Monoclonal Antibody for the Detection of SNAP/CLIP tag
The present invention relates t o an antibody for the detection of SNAP/CLIP tags,
to nucleic acids coding for such an antibody, and to the use of such an antibody for
the detection of proteins containing SNAP/CLIP tags.
The SNAP and CLIP tag technology is a relatively young technology. It is an ele
gant way to provide target proteins, especially fusion proteins, with desired ligands.
WO 20009/114748 Al discloses SNAP-25 compositions, methods of making
a-SNAP-25 antibodies that bind an epitope comprising a carboxyl-terminus at
the PI residue from the Bo NT/A cleavage site scissile bond from a SNAP-25
cleavage product, -SNAP-25 antibodies that bind an epitope comprising a
carboxyl-terminus at the PI residue from the BoNT/A cleavage site scissile bond
from a SNAP-25 cleavage product, methods of detecting BoNT/A activity, and
methods of detecting neutralizing a-Bo NT/A antibodies.
M. Yamamoto, L. Hassinger, J. E. Crandall report in Journal of Neurocytology 19,
619-627 (1990) about ultrastructural localization of stage-specific neuriteassociated
proteins in the developing rat cerebral and cerebellar cortices.
SNAP/TAG-1 is a glycoprotein of 135 kDa and is expressed on the surface of a
subset of growing axons in the developing rodent CNS. The ultrastructural
localization of this antigen was analysed in embryonic day 17 cerebral cortex and
postnatal days 4 and 8 cerebellar cortex of rats using immunoelectron
microscopy with a monoclonal antibody which recognizes SNAP/TAG-1 (4D7),
and peroxidase-conjugated secondary antibody. In the embryonic cortex,
immunoreactivity was associated with the plasma membranes of restricted
groups of axons, neuronal somata and their leading processes located in the
intermediate zone, subplate and cortical plate. Immunoreactive axons were
bundled together in groups of 10-20 and were separated from nonimmunoreactive
axons. Some growth cones were immunoreactive; however, not
all growth cones of 4D7-immunoreactive axons showed staining. I n the postnatal
cerebellum, immunoreactivity was associated with the somata and axons of
granule cells that are located in the most internal portion of the external granule
cell layer. I n cerebral and cerebellar cortices, immunoreactivity appeared in
corresponding points of adjacent cell membranes in punctuate fashion and with
a regular periodicity of 100-200 nm. The possibility that SNAP/TAG-1 is acting
as an adhesion molecule among specific subgroups of axons in the developing
CNS is discussed.
Richard J Ward, John D Pediani, and Graeme Milligan report in British Journal
Pharmacology (2011), 162, 1439-1452 about Ligand-induced internalization of
the orexin OXi and cannabinoid CBi receptors assessed via N-terminal SNAP and
CLIP-tagging. Cell surface forms of each receptor construct were detected by
both antibody recognition of the epitope tags and covalent binding of
fluorophores to the 0 -alkylguanine-DNA-alkyltransferase variants. Receptor
internalization in response to agonists but not antagonists could be monitored by
each approach but sensitivity was up to six- t o 10-fold greater than other
approaches when employing a novel, time-resolved fluorescence probe for the
SNAP tag. Sensitivity was not enhanced, however, for the CLIP tag, possibly due
t o higher levels of nonspecific binding.
The SNAP tag is based on the human DNA repair enzyme 0(6)-alkylguanine DNA
alkyltransferase. The latter has been altered by introducing mutations to such an
extent that a protein variant having a smaller molecular size and extremely high
affinity for benzylguanine could be selected. The SNAP tag undergoes a highly spe¬
cific reaction with benzylguanine derivatives, binding the benzyl radical with the
substrate coupled thereto covalently to itself with cleavage of guanine. As a re¬
combinant protein tag, it enables the covalent and stoichiometrically defined coupling
of various benzylguanine-modified substrates to the fusion protein. The CLIP
tag was developed from the SNAP tag by mutagenesis and undergoes a highly
specific reaction with benzylcytosine derivatives rather than benzylguanine. Thus,
the simultaneous differentiated labeling of SNAP and CLIP tags in one experimental
approach is possible. The SNAP technology (SNAP/CLIP plasmids and substrates) is
distributed by New England Biolabs (NEB).
I n "Journal of Biomedicine and Biotechnology", Vol. 2010, Article ID658954,
doi: 10. 1155/2010/658954, Aliprandi et al. disclose a recombinant anti-SNAP
antibody in a VHH format.
I t is desirable to have an analytical tool by which both CLIP and SNAP tags can be
detected.
