Cellular Labeling (E9230)


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. 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.


Protocol for Cell Surface Labeling Reaction

  1. Dilute the labeling stock solution 1:200 in medium to yield a labeling medium of 5 μM CLIP-Surface 488 or CLIP-Surface 547. 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.
  4. Image the cells using an appropriate filter set. CLIPf fusion proteins labeled with CLIP-Surface 488 should have an excitation maximum at 506 nm and an emission maximum at 526 nm, and can be imaged with standard fluorescein filter sets. CLIPf fusion proteins labeled with CLIP-Surface 547 should have an excitation maximum at 554 nm and an emission maximum at 568 nm, and can be imaged with standard TAMRA and Cy3 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 SNAP-tag with SNAP-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.


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 labeling medium after the 30 minutes incubation (Step 2 above) as a DNA counterstain for nuclear visualization. Counterstaining of cells is also possible after fixation and permeabilization.


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. An alternate explanation is that the CLIPf is fused to the end of the protein that is not localized on the extracellular surface of the cell membrane; reversing the orientation of the fusion protein may solve this problem.

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-Surface 488 and CLIP-Surface 547 are very photostable. However, if you experience problems with photobleaching, addition of a commercially available anti-fade reagent may be helpful.