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Protocol: Aminooxy Labeling of Glycoproteins

Dyes functionalized with an aminooxy reactive group can be used to label molecules with a carbonyl group (aldehyde or ketone) to form a stable oxime bond. Aminooxy labeling can be used to conjugate glycoproteins after oxidation of the carbohydrates to generate aldhehyde groups. Aminooxy labeling of antibody glycosylation sites can be used as an alternative to succinimidyl ester labeling of amines, for antibodies where amine labeling affects the antibody binding affinity. Also see our protocols for Succinimidyl Ester Labeling of Protein Amines and Maleimide Labeling of Protein Thiols.

The protocol below is a typical procedure for oxidation and aminooxy labeling of IgG antibodies. Protocols for labeling other carbonyl-containing molecules are similar, except that the oxidation step is not necessary for molecules with free aldehyde or ketone groups. In addition, the purification procedures may need to be modified for different labeled targets. The labeling reaction may be scaled up or down for any amount of protein as long as the ratios of the reagents are maintained.

Materials required:

Workflow overview:

  1. Prepare the antibody for labeling
  2. Oxidize carbohydrate groups (10-30 minutes)
  3. Prepare the dye stock solution
  4. Perform the labeling reaction (2 hours)
  5. Purify the conjugated antibody
  6. Calculate the degree of labeling
  7. Add antibody stabilizers to conjugate


1 – Prepare antibody solution for labeling

Dissolve the antibody in 1X PBS buffer, preferably at 20-100 uM (3-15 mg/mL for IgG). Low protein concentration may result in poor protein recovery yield or inefficient labeling.

2 – Oxidize antibody carbohydrate groups

2.1 – Prepare 100 mM sodium periodate (NaIO4) stock solution in dH2O.

2.2 – To the antibody solution from step 1, add 1/10 volume of 10X reaction buffer (1 M sodium acetate, 1.5 M NaCl, pH 5.5) and 1/10 volume of NaIO4 stock solution. For example, if you have 100 uL of protein solution, add 10 uL of 10X reaction buffer and 10 uL of NaIO4 stock solution.

2.3 – Incubate for 10 minutes at room temperature or 30 minutes on ice.

2.4 – Add ethylene glycol to the reaction to a final concentration of 100 mM to quench the periodate. The molarity of pure ethylene glycol is 14.5M, so add 0.69 uL of ethylene glycol for every 100 uL of reaction mixture. Incubate for 10 minutes at room temperature.

3 -Prepare the dye stock solution

Prepare a 5 mM stock solution of CF® Dye Aminooxy in water, DMSO or DMF. Aminooxy dyes are stable in solution and can be stored at -20°C, protected from light, for at least one year.

4- Carry out the labeling reaction

4.1 – Add 50 molar equivalents of CF aminoooxy reagent to the reaction from step 2. For example, to 100 uL of oxidized IgG at 50 uM add 50 uL of 5 mM dye stock. This corresponds to 5 nmol protein aldehyde and 250 nmol dye.

4.2 – Optional, but recommended: add 1/10 volume of Aniline, 10X in acetate buffer to catalyze the reaction. For example, if the mixture from step 4-1 is 150 uL in total, add 15 uL of 10X Aniline.

4.3 – Mix by vortexing the solution and incubate at room temperature with rocking or shaking for 2 hours, protected from light.

5 – Separate the labeled protein from the free dye

Prepare a Sephadex® column (10 mm x 300 mm) equilibrated in 1X PBS buffer. Load the reaction solution from step 3 onto the column and elute with PBS buffer. The first band excluded from the column corresponds to the antibody conjugate.

  • For small scale labeling reactions, you may use an ultrafiltration vial to remove the free dye from the conjugate in order to avoid an overly dilute product. 10K MWCO can be used for IgG; proteins with different molecular weights may require different MWCO.

6 – Determination of degree of labeling (DOL)

Degree of labeling (DOL) is the average number of dye molecules conjugated to each antibody molecule. Measure the absorbance of the eluted antibody conjugate solution at 280 nm and at the absorption maximum of the dye used for labeling. The optimal range of DOL for each dye is listed in Table 1, although a DOL slightly above or below this range will also produce good results.

