Clontech Laboratories, Inc.

iDimerize™ Inducible
Heterodimer System
User Manual

PT5179-1
Cat. Nos. 635067, 635055, 635056, 635057, 635065, 635089 & 635091
Published 1/10/2013

Clontech® Laboratories, Inc.

A Takara Bio Company
1290 Terra Bella Avenue, Mountain View, CA 94043, USA
U.S. Technical Support: tech@[Link]

United States/Canada Asia Pacific Europe Japan

800.662.2566 +1.650.919.7300 +33.(0)1.3904.6880 +81.(0)77.543.6116
iDimerize™ Inducible Heterodimer System User Manual PT5179-1
Table of Contents
I. Introduction..................................................................................................................................................................... 3
II. List of Components......................................................................................................................................................... 5
III. Additional Materials Required........................................................................................................................................ 6
A. A/C Heterodimerizer ................................................................................................................................................ 6
B. DmrA & DmrC Antibodies ...................................................................................................................................... 6
C. Mammalian Cell Culture Supplies ........................................................................................................................... 6
D. Antibiotics for Selecting Stable Cell Lines .............................................................................................................. 6
E. Xfect™ Transfection Reagents ................................................................................................................................ 6
F. In-Fusion® HD Cloning System ............................................................................................................................... 7
IV. Creating Fusion Proteins Containing Dimerization Domains......................................................................................... 7
A. General Considerations ............................................................................................................................................ 7
B. Protocol: Cloning Strategy for Creating Fusion Proteins ......................................................................................... 9
V. In Vitro Inducible Heterodimerization .......................................................................................................................... 12
A. Protocol: Transient Transfection of Heterodimerizer............................................................................................. 12
B. Protocol: Stable Expression of Heterodimerizer Constructs .................................................................................. 13
C. Protocol: Washout Experiment—Removing A/C Heterodimerizer from Cells ..................................................... 14
D. Results Obtained Using In Vitro Heterodimerization ............................................................................................ 14
VI. In Vivo Inducible Heterodimerization........................................................................................................................... 15
A. General Guidelines ................................................................................................................................................. 15
B. Results Obtained Using In Vivo Heterodimerization ............................................................................................. 15
VII. References..................................................................................................................................................................... 15
VIII. Troubleshooting ............................................................................................................................................................ 15

Table of Figures
Figure 1. Different iDimerize kits use different dimerization strategies: homodimerization, heterodimerization, and reverse
dimerization.. .......................................................................................................................................................................... 4
Figure 2. Controlling signal transduction using regulated heterodimerization. ...................................................................... 4
Figure 3. pHet-1, pHet-Nuc1, and pHet-Mem1 Vector Maps: Cloning Strategy. .................................................................. 8

Table of Tables
Table 1. ARGENT and Clontech Nomenclature for iDimerize Inducible Heterodimer System Components ....................... 5
Table 2. Recommended Antibiotic Concentrations for Selecting & Maintaining Stable Cell Lines .................................... 13

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iDimerize™ Inducible Heterodimer System User Manual PT5179-1
I. Introduction
A. Summary
ARGENT cell signaling regulation kits from ARIAD are now available exclusively from Clontech, as the
iDimerize Inducible Dimerization Systems. This manual describes the iDimerize Inducible Heterodimer
System (Cat. No. 635067), which contains reagents for bringing together two molecules of an engineered
fusion protein by adding a small molecule "dimerizer". The kit can be used to create conditional alleles of
receptors, signaling molecules, and any other protein normally regulated by protein-protein interactions,
allowing complex cellular events to be brought under small molecule control. The iDimerize Inducible
Heterodimer System consists of components identical to those previously supplied in the ARGENT
Regulated Heterodimerization Kit from ARIAD. The names of the plasmids, dimerization domains, and
dimerization ligands have been changed by Clontech but are identical to those previously supplied in the
ARGENT kit. For a comparison of iDimerize vs ARGENT nomenclature, see Section II of this manual.

