Cyanine3 (cy3)

Manufactured by Nikon

Cy3 is a fluorescent dye commonly used in laboratory applications for labeling and detecting biomolecules. It has an excitation maximum at 550 nm and an emission maximum at 570 nm, making it suitable for a variety of detection methods.

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Lab products found in correlation

Cyanine3 (cy3), by Thermo Fisher Scientific (3 mentions) Eub338 16s rrna gene probe, by Thermo Fisher Scientific (3 mentions) Eclipse 90i confocal microscope, by Nikon (3 mentions) Fluorescence microscopy, by Nikon (1 mentions) Cyanine3 (cy3), by Beyotime (1 mentions) Cyanine3 (cy3), by Wuhan Servicebio Technology (1 mentions) Dapi g1012, by Wuhan Servicebio Technology (1 mentions) Intensilight c hgfie, by Nikon (1 mentions) Smartshutter, by Sutter Instruments (1 mentions) 4 6 diamidino 2 phenylindole (dapi), by Nikon (1 mentions) Elements software, by Nikon (1 mentions)

6 protocols using cyanine3 (cy3)

Bacterial Colonization Detection in Liver Tissues

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The EUB338 16S rRNA gene probe labeled with the fluorophore Cy3 (excitation wavelength, 555 nm; emission wavelength, 570 nm; Molecular Probes) was used to detect the bacterial colonization within liver tissues by FISH. In situ hybridization was confirmed using E. coli (ATCC, catalog PTA-7555) cultured under standard conditions, and fluorescence was compared with the unstained condition. Fluorescence microscopic analysis was conducted with the Nikon Eclipse 90i confocal microscope (Nikon) using a Cy3-labeled probe at 50 pmol/mL, as described (71 (link)–73 (link)).

Leinwand J.C., Paul B., Chen R., Xu F., Sierra M.A., Paluru M.M., Nanduri S., Alcantara C.G., Shadaloey S.A., Yang F., Adam S.A., Li Q., Bandel M., Gakhal I., Appiah L., Guo Y., Vardhan M., Flaminio Z., Grodman E.R., Mermelstein A., Wang W., Diskin B., Aykut B., Khan M., Werba G., Pushalkar S., McKinstry M., Kluger Z., Park J.J., Hsieh B., Dancel-Manning K., Liang F.X., Park J.S., Saxena A., Li X., Theise N.D., Saxena D, & Miller G. (2022). Intrahepatic microbes govern liver immunity by programming NKT cells. The Journal of Clinical Investigation, 132(8), e151725.

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Tracking Exosome-Mediated miRNA Delivery

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According to the manufacturer’s protocol, macrophage derived-exosomes were labeled with the fluorochrome DiI (Beyotime, cat#C1036). Airway epithelial cells were incubated with DMEM containing DiI-labeled exosomes for 24 h. After washing the cells, DAPI was used to stain the nucleus, and the results were analyzed with fluorescence microscopy (Nikon).
M2 macrophage was transfected with Cy3-labeled (Beyotime, cat#A0516) miR-30b-5p mimics, and exosomes were isolated. Airway epithelial cells were incubated with M2Φ-Exos transfected with Cy3-labeled miR-30b-5p mimics for 24 h. Cells were observed by fluorescence microscopy (Nikon) to internalize miR-30b-5p-containing exosomes.

Tang B., Wu Y., Zhang Y., Cheng Y., Wu Y, & Fang H. (2022). Scorpion and centipede alleviates severe asthma through M2 macrophage-derived exosomal miR-30b-5p. Aging (Albany NY), 14(9), 3921-3940.

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Bacterial Colonization Detection in Pancreatic Tissues

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The EUB338 16S rRNA gene probe or a Bifidobacterium specific probe labeled with the fluorophore Cy3 (extinction wavelength, 555 nm; emission wavelength, 570 nm; Molecular Probes, Eugene, OR) was used to detect the bacterial colonization within human and mouse pancreatic tissues by FISH. Fluorescence microscopic analysis was conducted with Nikon Eclipse 90i confocal microscope (Nikon, Melville, NY) using a Cy3 labeled-probe at 50 pmol/ml as described (36 (link)–38 (link)).

