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Cy3 mono reactive dye pack

Manufactured by GE Healthcare
Sourced in France, Japan

The Cy3 Mono-Reactive Dye Pack is a fluorescent labeling reagent used in various biotechnology applications. It is designed to covalently bind to primary amine groups in biomolecules, enabling their detection and visualization in techniques such as Western blotting, immunohistochemistry, and microarray analysis.

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13 protocols using cy3 mono reactive dye pack

1

Embryonic Brain Hypoxia-Reoxygenation Injury

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Initially, the chorioallantoic vein of the embryos was exposed by cutting a window (5 × 5 mm) in the eggshell with a drill in a dark room, using a lamp. Then, experimental hypoxic conditions were induced by enveloping half of the chicken embryo air chamber with a polyvinyl layer for 24 h at 39 °C, to limit gas exchange. Hypoxic conditions were terminated by removing the polyvinyl layer, and then, the embryos were further re-oxygenated for 24 h at 37 °C (H+Ox). The normoxic (Nx) control group was incubated under normal air conditions at 37 °C for 48 h. At the end of the first 24 h period, the embryos were microinjected through the chorioallantoic vein with 100 µL of either Cy3-labeled GH (Cy3-GH; 0.15 µg/g of body weight, for 2 h, to determine BBB crossing and distribution within several CNS areas, Figure 1A) or recombinant chicken GH (rcGH, American Cyanamid AC 4797-100, Wayne, NJ, USA, 0.15 µg/g) to study the neuroprotective effects 24 h after hypoxia/reoxygenation injury by analyzing apoptosis, lipid peroxidation, inflammatory mediators and the expression of several neurotrophic factors (Figure 1B). The control groups received 100 µL of a saline solution as a vehicle.
Cy3 conjugation to GH (Cy3-GH) was performed according to the Cy3 Mono-Reactive dye pack manufacturer’s instructions (GE Healthcare Life Sciences, Amersham, ON, Canada).
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2

Bacterial Strains and Fixation Protocol

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Staphylococcus aureus, Streptococcus pneumoniae, and Escherichia coli strains used in this work were clinical isolates from the Russian Ministry of Health Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology collection. Listeria monocytogenes type strain EGDe (serovar 1/2a) was cultivated in the Brain Heart Infusion medium (BHI, BD, USA) at 37°C.
For fixation, bacteria from overnight cultures were precipitated by centrifugation for 5 min at 5000 rpm; the pellet was resuspended in PBS, bacteria were precipitated again, resuspended in 2.5% glutaraldehyde in PBS and incubated for 2 h at 4°C. The final concentration of bacteria was 109 cells/ml. Fixed or live L. monocytogenes cells were labelled with Cy3 (Mono-Reactive Dye Pack, GE Healthcare, Sweden) in accordance with the recommendations of the manufacturer.
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3

Microarray-based IgE Detection

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IgE (Fitzgerald), Illustra NAP-25 desalting columns and Cy3 Mono-Reactive Dye Pack (GE Healthcare), NanoDrop (Thermo Scientific), and nuclease free water (Gibco) were used. Microarray equipment is as follows: custom 8×15k and 1×1M DNA microarrays, 8×15k and 1×1M gasket slides, ozone barrier slides, hybridization chambers, scanner cassettes, hybridization oven, and High-resolution Microarray Scanner (all Agilent), Slide rack and wash dishes (Shandon), and Kimtech polypropylene wipes (Kimberly-Clark). FluoReporter Mini-Biotin-XX Protein Labeling Kit (Invitrogen), Streptavidin-Cy3 Conjugate and HABA/Avidin Reagent (Sigma), and dialysis cassettes (3.5k MWCO, Thermo Scientific) were also used.
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4

Antigen Internalization Assay using Flow Cytometry

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Goat F(ab′)2 anti-mouse Igκ (Southern Biotech) was biotinylated with 20-fold molar excess of NHS-LC-LC-biotin (Thermo Fisher Scientific, Inc.) and labeled with Cy3 monoreactive dye pack (GE Healthcare) in sodium carbonate buffer (biotinylated anti-κ-Cy3). Excess dye was removed using Zeba 7K MWCO desalting columns (Thermo Fisher Scientific, Inc.). Splenocytes were incubated with biotinylated anti-κ-Cy3 for 30 min on ice. Samples were incubated at 37°C for the times indicated before fixation with 2% PFA on ice for 20 min. Cells were stained with fluorescently labeled streptavidin to label the biotinylated anti-κ-Cy3 on the surface. Flow cytometry was used to determine antigen internalization defined as the reduction in the amount of biotinylated anti-κ-Cy3 remaining on the surface as a percentage of the amount on the surface of cells that had been left on ice.
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5

Quantifying Laminin Chain Secretion

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The relative abundance of the secreted laminin chains was determined with ImmunoCruz Cell Adhesion-2 MicroArray (sc-200006, Santa Cruz Biotechnologies, Santa Cruz, CA, USA) according to the manufacturer’s protocol. Briefly, cells were plated at 2 × 106/100-mm plate and maintained overnight. Cells were maintained in the fresh medium containing 5% Matrigel for 24 hr. The CM was harvested and spun to remove the Matrigel drip. The medium was concentrated to 1 ml using Amicon Ultra-15 centrifugal filter units (3 kDa cut off, Millipore). The protein concentration was determined with DC Protein Assay reagent (Bio-Rad) and normalized to 1 mg/ml. 250 μg protein was labeled with Cy3 dye (Cy3 Mono-Reactive Dye Pack, GE Healthcare, Milwaukee, WI, USA). The labeled protein was dissolved in 1.5 ml desalting buffer, and unbound dye was removed by using Amicon Ultra-15 centrifugal filter units that concentrated the protein to 500 μl. The labeled protein was hybridized with array slides, and slides were scanned and analyzed by the CruzScan Scanning service (sc-200215, Santa Cruz).
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6

