pGEM-T Easy

Technical Manual
pGEM-T and pGEM-T

Easy Vector Systems
INSTRUCTIONS FOR USE OF PRODUCTS A1360, A1380, A3600 AND
A3610.
pGEM-T and pGEM-T Easy

Vector Systems
All technical literature is available on the Internet at www.promega.com/tbs/
Please visit the web site to verify that you are using the most current version of this
Technical Manual. Please contact Promega Technical Services if you have questions on use
of this system. E-mail techserv@promega.com.
1. Description..........................................................................................................2
2. pGEM-T and pGEM-T Easy Vector
Multiple Cloning Sequences and Maps .......................................................4
A. Multiple Cloning Sequences ..............................................................................4
B. pGEM-T Vector Map and Sequence Reference Points .................................5
C. pGEM-T Easy Vector Map and Sequence Reference Points........................6
3. Product Components and Storage Conditions ............................................7

4. Protocol for Ligations Using the pGEM-T and
pGEM-T Easy Vectors and the 2X Rapid Ligation Buffer.......................8
5. Protocol for Transformations Using the pGEM-T
and pGEM-T Easy Vector Ligation Reactions ...........................................9
6. General Considerations..................................................................................11
A.
B.
C.
D.
E.
PCR Product Purity............................................................................................11

Blunt-Ended PCR Products...............................................................................11
Optimizing Insert:Vector Molar Ratios...........................................................13
Screening Transformants for Inserts ...............................................................14
Experimental Controls.......................................................................................14
7. Isolation of Recombinant Plasmid DNA....................................................15

8. Generation of Single-Stranded DNA from
the pGEM-T and pGEM-T Easy Vectors.................................................16
9. Troubleshooting...............................................................................................16
10. References .........................................................................................................20
11. Appendix ..........................................................................................................20
A.
B.
C.
D.
PRINTED IN USA.
Revised 3/09
pGEM-T Vector Restriction Enzyme Sites....................................................20

pGEM-T Easy Vector Restriction Enzyme Sites ..........................................22
Composition of Buffers and Solutions ............................................................25
Related Products.................................................................................................26
Promega Corporation 2800 Woods Hollow Road Madison, WI 53711-5399 USA

Toll Free in USA 800-356-9526 Phone 608-274-4330 Fax 608-277-2516 www.promega.com
Part# TM042
Printed in USA.
Revised 3/09
Part# TM042
Page 1
1.
Description
Table 1. Comparison of PCR Product Properties for Thermostable DNA Polymerases.
The pGEM-T and pGEM-T Easy Vector Systems(a,b) are convenient systems for
the cloning of PCR products. The vectors are prepared by cutting the pGEM5Zf(+) and pGEM-T Easy Vectors, respectively, with EcoRV and adding a 3
terminal thymidine to both ends. These single 3-T overhangs at the insertion site
greatly improve the efficiency of ligation of a PCR product into the plasmids by
preventing recircularization of the vector and providing a compatible overhang
for PCR products generated by certain thermostable polymerases (1,2). As
summarized in Table 1, these polymerases often add a single deoxyadenosine, in
a template-independent fashion, to the 3-ends of the amplified fragments (3,4).
The high-copy-number pGEM-T and pGEM-T Easy Vectors contain T7 and SP6
RNA polymerase promoters flanking a multiple cloning region within the peptide coding region of the enzyme -galactosidase. Insertional inactivation of
the -peptide allows recombinant clones to be directly identified by color
screening on indicator plates. The multiple cloning region of the two vectors
includes restriction sites conveniently arranged for use with the Erase-a-Base
System (Cat.# E5750) for generating nested sets of deletions.
Both the pGEM-T and pGEM-T Easy Vector contain multiple restriction sites
within the multiple cloning region. The pGEM-T Easy Vector multiple cloning
region is flanked by recognition sites for the restriction enzymes EcoRI, BstZI and
NotI, thus providing three single-enzyme digestions for release of the insert. The
pGEM-T Vector cloning region is flanked by recognition sites for the enzyme
BstZI. Alternatively, a double-digestion may be used to release the insert from
either vector.
Characteristic
Resulting DNA ends
53 exonuclease activity
35 exonuclease activity
Taq/
AmpliTaq
3A
Yes
No
Thermostable DNA Polymerase

Vent Deep
Tfl
Tth
(Tli) Vent Pfu
>95% >95%
3A
3A Blunt Blunt Blunt
Yes
Yes
No
No
No
No
No
Yes
Yes
Yes
Pwo
Blunt
No
Yes
Specialized Applications of the pGEM-T and pGEM-T Easy Vectors:
Cloning PCR products.

