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What GFP-Trap should I use for my immunoprecipitation?

What GFP-Trap should I use for my immunoprecipitation?

GFP-Trap Agarose, GFP-Trap Magnetic Agarose,GFP-Trap Magnetic Particles M-270, GFP-Trap 96 Multiwell Plate

ChromoTek GFP-Trap^® is optimized for the immunoprecipitation of GFP-tagged proteins and their interacting factors. The GFP-Trap consists of the ChromoTek anti-GFP Nanobody/ V_HH that is coupled to 3 different types of beads or is immobilized in a 96 multiwell plate:

Agarose beads
Magnetic Agarose beads
Magnetic Particles M-270
96 Multiwell Plate

Immunoprecipitation with GFP-Trap.
I: Input, FT: Flow-Through, B: Bound

Based on the properties of the different matrices (see table), we recommend:

GFP-Trap Agarose for very low background and high binding capacity IP
GFP-Trap Magnetic Agarose for magnetic separation and high binding capacity IP
GFP-Trap Magnetic Particles M-270 for IP of very large proteins/complexes
GFP-Trap Multiwell Plates for high throughput analysis

GFP-Trap	Agarose	Magnetic Agarose	Magnetic Particles M-270	Multiwell Plate
Low background*	+++	++	++	++
Binding capacity	+++	+++	+	+
Size GFP-tagged protein*	Small to large	Small to large	Small to very large	Small to very large
Bead separation	centrifugation	magnetic	magnetic	Nanobody directly immobolised to multiwell plate

*Please note that these are general guidelines. For a specific protein or complex, the optimal experimental conditions/ GFP-Trap must be tested.

In detail, all types of GFP-Trap have very low background binding due to the highly specific binding of GFP (fusion proteins). In comparison, GFP-Trap Agarose has the lowest background. The background of GFP-Trap Magnetic Agarose and GFP-Trap Magnetic Particles M-270 is at slightly elevated levels. Hence, GFP-Trap Agarose is recommended if a very low background is needed.

The size and shape of the actual GFP-fusion protein, multimer or complex may require the use of the non-porous GFP-Trap Magnetic Particles M-270, because larger GFP-fusion proteins can’t access the GFP V_HH ligands inside the pores of agarose and magnetic agarose beads. Note that smaller proteins may form multimers or may be part of larger complexes and hence have larger sizes than expected.

Transparent GFP-Trap Multiwell Plates are pre-blocked and the GFP Nanobody is immobilized within the wells on solid polystyrene surface. They can be used for for high throughput analysis and immunoprecipitation of even very large proteins/ protein complexes.

	GFP-Trap beads
	Agarose	Magnetic Agarose	Magnetic Particles M-270
Matrix	Agarose (4% cross-linked)	Magnetic agarose (6% cross linked)	Magnetic Particles M-270
Bead form	Porous	Porous; sold iron core	Solid
Ligand	GFP V_HH	GFP V_HH	GFP V_HH
Affinity to GFP	1 pM	1 pM	1 pM
GFP-tagged protein size*	Small to large size	Small to large size	Small to very large size; all sizes
Color	White	Black	Brown
Medium particle size	~90 µm	~40 µm	2.8 µm
Binding capacity	12 µg/ 10 µL	8 µg/ 10 µL	1 μg/ 10 μL
Background	Very low	Low	Low
Magnetic separation & automation	no	Yes	Yes
May be centrifuged up to	2,500 x g	800 x g	8,000 x g