Cellular Labeling (S9102)


SNAP-tag fusion proteins can be expressed by transient or by stable transfection. For expression of fusion proteins with the SNAP-tag, refer to instructions supplied with the SNAP-tag plasmids. For cell culture and transfection methods, refer to established protocols.

Dissolve one vial of SNAP-tag substrate (30 nmol) in 50 μl of DMSO to give a solution of 0.6 mM SNAP-tag substrate in DMSO. Mix by vortexing for 10 minutes until all the SNAP-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 substrate is soluble up to at least 10 mM.


  1. Dilute the labeling stock solution 1:200 in medium to yield a labeling medium of 3 μM dye substrate. Mix dye with medium thoroughly by pipetting up and down 10 times (necessary for reducing backgrounds). For best performance, add the SNAP-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 SNAP-tag substrate than you will consume within one hour.
  2. Replace the medium on the cells expressing a SNAP-tag fusion protein with the SNAP-tag labeling medium and incubate at 37°C, 5% CO2 for 30 minutes.
    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
  3. Wash the cells three times with tissue culture medium with serum and incubate them in fresh medium for 30 minutes. Replace the medium one more time to remove unreacted SNAP-tag substrate that has diffused out of the cells.
  4. Image the cells using an appropriate filter set. SNAP-tag fusion proteins labeled with SNAPCell 647-SiR should have an excitation maximum at 645 nm and an emission maximum at 661 nm, and can be imaged with standard Cy5 filter sets.

    We recommend routinely labeling one well of non-transfected or mock-transfected cells as a negative control.


    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 SNAP-tag activity in a cell sample expressing the SNAP-tag fusion protein to generate a control. This can be achieved using a nonfluorescent SNAP-tag substrate, SNAP-Cell Block (bromothenylpteridine, BTP). SNAP-Cell Block may also be used in pulse-chase experiments to block the SNAP-tag reactivity during the chase between two pulse-labeling steps. A protocol for BTP blocking is included with SNAP-Cell Block (NEB #S9106).

    Optimizing Labeling 

    Optimal substrate concentrations and reaction times range from 1–10 µM and 15–60 minutes, respectively, depending on experimental conditions and expression levels of the SNAP-tag 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 and does not necessarily increase the signal to background ratio.

    Stability of Signal 

    The turnover rates of the SNAP-tag 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, SNAP-tag 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 SNAP-tag 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 SNAP-tag label with any fixation method.


    Cells can be counterstained with any live-cell dye that is compatible with the fluorescent properties of the SNAP-tag substrate for simultaneous microscopic detection. We routinely add 5 µM Hoechst 33342 to the medium prior to the first wash step (Step 3) as a DNA counterstain for nuclear visualization and leave this on the cells for 2 minutes prior to completing the wash steps. Counterstaining of cells is also possible after fixation and permeabilization.


    Antibody labeling can be performed after SNAP-tag labeling and fixation of the cells according to standard protocols without loss of the SNAP-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.  


    No Labeling 

    If no labeling is seen, the most likely explanation is that the fusion protein is not expressed. Verify the transfection method to confirm that the cells contain the fusion gene of interest. If this is confirmed, check for expression of the SNAP-tag fusion protein. If no antibody against the fusion partner is available, Anti-SNAP-tag Antibody (NEB #P9310) can be used. Alternatively, SNAP-Vista Green (NEB #S9147) can be used to confirm the presence of SNAP-tag 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 SNAP-tag substrate and/or the incubation time, following the guidelines described above. 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 SNAP-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 SNAP-tag from the N- to the C-terminus or vice versa. 

    Photobleaching is generally not a problem as SNAP-Cell 647-SiR is very photostable. However, if problems with photobleaching arise, addition of a commercially available anti-fade reagent may be helpful.