The object of the invention is achieved by the antibody according to claim 1. The
monoclonal antibody of the invention that binds specifically to the SNAP tag motif
and to the CLIP tag and comprises CDRs with the amino acid sequences SEQ ID
Nos. 3, 4, 5, and 8, 9, 10. I n particular, the antibody of the invention is a murine
antibody.
Subject matter of the invention is also a nucleic acid coding for the antibody of the
invention, in particular a nucleic acid having the nucleic acid sequence of SEQ ID
Nos. 1 or 6.
The antibody of the invention is obtainable by a process of the invention, in which
an immunization is effected by means of a SNAP tag protein in non-human mam
mals, especially mice, and hybridoma cells are obtained therefrom, from which the
antibody cell lines that recognize both the SNAP and the CLIP tags are identified by
binding assays.
Also the use of the antibody of the invention for the detection of both a SNAP and
CLIP tag Aliprandi et al. describe a recombinant antibody that recognizes the
SNAP tag. The antibody according to the invention can be used for staining t is
sue sections. The murine anti-SNAP antibody according to the present invention
can be used, in particular, for staining cryosections and paraffin sections. An ad
vantage of the antibody according to the invention over the antibody already
published in Aliprandi et al. is its greater valence; the recombinant protein can
recognize only one epitope, while the antibody according t o the invention can
recognize two epitopes.
Figure 1: Immunohistochemistry; staining of cryosections of an A431 tumor ob
tained from mice with HAI SNAP (anti-EGFR) and M2D11.
Figure 2: Flow cytometry; the Figure shows the binding of M2D11 to two different
SNAP fusion proteins in flow cytometry.
Figure 3 : Western blot analysis; the two Figures show, on the one hand, the bind
ing of M2D11 to the two proteins SNAP and CLIP-EGF in a denaturing gel.
Figure 4 : Western blot analysis; this Figure shows the blot of a native polyacrylamide
gel for detecting the binding of M2D11 and SNAP protein in solution.
The antibody according to the invention is able to detect both the SNAP tag and
the CLIP tag. The antibody according to the invention has the advantage that the
SNAP fusion proteins can be detected in flow cytometry. The sensitivity of the ant i
body in ELISA (enzyme-linked immunosorbent assay) and Western blot is similar
to that of the antibody described by Aliprandi et al.
I n addition to the methods described, the antibody according t o the invention was
tested in immunohistochemical experiments. It can be employed for the detection
of SNAP fusion proteins in cryosections and in paraffin sections.
I n a specific embodiment, the antibody is a monoclonal antibody. In particular, the
antibody may be of murine origin. The murine antibody is advantageous because
murine IgG antibodies belong to the most frequently employed antibody formats in
molecular-biological research. Thus, the work with such antibodies and the detec
tion of murine IgG antibodies is familiar to the skilled persons in many laborato¬
ries.
The heavy chain variable region of the antibody according to the invention is
shown in SEQ ID No. 2, and SEQ ID No. 1 relates to the nucleic acid coding for this
region.
The light chain variable region of the antibody according to the invention is shown
in SEQ ID No. 7, and SEQ ID No. 6 relates to the nucleic acid coding for this re¬
gion.
CDRs of the heavy chain of the antibody according to the invention are listed in
amino acid sequences SEQ ID Nos. 3-5. CDRs of the light chain of the antibody ac
cording to the invention are listed in amino acid sequences SEQ ID Nos. 8-10.
The invention also relates to nucleic acids coding for the mentioned proteins, espe¬
cially SEQ ID Nos. 1 and 6.
The present invention also relates to a process for preparing the antibody according
to the invention, in which an immunization is effected by means of a SNAP tag
protein in non-human mammals, especially mice. From these, hybridoma cell lines
are obtained, and the antibody cell lines that recognize both the SNAP and the
CLIP tags are identified by corresponding binding assays.
The antibodies according to the invention can be used for the detection of SNAP
and CLIP tags individually, but also of a combination thereof.
Examples
Polyacrylamide gel electrophoresis and Western blot
The samples to be analyzed were denatured in Laemmli buffer (or in a native sam¬
ple buffer without SDS) and electrophoresed on a 12% (w/v) SDS polyacrylamide
gel and a polyacrylamide gel (160 V, 60 min). The proteins were visualized by
Coomassie staining or transferred to a nitrocellulose membrane (Whatman, Schlei¬
cher & Schuell, Dassel, Germany) (350 mA, 70 min). After the transfer, the mem
brane was blocked at room temperature in 1% (w/v) BSA for 1 hour. After wash
ing three times in PBS-T, the blot was incubated with the primary antibody ( 1
hour). After three further washing steps, the specific binding was detected with an
enzyme-conjugated secondary antibody ( 1 hour) and the corresponding substrate
(10 min). I n the analysis of SNAP or CLIP proteins, the samples were incubated
with BG or BC substrates before denaturing. The results are shown in Figure 3.