  • The protein solution eluted from the column may be too concentrated for accurate absorbance measurement and thus must be diluted to approximately ~0.1 mg/mL. The fold of dilution (“dilution factor”) necessary can be estimated from the amount of starting antibody (i.e., 5 mg) and the total volume of the protein solution collected from the column.

6a. Determine the protein concentration

The concentration of the antibody conjugate can be calculated from the formula:
[conjugate] = {[A280 – (Amax x Cf)]/1.4} x dilution factor

where [conjugate] is the concentration in mg/mL of the antibody conjugate collected from the column; “dilution factor” is the fold of dilution used for spectral measurement; A280 and Amax are the absorbance readings of the conjugate at 280 nm and the absorption maximum respectively; Cf is the absorbance correction factor; and the value 1.4 is the extinction coefficient of IgG in mL/mg. See Table 1 for the Amax and correction factor for each CF® dye.

  • If labeling a protein other than IgG, use the extinction coefficient for that specific protein.
  • If using a dye other than a CF® dye, use the Amax and correction factor for that specific dye.

6b. Calculate the degree of labeling (DOL):

The DOL is calculated according to the formula:
DOL = (Amax x Mwt x dilution factor)/(ε x [conjugate])

where Amax, “dilution factor” and [conjugate] are as defined in Step 6a, Mwt is the molecular weight of IgG (~150,000), and ε is the molar extinction coefficient of the dye (see Table 1).

  • If labeling a protein other than IgG, use the molecular weight for that specific protein.
  • If using a dye other than a CF® dye, use the extinction coefficient for that specific dye.

7 – Storage and handling of labeled antibody

For long-term storage, we recommend adding 5-10 mg/mL BSA and 0.01-0.03% sodium azide to the conjugate solution to prevent denaturation and microbial growth. The conjugate should be stored at 4°C, protected from light. If glycerol is added to a final concentration of 50%, the conjugate can be stored at -20°C. Under these conditions, antibody conjugates are stable for a year or longer.

Table 1: CF® Dye Technical Data

Dye Abs/Em (nm) Sephadex® media Amax (nm) Cf (protein) ε Optimal DOL (IgG)
CF®350 347/448 G-25 347 0.14 18,000 4-6
CF®405S 404/431 G-25 404 0.7 33,000 5-10
CF®405M 408/452 G-25 408 0.13 41,000 4-6
CF®405L 395/545 G-25 395 0.5 24,000 8-12
CF®430 426/498 G-25 426 0.044 40,000 5-8
CF®440 440/515 G-25 440 0.044 40,000 5-8
CF®450 405/460 G-25 450 0.2 40,000 5-8
CF®488A 490/515 G-25 490 0.1 70,000 7-9
CF®514 516/548 G-25 516 0.073 105,000 5-8
CF®532 527/558 G-25 527 0.06 96,000 4-7
CF®543 541/560 G-25 541 0.095 100,000 4-7
CF®555 555/565 G-25 555 0.08 150,000 4-5, 3-6 ok
CF®568 562/583 G-25 562 0.08 100,000 5-6
CF®570 568/591 G-25 568 0.1 150,000 5-6
CF®583 583/606 G-25 583 0.223 150,000 5-6
CF®594 593/614 G-25 593 0.08 115,000 4-7
CF®620R 617/639 G-25 617 0.45 115,000 5-6
CF®633 630/650 G-25 630 0.48 100,000 4-7
CF®640R 642/662 G-50 642 0.37 105,000 4-7
CF®647 650/665 G-25 650 0.03 240,000 4-5, 3-6 ok
CF®660C 667/685 G-75 667 0.08 200,000 3-6, 2-3 ok
CF®660R 663/682 G-25 663 0.51 100,000 4-7
CF®680 681/698 G-75 681 0.09 210,000 3-5, 2-3 ok
CF®680R 680/701 G-25 680 0.32 140,000 5-6
CF®750 755/777 G-75 755 0.03 250,000 3-5, 2-3 ok
CF®770 770/797 G-75 770 0.06 220,000 3-5, 2-3 ok
CF®790 784/806 G-75 784 0.07 210,000 3-5
CF®800 797/816 G-75 797 0.08 210,000 3-5
Sephadex is a registered trademark of Cytiva.

For information on dye charge, download the CF® Dye Aminooxy Product Information Sheet.