B. Overview of Dimerization
Many cellular processes are triggered by the induced interaction, or “dimerization”, of signaling proteins
(Crabtree, et al., 1996). Examples include the clustering of cell surface receptors by extracellular growth
factors, and the subsequent stepwise recruitment and activation of intracellular signaling proteins. A
chemical inducer of dimerization, or “dimerizer”, is a cell-permeant organic molecule with two separate
motifs that each bind with high affinity to a specific protein module tagged onto the protein of interest.
Any cellular process activated by protein-protein interactions can in principle be brought under dimerizer
control, by fusing the protein(s) of interest to the binding module. Addition of the dimerizer then brings
the chimeric signaling protein subunits into very close proximity to each other, mimicking the activation
of the cellular event that the protein of interest controls. Different types of dimerizer (Figures 1 & 2) are
available:
 Heterodimerizers contain two different binding motifs, allowing the dimerization of two
different proteins of interest when each is fused to a different dimerization domain recognized by
the heterodimerizer. The iDimerize Inducible Heterodimer System provides the heterodimerizer
ligand—as well as DNA vectors that enable each dimerization domain to be fused to a different
protein of interest. The two different dimerization domains (DmrA & DmrC) are each able to
bind to the A/C Heterodimerizer ligand.
 Homodimerizers incorporate two identical binding motifs, and can therefore be used to induce
self-association of a single signaling domain or other protein of interest. For applications
requiring homodimerization, we provide a separate kit, the iDimerize Inducible Homodimer
System (Cat. No. 635068), that includes the homodimerizer ligand,.
 Reverse dimerizers promote the dissociation of proteins that have been engineered to self-
associate because they are tagged with “conditional aggregation domains” (DmrD), as in our
iDimerize Reverse Dimerization System (Cat. No. 635066).
 Another dimerization system, our iDimerize Regulated Transcription System (Cat. No.
635081), places the transcription of a target gene under the control of a “dimerizer”, which causes
the assembly of a functional transcription factor in order to achieve tightly regulated conditional
expression of genes of interest.

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Figure 1. Different iDimerize kits use different dimerization strategies: homodimerization, heterodimerization, and
reverse dimerization. Separate kits are available from Clontech.

C. iDimerize Inducible Heterodimer System

The iDimerize Inducible Heterodimer System contains reagents to induce the heterodimerization of two
proteins of interest by the addition of a small molecule, the “A/C Heterodimerizer”. The system consists of
three vectors that are used to create two fusion proteins, one containing a DmrC dimerization domain (pHet-
1) and the other containing a Dmr A dimerization domain (pHet-Nuc1 or pHet-Mem1), each of which bind
A/C Heterodimerizer, also included in the kit. The resulting fusion proteins, which contain different
localization tags, are localized to the cytoplasm (pHet-1), nucleus (pHet-Nuc1), or plasma membrane (pHet-
Mem1). The addition of A/C Heterodimerizer to live cells expressing fusion proteins containing DmrA and
DmrC domains induce heterodimerization of the fusion proteins by promoting the interaction of these
dimerization domains (Graef et al., 1997, Castellano et al., 1999). The plasmids in this kit provide an
assortment of components (i.e., dimerization domains, an HA epitope tag, and localization sequences) that
can easily be customized and exchanged to generate protein fusions whose activity and localization can be
controlled by the heterodimerizer (Figure 2).

Figure 2. Controlling signal transduction using regulated heterodimerization.

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II. List of Components
Store all components at -20°C.
 1 each iDimerize Inducible Heterodimer Vector Set 1
− 20 µl pHet-1 Vector (500 ng/µl)
− 20 µl pHet-Mem1 Vector (500 ng/µl)
− 20 µl pHet-Nuc1 Vector (500 ng/µl)
− 40 µl Linear Hygromycin Marker (50 ng/µl) (also sold separately as Cat. No. 631625)
− 40 µl Linear Puromycin Marker (50 ng/µl) (also sold separately as Cat. No. 631626)
 500 µl A/C Heterodimerizer (0.5 mM)
(also sold separately as Cat. Nos. 635057, 635056 & 635055—see Section III.A)

The iDimerize Inducible Heterodimer System components are identical to those previously supplied in the
ARGENT Regulated Heterodimerization Kit from Ariad—only the names have been changed (Table 1).
Table 1. ARGENT and Clontech Nomenclature for iDimerize Inducible Heterodimer System Components