Construction of unidirectional nested deletions with the Erase-a-Base System.
Production of ssDNA.
Blue/white screening for recombinants.
In vitro transcription from dual-opposed promoters. (For protocol information,
please request the Riboprobe in vitro Transcription Systems Technical Manual
#TM016 (available at: www.promega.com/tbs/)
For peer-reviewed articles that cite use of the pGEM-T Vectors, visit:
www.promega.com/citations
The pGEM-T and pGEM-T Easy Vectors also contain the origin of replication
of the filamentous phage f1 for the preparation of single-stranded DNA (ssDNA;
see Section 8). The ssDNA molecule exported corresponds to the bottom strand
shown in Figure 1.
The pGEM-T and pGEM-T Easy Vector Systems include a 2X Rapid Ligation
Buffer for ligation of PCR products. Reactions using this buffer may be incubated
for 1 hour at room temperature. The incubation period may be extended to
increase the number of colonies after transformation. Generally, an overnight
incubation at 4C will produce the maximum number of transformants.


Part# TM042
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Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
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2.
2.B. pGEM-T Vector Map and Sequence Reference Points
pGEM-T and pGEM-T Easy Vector Multiple Cloning Sequences and Maps
2.A. Multiple Cloning Sequences

XmnI 1994
NaeI
2692
ScaI
1875
T7
f1 ori
T7 Transcription Start
5 . . . TGTAA TACGA CTCAC TATAG GGCGA ATTGG GCCCG ACGTC GCATG CTCCC GGCCG
3 . . . ACATT ATGCT GAGTG ATATC CCGCT TAACC CGGGC TGCAG CGTAC GAGGG CCGGC
T7 Promoter
ApaI
AatII
SphI
Amp r
BstZI
pGEM-T
Vector
lacZ
(3000bp)
CCATG GCCGC GGGATT3
ATCAC TAGTG CGGCC GCCTG CAGGT CGACC ATATG
cloned insert
GGTAC CGGCG CCCTA
3TTAGTG ATCAC GCCGG CGGAC GTCCA GCTGG TATAC
NcoI
SacII
SpeI
NotI
BstZI
PstI
SalI
NdeI
SP6 Transcription Start
SP6 Promoter
SacI
BstXI
NsiI
T7 RNA polymerase transcription initiation site

multiple cloning region
SP6 RNA polymerase promoter (17 to +3)
SP6 RNA polymerase transcription initiation site
pUC/M13 Reverse Sequencing Primer binding site
lacZ start codon
lac operator
-lactamase coding region
phage f1 region
lac operon sequences
pUC/M13 Forward Sequencing Primer binding site
T7 RNA polymerase promoter (17 to +3)
5 . . . TGTAA TACGA CTCAC TATAG GGCGA ATTGG GCCCG ACGTC GCATG CTCCC GGCCG CCATG
3 . . . ACATT ATGCT GAGTG ATATC CCGCT TAACC CGGGC TGCAG CGTAC GAGGG CCGGC GGTAC
T7 Promoter
ApaI
AatII
SphI
BstZI
NcoI
GCGGC CGCGG GAATT CGATT3

ATCAC TAGTG AATTC GCGGC CGCCT GCAGG TCGAC
cloned insert
CGCCG GCGCC CTTAA GCTA
3TTAGTG ATCAC TTAAG CGCCG GCGGA CGTCC AGCTG
EcoRI
SpeI
EcoRI
NotI
BstZI
PstI
SalI
CATAT GGGA GAGCT CCCAA CGCGT TGGAT GCATA GCT TG AGTAT TCTAT AGTGT CACCT AAAT . . . 3
GTATA CCCT CTCGA GGGTT GCGCA ACCTA CGTAT CGAAC T CATA AGATA TCACA GTGGA TT TA . . . 5
SP6 Promoter
SacI
BstXI
NsiI
1517MA
SP6 Transcription Start
NdeI
55
62
62
73
75
82
94
103
112
126
pGEM-T Vector sequence reference points:

