,8(4):465-469. doi: 10.1039/b822533h
26. [26]
  Lehmann M, Gottschalk B, Puchkov D. Multicolor Caged dSTORM Resolves the Ultrastructure of Synaptic Vesicles in the Brain[J]. J Angew Chem Int Ed, 2015,54(45):13230-13235. doi: 10.1002/anie.201505138
27. [27]
  Wombacher R, Heidbreder M, van de Linde S. Live-Cell Super-Resolution Imaging with Trimethoprim Conjugates[J]. Nat Methods, 2010,7(9):717-719. doi: 10.1038/nmeth.1489
28. [28]
  Benke A, Manley S. Live-Cell dSTORM of Cellular DNA Based on Direct DNA Labeling[J]. Chem Bio Chem, 2012,13(2):298-301. doi: 10.1002/cbic.201100679
29. [29]
  Shim S H, Xia C, Zhong G. Super-resolution Fluorescence Imaging of Organelles in Live Cells with Photoswitchable Membrane Probes[J]. Proc Natl Acad Sci USA, 2012,109(35):13978-13983. doi: 10.1073/pnas.1201882109
30. [30]
  Lukinavičius G, Umezawa K, Olivier N. A Near-Infrared Fluorophore for Live-Cell Super-Resolution Microscopy of Cellular Proteins[J]. Nat Chem, 2013,5(2):132-139. doi: 10.1038/nchem.1546
31. [31]
  Uno S, Kamiya M, Yoshihara T. A Spontaneously Blinking Fluorophore Based on Intramolecular Spirocyclization for Live-Cell Super-resolution Imaging[J]. Nat Chem, 2014,6(8):681-689. doi: 10.1038/nchem.2002
32. [32]
  Lee H D, Lord S J, Iwanaga S. Superresolution Imaging of Targeted Proteins in Fixed and Living Cells Using Photoactivatable Organic Fluorophores[J]. J Am Chem Soc, 2010,132(43):15099-15101. doi: 10.1021/ja1044192
33. [33]
  Fölling J, Belov V, Kunetsky R. Photochromic Rhodamines Provide Nanoscopy with Optical Sectioning[J]. Angew Chem Int Ed, 2007,46(33):6266-6270. doi: 10.1002/anie.v46:33
34. [34]
  Huang B, Wang W Q, Bates M. Three-Dimensional Super-resolution Imaging by Stochastic Optical Reconstruction Microscopy[J]. Science, 2008,319(5864):810-813. doi: 10.1126/science.1153529
35. [35]
  Lee M K, Rai P, Williams J. Small-Molecule Labeling of Live Cell Surfaces for Three-Dimensional Super-resolution Microscopy[J]. J Am Chem Soc, 2014,136(40):14003-14006. doi: 10.1021/ja508028h
36. [36]
  Halabi E A, Thiel Z, Trapp N. A Photoactivatable Probe for Super-resolution Imaging of Enzymatic Activity in Live Cells[J]. J Am Chem Soc, 2017,139(37):13200-13207. doi: 10.1021/jacs.7b07748
37. [37]
  Banala S, Maurel D, Manley S. A Caged, Localizable Rhodamine Derivative for Superresolution Microscopy[J]. ACS Chem Biol, 2012,7(2):289-293. doi: 10.1021/cb2002889
38. [38]
  Grimm J B, Sung A J, Legant W R. Carbofluoresceins and Carborhodamines as Scaffolds for High Contrast Fluorogenic Probes[J]. ACS Chem Biol, 2013,8(6):1303-1310. doi: 10.1021/cb4000822
39. [39]
  Grimm J B, Klein T, Kopek B G. Synthesis of a Far-Red Photoactivatable Silicon-Containing Rhodamine for Super-resolution Microscopy[J]. Angew Chem Int Ed, 2016,55(5):1723-1727. doi: 10.1002/anie.201509649
40. [40]
  Nevskyi O, Sysoiev D, Oppermann A. Nanoscopic Visualization of Soft Matter Using Fluorescent Diarylethene Photoswitches[J]. Angew Chem Int Ed, 2016,55(41):12698-12702. doi: 10.1002/anie.201606791