Ligand Name in ARIAD Kit Ligand Name in Clontech Kit

AP21967 A/C Heterodimerizer
Plasmid Name in ARIAD Kit Plasmid Name in Clontech Kit
pC4-RHE pHet-1
pC4M-F2E pHet-Mem1
pC4EN-F1 pHet-Nuc1
Dimerization Domain Name in ARIAD Kit Dimerization Domain Name in Clontech Kit
F DmrA
F' DmrA
FRB DmrC
NOTES:
 The A/C Heterodimerizer is so named because it induces dimerization of a protein possessing the DmrA
domain and a second protein containing the DmrC domain..
 The amino acid sequences for the F and F’’ domains are identical. However, there are significant differences
at the nucleotide sequence level to reduce the potential for recombination between the repeating domain
within the pC4M-F2E plasmid (pHet-Mem1).

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III. Additional Materials Required
A. A/C Heterodimerizer
Each iDimerize Inducible Heterodimer System includes 500 μl A/C Heterodimerizer (0.5 mM; see
Section II). Additional A/C Heterodimerizer can also be purchased separately in the following sizes:

Cat. No. Product Name Size

635057 A/C Heterodimerizer (0.5 mM) 500 µl
635056 A/C Heterodimerizer (0.5 mM) 5 x 500 µl

635055 A/C Heterodimerizer* 5 mg

*Designed for in vivo use; supplied in a dry-down format (see Section VI).

B. DmrA & DmrC Antibodies

The DmrA and DmrC Antibodies recognize the respective DmrA and Dmr C dimerization domains
expressed using any iDimerize Inducible Heterodimer System, and are recommended for Western blot
analysis.

Cat. No. Product Name Size

635089 DmrA Monoclonal Antibody (0.5 µg/µl) 100 µg
635091 DmrC Polyclonal Antibody (0.5 µg/µl) 100 µg

C. Mammalian Cell Culture Supplies

 Culture medium, supplies, and additives specific for your target cells
 Trypsin/EDTA (e.g., Sigma, Cat. No. T4049)
 Cloning cylinders or discs for isolating colonies of adherent cell lines (Sigma, Cat. No. C1059)
 Cell Freezing Medium, with or without DMSO (Sigma, Cat. Nos. C6164 or C6039)
 Dulbecco’s phosphate buffered saline (DPBS; VWR, Cat. No. 82020-066 or Sigma, Cat. No. D8662)

D. Antibiotics for Selecting Stable Cell Lines

Cat. No. Antibiotic
631306 Puromycin (100 mg)
631305 Puromycin (25 mg)
631309 Hygromycin B (1 g)

E. Xfect™ Transfection Reagents

Xfect Transfection Reagent provides high transfection efficiency and low cytotoxicity for most
commonly used cell types. Xfect mESC Transfection Reagent is optimized for mouse embryonic stem
cells.
Cat. No. Transfection Reagent
631317 Xfect Transfection Reagent (100 rxns)
631318 Xfect Transfection Reagent (300 rxns)
631320 Xfect mESC Transfection Reagent (100 rxns)
631321 Xfect mESC Transfection Reagent (300 rxns)

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®
F. In-Fusion HD Cloning System
In-Fusion is a revolutionary technology that greatly simplifies cloning.
For more information, visit [Link]/infusion
Cat. No. In-Fusion Cloning Kit
639645 In-Fusion HD Cloning System (10 rxns)
639646 In-Fusion HD Cloning System (50 rxns)
639647 In-Fusion HD Cloning System (100 rxns)