Pushalkar S., Hundeyin M., Daley D., Zambirinis C.P., Kurz E., Mishra A., Mohan N., Aykut B., Usyk M., Torres L.E., Werba G., Zhang K., Guo Y., Li Q., Akkad N., Lall S., Wadowski B., Gutierrez J., Rossi J.A., Herzog J.W., Diskin B., Torres-Hernandez A., Leinwand J., Wang W., Taunk P.S., Savadkar S., Janal M., Saxena A., Li X., Cohen D., Sartor R.B., Saxena D, & Miller G. (2018). The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression. Cancer discovery, 8(4), 403-416.

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Mouse Pancreatic Bacterial Colonization Detection

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The EUB338 16S rRNA gene probe labeled with the fluorophore Cy3 (extinction wavelength, 555 nm; emission wavelength, 570 nm; Molecular Probes, Eugene, OR) was used to detect the bacterial colonization within mouse pancreatic tissues by FISH. Fluorescence microscopic analysis was conducted with Nikon Eclipse 90i confocal microscope (Nikon, Melville, NY) using a Cy3 labeled-probe at 50 pmol/ml as described (34 (link)–36 (link)).

Hundeyin M., Kurz E., Mishra A., Kochen Rossi J.A., Liudahl S.M., Leis K.R., Mehrotra H., Kim M., Torres L.E., Ogunsakin A., Link J., Sears R.C., Sivagnanam S., Goecks J., Islam K.S., Dolgalev I., Savadkar S., Wang W., Aykut B., Leinwand J., Diskin B., Adam S., Israr M., Gelas M., Lish J., Chin K., Farooq M.S., Wadowski B., Wu J., Shah S., Adeegbe D.O., Pushalkar S., Vasudevaraja V., Saxena D., Wong K.K., Coussens L.M, & Miller G. (2019). Innate αβ T cells Mediate Anti-tumor Immunity by Orchestrating Immunogenic Macrophage Programming. Cancer discovery, 9(9), 1288-1305.

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Fluorescent Visualization of Bacterial Colonization in Mouse Pancreas

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The EUB338 16S rRNA probe labeled with the fluorophore Cy3 (extinction wavelength, 555 nm; emission wavelength, 570 nm; Servicebio, China) was used to detect the bacterial colonization within mouse pancreatic tissues by FISH. Nuclei were stained with DAPI (G1012, Servicebio). Fluorescence microscopic analysis was conducted with Nikon Eclipse 90i confocal microscope (Nikon, Melville, NY) using a Cy3 labeled-probe at 1μM as described [51 (link)–53 ].

Yang X., Wang Z., Niu J., Zhai R., Xue X., Wu G., Fang Y., Meng G., Yuan H., Zhao L, & Zhang C. (2023). Pathobionts from chemically disrupted gut microbiota induce insulin-dependent diabetes in mice. Microbiome, 11, 62.

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Fluorescence Microscopy Imaging Protocol

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The samples were imaged using an inverted epifluorescence microscope
(Nikon, Melville, NY, Eclipse Ti) equipped with a cooled EM-CCD camera
(Photometrics, Tucson, AZ, Cascade II:1024) and motorized stage control
(Prior, Rockland, MA, Proscan III). A mercury lamp was used as the light source
(Nikon, Intensilight C-HGFIE) with band-pass filter sets (Cy3, Nikon Instruments,
96323; Cy5, Nikon Instruments, 96324; DAPI, Nikon Instruments, 96310). A fast
motorized optical shutter (Sutter Instruments, Novato, CA, SmartShutter) was used
to control the fluorescence illumination exposure time. A 40×, 1.30 numerical
aperture, oil-immersion differential interference contrast (DIC) objective (Nikon,
MRH01400) was used with an additional 2.5× lens in front of the camera. The
coverslip containing the sample was mounted on a universal specimen holder. The
microscope was installed on an optical table (TMC, Peabody, MA, breadboard and
four-post support) to dampen mechanical vibrations. 'Elements' software (Nikon)
was used to control the microscopy setup. The same imaging protocol was also used
with an alternative camera (Photometrics, Evolve 512).

Skinner S.O., Xu H., Nagarkar-Jaiswal S., Freire P.R., Zwaka T.P, & Golding I. (2016). Single-cell analysis of transcription kinetics across the cell cycle. eLife, 5, e12175.

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