Scalable smFISH Probe Production

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smiFISH primary probes and FLAPs (secondary probes, either fluorescent or conjugated to digoxigenin) were produced and purchased from Integrated DNA Technologies (IDT), with the following production details. The primary probes are produced using high-throughput oligonucleotides synthesis in 96-well plates. To make use of low-scale synthesis (25 nmol), the total length of primary probes (transcript-binding + FLAP-binding) should not exceed 60 nucleotides for cheaper synthesis. At this scale, oligonucleotides synthesis is possible at the price of ∼0.1 Euros per base at the time of the writing of the paper (∼150 Euros for 24 primary probes). The secondary probes are conjugated to two Cy3, Cy5 or digoxygenin moieties through 5′ and 3′ amino modifications. smFISH probes were synthesized by J.M. Escudier (SPCMIB, Toulouse, France) and labelled with Cy3 mono-reactive dye pack (GE Healthcare).
All primary probes sequences are available online at https://bitbucket.org/muellerflorian/fish_quant in the Oligostan folder. FLAP sequences are listed in Supplementary Note 1.
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7

Synthesis and Labeling of smFISH Probes

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smiFISH probes were purchased from Integrated DNA Technologies. smFISH probes were synthesized by J.M. Escudier (SPCMIB, Toulouse, France) and labeled with Cy3 mono-reactive dye pack (GE Healthcare). Probe sequences are available in Supplementary Data 1.
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8

Mouse Tissue RNA Extraction and Labeling

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RNA isolation, amplification and labelling procedures were carried out essentially as described elsewhere [14 (link)]. Quality of tRNA was checked with a Bioanalyzer assay (RNA 6000 Pico Kit, Agilent Technologies, Amstelveen, The Netherlands). RNA integrity numbers of tRNA of mouse CH ranged from 4.9 to 6.9, of the mouse RPE ranged from 4.9 to 7.2 and of mouse PR ranged from 5.5 to 7.6. In our microarray study we used a common reference design. The common reference was prepared from mouse RPE/choroid that was isolated, amplified using the same methodology as our experimental samples, and labelled with Cy3 (Cy3 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK).
See Janssen et al. [14 (link)] for a more detailed description of the laser dissection procedures, RNA processing and microarray procedures.
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9

DNA Microarray Protein-Binding Assay

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The chemicals used were IgE (Fitzgerald), Thrombin (Haematologic Technologies, Inc.), BSA and HSA (Sigma), neuropeptide Y (Pheonix Pharmaceuticals), Illustra NAP-25 desalting columns and Cy3 Mono-Reactive Dye Pack (GE Healthcare), NanoDrop (Thermo Scientific), nuclease free water (Gibco). Microarray equipment consisted of the following: custom 8 × 15 k DNA microarrays, 8 × 15 k gasket slides, ozone barrier slides, hybridization chambers, scanner cassettes, hybridization oven, and High-resolution Microarray Scanner (all Agilent) and slide rack and wash dishes (Shandon) and Kimtech polypropylene wipes (Kimberly-Clark). All DNA was purchased through IDT:

4A018: GGTTGGTTTTTCAATCAGCGATCGCGGAATCCAGGGTTAGGCGGCCAACC (with and without 3′-T10-Biotin moiety).

TFBS: GGTTGGTGTGGTTGG.

Buffers: Binding [PBSMTB]-1x PBS (8.1 mM Na2HPO4, 1.1 mM KH2PO4, 2.7 mM KCl, 137 mM NaCl, pH 7.4) + 1 mM MgCl2 + 0.1% Tween-20 and 1% BSA; Washing [PBSM]-1x PBS (8.1 mM Na2HPO4, 1.1 mM KH2PO4, 2.7 mM KCl, 137 mM NaCl, pH 7.4) + 1 mM MgCl2; Rinse [R]-1/4 dilution of PBSM and nuclease free water.

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10

Lectin Microarray Analysis of MSC Membrane Proteins

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Plasma membrane proteins from MSCs and osteogenically differentiated MSCs were prepared using a Mem-PER™ Plus Membrane Protein Extraction Kit (Thermo Fisher Scientific). Cells and exosomes were labelled with a Cy3 Mono-Reactive dye pack (GE Healthcare Ltd., Tokyo, Japan). Samples were diluted with Probing Solution containing 0.005% Triton X-100 (GlycoTechnica, Yokohama, Japan) to 500–1000 ng/mL and then applied to each well of a lectin microarray chip (LecChip™; GlycoTechnica). After overnight incubation at room temperature, fluorescence images were obtained using a GlycoStation™ Reader 2200 (GlycoTechnica). Data were analysed using GlycoStation® Tools Pro Suite 1.5 (GlycoTechnica).
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