IV. Creating Fusion Proteins Containing Dimerization Domains

A. General Considerations
1. Controlling localization of fusion proteins
 Fusion proteins are created by cloning signaling proteins of interest into either the XbaI site
or the SpeI site of the pHet-1, pHet-Nuc1 and pHet-Mem-1 vectors (Figure 3). Cloning into
the XbaI site places the DmrA or DmrC domain(s) at the C-terminus and cloning into the
SpeI site places the DmrA or DmrC domain(s) at the N terminus of your protein of interest.
 If the sequence encoding your protein is cloned into the Xba1 site of the pHet-1 vector, it
must be in-frame with the start codon (ATG) located upstream of the Xba I site, and be in-
frame with the downstream DmrC domain. If your protein of interest is cloned into the Xba I
site of the pHet-Nuc1 or pHet-Mem-1 vector, it must be in-frame with the N-terminal nuclear
localization signal of pHet-Nuc1 or the N-terminal myristoylation signal of pHet-Mem-1. The
coding sequence of a protein that is cloned into the Xba1 site of either vector must not
contain a stop codon, and must be in-frame with the downstream DmrA or DmrC domain(s).
 Fusion proteins localize to the cytoplasm when created using pHet-1 (which contains no
targeting signal), to the nucleus when created using pHet-Nuc1 (which contains an N-
terminal nuclear localization signal between the EcoRI and XbaI sites), and to the inner
leaflet of the plasma membrane when created using pHet-Mem1 (which contains an N-
terminal myristoylation signal between the EcoRI and XbaI sites).
 A hemagglutinin (HA) epitope tag located between the SpeI and BamHI sites in the pHet-1
and pHet-Mem1 vectors is expressed at the C-terminus of fusion proteins created using any
of the three vectors. This tag is useful for determining subcellular protein localization,
facilitating protein purification, identifying associated proteins, and characterizing new
proteins by immunoprecipitation (HA-Tag Polyclonal Antibody, Cat. No. 631207).

2. How many DmrA and DmrC domains should I use?

The number of DmrA and DmrC domains best suited for each application varies. We have generally
found that fusing one DmrA domain or one DmrC domain to each signaling protein works well, although
in some cases multiple tandem DmrC domains are required (e.g., when the event studied requires the
formation of higher order oligomers). Often the optimal configuration is best determined empirically.

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Figure 3. pHet-1, pHet-Nuc1, and pHet-Mem1 Vector Maps: Cloning Strategy. Use the XbaI site to clone your gene of interest upstream of the
dimerizing domain(s), and the SpeI site to clone your gene of interest downstream of the domain(s) as described in Section IV.B.

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B. Protocol: Cloning Strategy for Creating Fusion Proteins
Create fusion proteins containing the DmrA/DmrC domains and your protein of interest in the supplied vectors
using the following cloning strategy (For vector map information, see Figure 3).

In-Fusion HD cloning is generally recommended over ligation-based cloning because In-Fusion HD cloning is
directional, is not affected by internal SpeI and XbaI sites, and is highly efficient (most clones contain the correct
insert). For In Fusion HD ordering information; see Section III.F.

1. Cloning options for pHet-1

 XbaI Site
 Clone here to place the DmrC domain at the C-terminus of your protein.
 Linearize the vector at the XbaI site and directionally clone using the In-Fusion HD
Cloning System. Alternatively, amplify your gene with flanking XbaI and SpeI sites
(SpeI and XbaI have compatible cohesive ends) and clone the digested fragment into the
XbaI site.
 Do not include a ATG start codon in your gene; the ATG will be supplied by the vector at
nucleotides 676–678.
 Do not include a stop codon in your gene.
 Make sure that the coding region of your gene is in frame with the ATG at nucleotides
676–678. Tip: If your gene is in frame with the XbaI site in your primers, it will
automatically be in the correct reading frame when cloned.
 The expressed protein will contain a C-terminal HA-tag
 SpeI Site
 Clone here to place the DmrC domain at the N-terminus of your protein.
 Linearize the vector at the SpeI site and directionally clone using Clontech’s In-Fusion
HD Cloning System. Alternatively, amplify your gene with flanking XbaI and SpeI sites
(SpeI and XbaI have compatible cohesive ends) and clone into the SpeI site.
 Make sure that the coding region of your gene is in frame with the last codon of the
DmrC sequence (nucleotides 964–966). Tip: If your gene is in frame with the SpeI site in
your primers, it will automatically be in the correct reading frame when cloned.
 If you wish to retain the HA-Tag, do not include a stop codon at the end of your gene.
 If you do not wish to retain the HA-Tag, you must include a stop codon at the end of your
gene.