Figure 3 : Western blot analysis. The two Figures 3A, 3B and 3C show, on the one
hand, the binding of M2D11 to the two proteins SNAP and CLIP EGF in a denaturing
gel. The antibody shows no cross-reactivity with other His6-tagged proteins
(GFP-Ki4). I n addition, Figure 3B shows that the antibody does not compete with
the SNAP substrate for the binding to SNAP. After biotinylation of the SNAP protein
with BG biotin, the protein can further be detected with M2D11. I n addition, Figure
3C shows the binding of the antibody to different SNAP-scFv fusions (H22-SNAP,
SNAP-2715) and to CLIP-scFv-SNAP fusion proteins.
Figure 4 : Western blot analysis. This Figure shows the blot of a native polyacrylamide
gel for detecting the binding of M2D11 and SNAP protein in solution. Part A
shows the existence of SNAP protein through the Myc tag of the protein. It be
comes clear that the protein is bound by M2D11 also in solution, and that free protein
is detectable only at an excess of 1:4. I n Figure Part B, antibody was addit ion
ally detected, so that a colocalization of both proteins could be shown.
Immunohistochemistry
The tissue sections were prepared from EGFR-positive subcutaneous tumors origi
nating from BALB/c mice with A-431 tumors (DSMZ No. ACC 91). After sacrificing
the animals, the tumors were embedded in "Jung tissue freezing medium" (Leica
Microsystems, Nussloch, Germany) and frozen in liquid nitrogen. Cryosections of
8 m were prepared with a Leica 3050S Kryostat and dried over night. The sec
tions were fixed in acetone for 10 min, dried and outlined with an Immunopen
(Sigma Aldrich). The tumor cells were stained with an EGFR-specific scFv fusion
protein 425scFv SNAP (0.034 mg/ml) as a primary antibody. After three washes in
PBST, the SNAP fusion protein was detected with different concentrations of the
peroxidase-labeled antibody M2D11 (stock solution: 657 ng/ m I) . Both antibody in
cubation steps were performed at room temperature for 4 5 min, and the washing
steps were performed with shaking at room temperature for 5 min. After two
washes in PBST and one wash in TBST, the tissue sections were incubated in 3-
amino-9-ethylcarbazole (AEC) solution until staining became visible. Subsequently,
counterstaining was performed with haematoxylin before the sections were
mounted in glycerol gel. The results are shown in Figure 1.
Figure 1; Immunohistochemistry. Staining of cryosections of an A431 tumor obtained
from mice with 425(scFv)-SNAP (anti-EGFR) and M2D11.
Flow cytometry
The functionality of M2D11 was analyzed by flow cytometry with FACSCalibur
(Becton & Dickinson) and CellQuest software. The non-specific binding to the cell
surface of different cell lines was detected, as was the specific binding of SNAP fusion
proteins bound to the cell. About 4*10 5 cells were incubated first in 100 m I of
PBS with 1-2 g of SNAP/CLIP fusion protein and then in 100 m of PBS with 3.3 ng
of 2D11 on ice for 30 min. For detection, the cells were incubated with GaM-PE
( 1: 100, Dianova, Hamburg, Germany) on ice for 30 min. The cells were then ana
lyzed by flow cytometry. The PBS washing steps were performed in a standard cell
wash centrifuge between all steps. The cells were resuspended in 300 m I of PBS for
the measurement. The results are shown in Figure 2.
Figure 2 : Flow cytometry. The Figure shows the binding of M2D11 to two different
SNAP fusion proteins in flow cytometry. On both cell lines, no or only very little
cross-reactivity of the antibody with the cell surface can be detected. Mono Mac 1
and A431 cells are shown here by way of example. The analyses were additionally
performed with cell lines PC-3, CHO-K1, Kasumi, Mcf-7, L3.6pl, L540 and FG.

CLAIMS
1. A monoclonal antibody that binds specifically to the SNAP tag motif and to
the CLIP tag comprising CDRs with the amino acid sequences SEQ ID Nos.
3, 4, 5, and 8, 9, 10.
2. The antibody according to claim 1, characterized by being a murine ant i
body.
3. A nucleic acid coding for the antibody according to claim 1 or 2 .
4. The nucleic acid according to claim 3, characterized by having the nucleic
acid sequence of SEQ ID Nos. 1 or 6 .
5. A process for preparing an antibody according to claim 1, in which an im
munization is effected by means of a SNAP tag protein in non-human
mammals, especially mice, and hybridoma cells are obtained therefrom,
from which the antibody cell lines that recognize both the SNAP and the
CLIP tags are identified by binding assays.
6. Use of the antibody according t o claim 1 or 2 for the detection of a SNAP
and/or CLIP tag.