41. [41]
  Zhang H, Wang C, Jiang T. Microtubule-Targetable Fluorescent Probe:Site-Specific Detection and Super-Resolution Imaging of Ultrace Tubulin in Microtubules of Living Cancer Cells[J]. Anal Chem, 2015,87(10):5216-5222. doi: 10.1021/acs.analchem.5b01089
42. [42]
  Hua Q, Xin B, Xiong Z. Super-resolution Imaging of Self-assembly of Amphiphilic Photoswitchable Macrocycles[J]. Chem Commun, 2017,53(18):2669-2672. doi: 10.1039/C7CC00044H
43. [43]
  He H, Ye Z, Xiao Y. Super-Resolution Monitoring of Mitochondrial Dynamics upon Time-Gated Photo-Triggered Release of Nitric Oxide[J]. Anal Chem, 2018,90(3):2164-2169. doi: 10.1021/acs.analchem.7b04510
44. [44]
  Gu X, Zhao E, Zhao T. Mitochondrion-Specific Photoactivatable Fluorescence Turn-On AIE-Based Bioprobe for Localization Super-Resolution Mic/roscope[J]. Adv Mater, 2016,28(25):5064-507. doi: 10.1002/adma.201505906
1. [1]
  Jinlong YAN , Weina WU , Yuan WANG . A simple Schiff base probe for the fluorescent turn-on detection of hypochlorite and its biological imaging application. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1653-1660. doi: 10.11862/CJIC.20240154
2. [2]
  Jun LUO , Baoshu LIU , Yunchang ZHANG , Bingkai WANG , Beibei GUO , Lan SHE , Tianheng CHEN . Europium(Ⅲ) metal-organic framework as a fluorescent probe for selectively and sensitively sensing Pb²⁺ in aqueous solution. Chinese Journal of Inorganic Chemistry, 2024, 40(12): 2438-2444. doi: 10.11862/CJIC.20240240
3. [3]
  Yu SU , Xinlian FAN , Yao YIN , Lin WANG . From synthesis to application: Development and prospects of InP quantum dots. Chinese Journal of Inorganic Chemistry, 2024, 40(11): 2105-2123. doi: 10.11862/CJIC.20240126
4. [4]
  Siyi ZHONG , Xiaowen LIN , Jiaxin LIU , Ruyi WANG , Tao LIANG , Zhengfeng DENG , Ao ZHONG , Cuiping HAN . Targeting imaging and detection of ovarian cancer cells based on fluorescent magnetic carbon dots. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1483-1490. doi: 10.11862/CJIC.20240093
5. [5]
  Liang TANG , Jingfei NI , Kang XIAO , Xiangmei LIU . Synthesis and X-ray imaging application of lanthanide-organic complex-based scintillators. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1892-1902. doi: 10.11862/CJIC.20240139
6. [6]
  Donghui PAN , Yuping XU , Xinyu WANG , Lizhen WANG , Junjie YAN , Dongjian SHI , Min YANG , Mingqing CHEN . Preparation and in vivo tracing of ⁶⁸Ga-labeled PM_2.5 mimetic particles for positron emission tomography imaging. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 669-676. doi: 10.11862/CJIC.20230468
7. [7]
  Zhiwen HUANG , Qi LIU , Jianping LANG . W/Cu/S cluster-based supramolecular macrocycles and their third-order nonlinear optical responses. Chinese Journal of Inorganic Chemistry, 2025, 41(1): 79-87. doi: 10.11862/CJIC.20240184
8. [8]
  Jin Tong , Shuyan Yu . Crystal Engineering for Supramolecular Chirality. University Chemistry, 2024, 39(3): 86-93. doi: 10.3866/PKU.DXHX202308113
9. [9]