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2. Cloning options for pHet-Mem1
 XbaI Site
 Clone here to place two DmrA domains at the C-terminus and an N-myr signal at the N-
terminus of your protein.
 Linearize the vector at the XbaI site and directionally clone using the In-Fusion HD
Cloning System. Alternatively, amplify your gene with flanking XbaI and SpeI sites
(SpeI and XbaI have compatible cohesive ends) and clone the digested fragment into the
XbaI site.
 Do not include a ATG start codon in your gene; the ATG will be supplied by the vector at
nucleotides 668–670.
 Do not include a stop codon in your gene.
 Make sure that the coding region of your gene is in frame with the ATG at nucleotides
668–670. Tip: if your gene sequence is in frame with the XbaI site in your primers, it will
automatically be in the correct reading frame when cloned.
 The expressed protein will contain a C-terminal HA-tag.
 SpeI Site
 Clone here to place two DmrA domains and the N-myr signal at the N-terminus of your
protein.
 Linearize the vector at the SpeI site and directionally clone using Clontech’s In-Fusion
HD Cloning System. Alternatively, amplify your gene with flanking XbaI and SpeI sites
(SpeI and XbaI have compatible cohesive ends) and clone into the SpeI site.
 Make sure that the coding region of your gene is in frame with the last codon of the
DmrA sequence (nucleotides 1361–1363). Tip: If your gene sequence is in frame with the
SpeI site in your primers, it will automatically be in the correct reading frame when
cloned.
 If you wish to retain the HA-Tag, do not include a stop codon at the end of your gene.
 If you do not wish to retain the HA-Tag, include a stop codon at the end of your gene.

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3. Cloning options for pHet-Nuc1
 XbaI Site
 Clone here to place a DmrA domain at the C-terminus and an HA-Tag and nuclear
localization signal (NLS) at the N-terminus of your protein.
 Linearize the vector at the XbaI site and directionally clone using the In-Fusion HD
Cloning System. Alternatively, amplify your gene with flanking XbaI and SpeI sites
(SpeI and XbaI have compatible cohesive ends) and clone the digested fragment into the
XbaI site.
 The first ATG start codon will be supplied by the HA-Tag at nucleotides 673-675, so
there is no need to include a start codon at the start of your gene of interest.
 Do not include a stop codon in your gene.
 Make sure that the coding region of your gene is in frame with the ATG at nucleotides
673-675. Tip: if your gene sequence is in frame with the XbaI site in your primers, it will
automatically be in the correct reading frame when cloned.
 SpeI Site
 Clone here to place a DmrA domain, HA-tag, and NLS at the N-terminus of your protein.
 Linearize the vector at the SpeI site and directionally clone using Clontech’s In-Fusion
HD Cloning System. Alternatively, amplify your gene with flanking XbaI and SpeI sites
(SpeI and XbaI have compatible cohesive ends) and clone into the SpeI site.
 Make sure that the coding region of your gene is in frame with the last codon of the
DmrA sequence (nucleotides 1084–1086). Tip: If your gene sequence is in frame with the
SpeI site in your primers, it will automatically be in the correct reading frame when
cloned.
 Include a stop codon at the end of your gene of interest.

4. Creating Fusion Proteins with Multiple Dimerization Domains

You may choose to add additional dimerization domains to your protein to allow for higher order
oligomerization. Additional DmrA or DmrC domains can be added to the XbaI (or SpeI) site of
any of the vectors by using In-Fusion HD or via traditional cloning of an XbaI-SpeI fragment.
Since the flanking XbaI and SpeI sites are maintained after cloning, additional domains can be
fused if desired.

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V. In Vitro Inducible Heterodimerization
Please read each protocol completely before starting. Successful results depend on understanding and performing
the following steps correctly.

