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  • Cellular Labeling (E9200)

    Preparation of Labeling Stock Solution

    Dissolve one vial of CLIP-tag substrate in 10 μl of fresh DMSO to yield a labeling stock solution of 1 mM CLIP-Cell 505 or 0.6 mM CLIP-Cell TMR-Star. Mix by vortexing for 10 minutes until all the CLIP-tag substrate is dissolved. Store this stock solution in the dark at 4°C, or for extended storage at -20°C. Different stock concentrations can be made, depending on your requirements. The substrates are soluble up to at least 10 mM.

    1. Protocol for Intracellular Labeling Reaction

      Dilute the labeling stock solution 1:200 in medium to yield a labeling medium of 5 μM CLIP-Cell-505 or 3 μM CLIP-Cell TMR-Star. Mix dye with medium thoroughly by pipetting up and down 10 times (necessary for reducing backgrounds). For best performance, add the CLIP-tag substrate to complete medium, including serum (0.5% BSA can be used for experiments carried out in serum-free media). Do not prepare more medium with CLIP-tag substrate than you will consume within one hour.
      Number of wells in plate Recommended Volume for Cell Labeling
      6 1 ml
      12 500 µl
      24 250 µl
      48 100 µl
      96 50 µl
      These recommendations are for culturing cells in polystyrene plates. For confocal imaging, we recommend using chambered coverglass such as Lab-Tek II Chambered Coverglass which is available in a 1, 2, 4 or 8 well format from Nunc.
    2. Replace the medium on the cells expressing a CLIPf fusion protein with the CLIP-tag labeling medium and incubate at 37°C, 5% CO2 for 30 minutes.
    3. Wash the cells three times with tissue culture medium containing serum and incubate in fresh medium for 30 minutes. Replace the medium one more time to remove unreacted CLIP-tag substrate that has diffused out of the cells.
    4. Image the cells using an appropriate filter set. CLIPf fusion proteins labeled with CLIP-Cell 505 should have an excitation maximum at 504 nm and an emission maximum at 532 nm, and can be imaged with standard fluorescein filter sets. CLIPf fusion proteins labeled with CLIP-Cell TMR-Star should have an excitation maximum at 554 nm and an emission maximum at 580 nm, and can be imaged with standard rhodamine filter sets.
    5. We recommend routinely labeling one well of non-transfected or mocktransfected cells as a negative control.
    Notes for Cellular Labeling 

    Blocking Unreacted CLIP-tag with CLIP-Cell Block 

    In many cases the labeling of a non-transfected cell sample or a mock-transfected cell sample will be completely sufficient as a control. In some cases, however, it may be desirable to block the CLIP-tag activity in a cell sample expressing the CLIPf fusion protein to generate a control. This can be achieved using the included nonfluorescent CLIP-tag substrate, CLIP-Cell Block (bromothenylcytosine, BTC). CLIP-Cell Block may also be used in pulse-chase experiments to block the CLIP-tag reactivity during the chase between two pulse-labeling steps.. 

    Optimizing Labeling 

    Optimal substrate concentrations and reaction times range from 1–20 μM and 5–30 minutes, respectively, depending on experimental conditions and expression levels of the CLIPf fusion protein. Best results are usually obtained at concentrations between 1 and 5 μM substrate and 30 minutes reaction time. Increasing substrate concentration and reaction time usually results in a higher background without necessarily increasing the signal to background ratio. 

    Stability of Signal

    The turnover rates of the CLIPf fusion protein under investigation may vary widely depending on the fusion partner. We have seen half-life values ranging from less than one hour to more than 12 hours. Where protein turnover is rapid, we recommend analyzing the cells under the microscope immediately after the labeling reaction or, if the application allows it, fixing the cells directly after labeling. As an alternative to visualize proteins with fast turnover rates, CLIPf fusion proteins can be labeled at lower temperatures (4 or 16°C). Labeling times may need to be optimized.

    Fixation of Cells

    After labeling the CLIPf fusion proteins, the cells can be fixed with standard fixation methods such as para-formaldehyde, ethanol, methanol, methanol/acetone etc., without loss of signal. We are not aware of any incompatibility of the CLIP-tag label with any fixation method.

    Counterstaining 

    Cells can be counterstained with any live-cell dye that is compatible with the fluorescent properties of the CLIP-tag substrate for simultaneous microscopic detection. We routinely add 5 μM Hoechst 33342 to the medium that is used prior to the final 30 minutes incubation (Step 3 above) as a DNA counterstain for nuclear visualization. Counterstaining of cells is also possible after fixation and permeabilization.

    Immunocytochemistry 

    Antibody labeling can be performed after CLIP-tag labeling and fixation of the cells according to standard protocols without loss of the CLIP-tag signal. The fixation conditions should be selected based on experience with the protein of interest. For example some fixation methods destroy epitopes of certain proteins and therefore do not allow antibody staining afterwards.

    Problems with Cellular Labeling 

    No Labeling 

    If no labeling is seen, the most likely explanation is that the fusion protein is not expressed. Verify your transfection method to confirm that the cells contain the fusion gene of interest. If this is confirmed, check for expression of the CLIPf fusion protein. If no antibody against the fusion partner is available, Anti-SNAP-tag Antibody (NEB #P9310) can be used. Alternatively, CLIP-Vista Green (NEB #S9235) can be used to confirm presence of CLIPf fusion in cell extracts following SDS-PAGE, without the need for Western blotting.

    Weak Labeling 

    Weak labeling may be caused by insufficient exposure of the fusion protein to the substrate. Try increasing the concentration of CLIP-tag substrate and/or the incubation time within the range of 1–20 μM and 5–30 minutes, respectively. Alternatively the protein may be poorly expressed and/or turn over rapidly. If the protein has limited stability in the cell, it may help to analyze the samples immediately after labeling.

    High Background 

    Background fluorescence may be controlled by reducing the concentration of CLIP-tag substrate used, and by shortening the incubation time. The presence of fetal calf serum or BSA during the labeling incubation should reduce non-specific binding of substrate to surfaces.

    Signal Strongly Reduced after Short Time 

    If the fluorescence signal decreases rapidly, it may be due to instability of the fusion protein. The signal may be stabilized by fixing the cells. Alternatively try switching the CLIP-tag from the N- to the C-terminus or vice versa. Photobleaching is generally not a problem as both CLIP-Cell 505 and CLIP-Cell TMR-Star are very photostable. However, if you experience problems with photobleaching, addition of a commercially available anti-fade reagent may be helpful.