  Meirong HAN , Xiaoyang WEI , Sisi FENG , Yuting BAI . A zinc-based metal-organic framework for fluorescence detection of trace Cu²⁺. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1603-1614. doi: 10.11862/CJIC.20240150
10. [10]
  Yuan ZHU , Xiaoda ZHANG , Shasha WANG , Peng WEI , Tao YI . Conditionally restricted fluorescent probe for Fe³⁺ and Cu²⁺ based on the naphthalimide structure. Chinese Journal of Inorganic Chemistry, 2025, 41(1): 183-192. doi: 10.11862/CJIC.20240232
11. [11]
  Shuwen SUN , Gaofeng WANG . Design and synthesis of a Zn(Ⅱ)-based coordination polymer as a fluorescent probe for trace monitoring 2, 4, 6-trinitrophenol. Chinese Journal of Inorganic Chemistry, 2025, 41(4): 753-760. doi: 10.11862/CJIC.20240399
12. [12]
  Zhifeng CAI , Ying WU , Yanan LI , Guiyu MENG , Tianyu MIAO , Yihao ZHANG . Effective detection of malachite green by folic acid stabilized silver nanoclusters. Chinese Journal of Inorganic Chemistry, 2025, 41(5): 983-993. doi: 10.11862/CJIC.20240394
13. [13]
  Qi Wang , Yicong Gao , Feng Lu , Quli Fan . Preparation and Performance Characterization of the Second Near-Infrared Phototheranostic Probe: A New Design and Teaching Practice of Polymer Chemistry Comprehensive Experiment. University Chemistry, 2024, 39(11): 342-349. doi: 10.12461/PKU.DXHX202404141
14. [14]
  Cen Zhou , Biqiong Hong , Yiting Chen . Application of Electrochemical Techniques in Supramolecular Chemistry. University Chemistry, 2025, 40(3): 308-317. doi: 10.12461/PKU.DXHX202406086
15. [15]
  Jia Yao , Xiaogang Peng . Theory of Macroscopic Molecular Systems: Theoretical Framework of the Physical Chemistry Course in the Chemistry “101 Plan”. University Chemistry, 2024, 39(10): 27-37. doi: 10.12461/PKU.DXHX202408117
16. [16]
  .
  CCS Chemistry | 超分子活化底物为自由基促进高效选择性光催化氧化
  . CCS Chemistry, 2025, 7(10.31635/ccschem.025.202405229): -.
17. [17]
  Jiakun BAI , Ting XU , Lu ZHANG , Jiang PENG , Yuqiang LI , Junhui JIA . A red-emitting fluorescent probe with a large Stokes shift for selective detection of hypochlorous acid. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1095-1104. doi: 10.11862/CJIC.20240002
18. [18]
  Rui Li , Jiayu Zhang , Anyang Li . Two Levels of Understanding of Chemical Bonds: a Case of the Bonding Model of Hypervalent Molecules. University Chemistry, 2024, 39(2): 392-398. doi: 10.3866/PKU.DXHX202308051
19. [19]
  Xiyuan Su , Zhenlin Hu , Ye Fan , Xianyuan Liu , Xianyong Lu . Change as You Want: Multi-Responsive Superhydrophobic Intelligent Actuation Material. University Chemistry, 2024, 39(5): 228-237. doi: 10.3866/PKU.DXHX202311059
20. [20]
  Cunming Yu , Dongliang Tian , Jing Chen , Qinglin Yang , Kesong Liu , Lei Jiang . Chemistry “101 Program” Synthetic Chemistry Experiment Course Construction: Synthesis and Properties of Bioinspired Superhydrophobic Functional Materials. University Chemistry, 2024, 39(10): 101-106. doi: 10.12461/PKU.DXHX202408008

Get Citation

PDF

XML

Metrics

PDF Downloads(74)
Abstract views(3005)
HTML views(1019)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142