A. Protocol: Transient Transfection of Heterodimerizer

Prior to establishing a stable cell line that expresses the pHet-1 and pHet-Nuc1 (or pHet-Mem1) constructs
containing your genes of interest, your constructs should be transiently transfected and tested for dimerization in
response to A/C Heterodimerizer. For your initial in vitro experiments, we recommend testing medium containing
different concentrations of A/C Heterodimerizer with your transfected cells in order to determine the sensitivity of
the system containing your protein(s) of interest.
1. In a well of a 6-well plate, use Xfect Transfection Reagent (Section III.E) to transfect your target cell
line with 5 µl of the pHet-1 and (pHet-Nuc or pHet-Mem1) constructs containing your gene of
interest. Follow the Xfect Protocol (Type PT5003-2 in the keyword field at
[Link]/manuals).
2. At 12 hours after transfection, split transfected cells into different plates or separate wells of a 6-well
plate, or your preferred plate format.
To begin incubation of the transfected cells with A/C Heterodimerizer at specific time intervals and
concentrations, replace the medium in the plates containing the transfected cells with medium
containing the appropriate amount of A/C Heterodimerizer, diluted as described below. Maintain at
least one culture in medium containing no A/C Heterodimerizer as a negative control.
NOTE: In the case of adherent cells, let the cells reattach after the split before removing the medium.
a. Recommended A/C Heterodimerizer Concentrations and Time Points
 Try A/C Heterodimerizer concentrations between 0.1 nM and 500 nM for different
lengths of time (30 minutes to 12+ hours) to determine the best experimental conditions.
b. General Guidelines for Preparing Medium Containing A/C Heterodimerizer
 Dilute the supplied A/C Heterodimerizer stock solution (0.5 mM, supplied in ethanol) in
tissue culture media to the final concentration(s) needed in your experiment.
EXAMPLE: Preparation of 10 ml of medium containing 500 nM of A/C
Heterodimerizer: Dilute 10 µl of A/C Heterodimerizer stock solution (500 µM) in 10 ml
of medium to yield a final concentration of 500 nM.
 Working concentrations of A/C Heterodimerizer can be obtained by adding it directly
from ethanol stocks, or by diluting it serially in culture medium just before use.
 If you are making serial dilutions of A/C Heterodimerizer into culture medium, we
recommend that the highest concentration not exceed 5 μM, to ensure complete solubility
in the (aqueous) culture medium.
 In either case, the final concentration of ethanol in the medium added to mammalian cells
should be kept below 0.5% (a 200-fold dilution of a 100% ethanol solution) to prevent
this solvent from having a detrimental effect on the cells.

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3. After adding the medium containing A/C Heterodimerizer at the appropriate concentration and for the
appropriate length of time, the effect of dimerization can be analyzed with an assay that is appropriate
for your experiment.

B. Protocol: Stable Expression of Heterodimerizer Constructs

To select for stable clones that express the pHet-1 and pHet-Nuc1 (or pHet-Mem1) constructs containing your
gene of interest (and have been shown to be responsive to A/C Heterodimerizer in Section V.A), cotransfect the
construct into your target cell line along with a linear selection marker (Purr or Hygr), and select stable
transfectants by screening for hygromycin or puromycin resistance, as follows:
1. Seed your target cells in a single well of a 6-well plate at a density sufficient to reach near confluence
at 48 hr after transfection.
2. Transfect the pHet-1 and pHet-Nuc1 (or pHet-Mem1) constructs into your target cells using Xfect
Transfection Reagent. Follow the Xfect Protocol (PT5003-2 from [Link]/manuals),
except use 2 μg of your pHet-1 and pHet-Nuc1 (or pHet-Mem1) constructs per well together with 100
ng of one of the supplied linear selection markers (puromycin or hygromycin).
NOTE: We use less DNA for stable transfections than is required by the general Xfect protocol, to
ensure that individual colonies are well-separated after puromycin or hygromycin selection.
3. After 48 hr, split the confluent well into 4 x 10 cm dishes (do not add the selective antibiotic yet).
4. After an additional 48 hr, add either puromycin or hygromycin at the selection concentration that is
optimal for your cell line (Table 2).
Table 2. Recommended Antibiotic Concentrations for Selecting & Maintaining Stable Cell Lines

Recommended Concentration (µg/ml)

1
Cat. No. Antibiotic Selecting Colonies Maintenance
631306 Puromycin (100 mg)
0.25–10 0.25
631305 Puromycin (25 mg)
631309 Hygromycin B (1 g) 50–400 100
1
When selecting for single colonies, the appropriate dose must be determined empirically for your specific cell
line. Test a dosage range using dishes of untransfected cells and choose the dose that kills all of the cells in 3–5
days. If all the cells die in less than 24 hr, you should use a lower dose.

5. Replace medium with fresh complete medium plus hygromycin or puromycin every four days, or
more often if necessary.
6. Cells that have not integrated the plasmid should begin to die after ~3–5 days.
NOTE: Avoid passaging the cells a second time, since replating cells under selection may result in
plates containing too many colonies for effective colony isolation (because individual colonies are not
well-separated).
7. After ~2 weeks, resistant colonies should begin to appear.
8. When the colonies are large enough to transfer, use cloning cylinders or disks to harvest (i.e., pick)
large, healthy colonies, and transfer each into a separate well of a 24-well plate.

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9. Culture 3-4 clones in a maintenance concentration of antibiotic (Table 2). Expand and test clones
using your preferred assay, after treating them with A/C Heterodimerizer according to the
concentrations and incubation conditions determined in Section V.A.

C. Protocol: Washout Experiment—Removing A/C Heterodimerizer from Cells

Perform this experiment to compare target cells before and after A/C Heterodimerizer treatment.
Instructions are provided for both adherent and suspension cells.
1. Adherent cells
a. Remove the medium from your transfected and compound treated cells.
b. Rinse cells with warm PBS with Ca2+ and Mg2+.
c. Detach cells by your method of choice (trypsin, cell dissociation buffer, etc.).
d. Split cells into at least two new cell culture plates.
e. Culture cells in one plate in the presence of A/C Heterodimerizer in medium at a
concentration of your choice (positive control) and culture the second plate without A/C
Heterodimerizer (negative control).
f. Collect cells at a specific time after splitting that is defined by your needs, in order to analyze
and compare cells cultured under the different conditions described above.
2. Suspension cells
a. Collect the cells via centrifugation.
b. Resuspend one portion of the cells in medium with A/C Heterodimerizer and another portion
of the cells in medium without A/C Heterodimerizer.
c. Analyze the cells using an assay that is appropriate for your experiment.

D. Results Obtained Using In Vitro Heterodimerization

Peak effects of induced heterodimerization of two proteins using A/C Hetrodimerizer are generally seen
at concentrations of 500 nM (Muthuswamy, et al., 1999; Castellano et al., 1999; unpublished data). In
initial experiments we recommend that A/C Hetrodimerizer be tested across a broad range of
concentrations (e.g. 0.5 nM to 500 nM) to provide a complete dose-response profile.

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iDimerize™ Inducible Heterodimer System User Manual PT5179-1
VI. In Vivo Inducible Heterodimerization
A. General Guidelines
For in vivo use, reconstitute the 5 mg format of A/C Heterodimerizer (Cat. No. 635055) following your
established injection protocol (for 5 mg format—see Section III.A).

B. Results Obtained Using In Vivo Heterodimerization

The ligand has been successfully used in mice with maximal effects seen at doses in the range of 0.5–10
mg/kg delivered intraveneously.

VII. References
Castellano, F., Montcourrier, P., Guillemot, J. C., Gouin, E., Machesky, L., Cossart, P. & Chavrier, P. (1999) Inducible
recruitment of Cdc42 or WASP to a cell-surface receptor triggers actin polymerization and filopodium formation. Curr.
Biol. 9(7): 351–360.
Crabtree, G. R. & Schreiber, S. L. (1996) Three-part inventions: intracellular signaling and induced proximity. Trends
Biochem. Sci. 21(11): 418–422.
Graef, I. A., Holsinger, L. J., Diver, S., Schreiber, S. L. & Crabtree, G. R. (1997) Proximity and orientation underlie
signaling by the non-receptor tyrosine kinase ZAP70. Embo. J. 16(18): 5618–5628.

Muthuswamy, S. K., Gilman, M. & Brugge, J. S. (1999) Controlled dimerization of ErbB receptors provides evidence for
differential signaling by homo- and heterodimers. Mol. Cell. Biol. 19(10): 6845–6857.

VIII. Troubleshooting

Description of Problem Possible Explanation Solution

The expression level of the protein(s)
of interest fused to the DmrA and/or Transfect cells with a lower amount of
Dimerization is observed in
DmrC domain(s) is too high, especially plasmid (in the case of transient
the absence of the A/C
in the case of a DmrA-tagged protein of transfection) or establish stable clones and
Heterodimerizer
interest localized to the plasma screen for the lowest background.
membrane.
 Increase the amount of A/C
 The A/C Heterodimerizer Heterodimerizer added.
concentration is too low.  Make sure to include a positive control
Addition of A/C  The monitoring assay is not when performing your assay.
Heterodimerizer does not sensitive enough.  Prepare a more concentrated stock
result in any of the expected  The volume of A/C Heterodimerizer solution.
effects used causes cells to die due to  Monitor protein expression in your cells
high solvent concentration. by Western blot using the anti-DmrA
 Expression level too low and anti-DmrC antibodies (Section
III.B).

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