T7 Transcription Start
SacII
1 start
14
20
26
31
37
46
Figure 2. pGEM-T Vector circle map and sequence reference points.
pGEM-T Easy Vector
NotI
BstZI
SpeI
NotI
BstZI
PstI
SalI
NdeI
SacI
BstXI
NsiI
SP6
0357MA06_2A
GGAGA GCTCC CAACG CGTTG GATGC ATAGC TTGAG TATTC TATAG TGTCA CCTAA AT . . . 3
CCTCT CGAGG GTTGC GCAAC CTACG TATCG AACTC ATAAG ATATC ACAGT GGATT TA . . . 5
ori
ApaI
AatII
SphI
BstZI
NcoI
SacII
0356VA04_3A
pGEM-T Vector
Figure 1. The promoter and multiple cloning sequence of the pGEM-T and pGEM-T
Easy Vectors. The top strand of the sequence shown corresponds to the RNA synthesized
by T7 RNA polymerase. The bottom strand corresponds to the RNA synthesized by SP6
RNA polymerase.
1
10113
124143
126
161177
165
185201
13222182
23652820
28212981, 151380
29412957
29843
Note: Inserts can be sequenced using the SP6 Promoter Primer (Cat.# Q5011), T7
Promoter Primer (Cat.# Q5021), pUC/M13 Forward Primer (Cat.# Q5601), or
pUC/M13 Reverse Primer (Cat.# Q5421).
Note: A single digest with BstZI (Cat.# R6881) will release inserts cloned into the
pGEM-T Vector. Double digests can also be used to release inserts.


Part# TM042
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Printed in USA.
Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
Page 5
3.
2.C. pGEM-T Easy Vector Map and Sequence Reference Points
XmnI 2009
ScaI 1890
NaeI 2707
f1 ori
Ampr
pGEM-T Easy
Vector
lacZ
T
T7
ApaI
AatII
SphI
BstZI
NcoI
BstZI
NotI
SacII
EcoRI
1 start
14
20
26
31
37
43
43
49
52
ori
SpeI
EcoRI
NotI
BstZI
PstI
SalI
NdeI
SacI
BstXI
NsiI
SP6
64
70
77
77
88
90
97
109
118
127
141
1473VA05_6A
(3015bp)
Figure 3. pGEM-T Easy Vector circle map and sequence reference points.
pGEM-T Easy Vector sequence reference points:
T7 RNA polymerase transcription initiation site
multiple cloning region
SP6 RNA polymerase promoter (17 to +3)
SP6 RNA polymerase transcription initiation site
pUC/M13 Reverse Sequencing Primer binding site
lacZ start codon
lac operator
-lactamase coding region
phage f1 region
lac operon sequences
pUC/M13 Forward Sequencing Primer binding site
T7 RNA polymerase promoter (17 to +3)
1
10128
139158
141
176197
180
200216
13372197
23802835
28362996, 166395
29492972
29993
Note: Inserts can be sequenced using the SP6 Promoter Primer (Cat.# Q5011), T7
Promoter Primer (Cat.# Q5021), pUC/M13 Forward Primer (Cat.# Q5601), or
pUC/M13 Reverse Primer (Cat.# Q5421).
Note: A single digest with BstZI (Cat.# R6881), EcoRI (Cat.# R6011) or NotI (Cat.#
R6431) will release inserts cloned into the pGEM-T Easy Vector. Double digests can
also be used to release inserts.
Product Components and Storage Conditions
Product
Size
pGEM-T Vector System I
20 reactions
For Laboratory Use. Includes:
1.2g pGEM-T Vector (50ng/l)
12l Control Insert DNA (4ng/l)
100u T4 DNA Ligase
200l 2X Rapid Ligation Buffer, T4 DNA Ligase
Cat.#
A3600
Product
Size
pGEM-T Vector System II
20 reactions
1.2g pGEM-T Vector (50ng/l)
100u T4 DNA Ligase
1.2ml JM109 Competent Cells, High Efficiency (6 200l)
Cat.#
A3610
Product
Size
pGEM-T Easy Vector System I
20 reactions
1.2g pGEM-T Easy Vector (50ng/l)
100u T4 DNA Ligase
Cat.#
A1360
Product
Size
pGEM-T Easy Vector System II
20 reactions
1.2g pGEM-T Easy Vector (50ng/l)
100u T4 DNA Ligase
1.2ml JM109 Competent Cells, High Efficiency (6 200l)
Cat.#
A1380
Storage Conditions: For Cat.# A3610, A1380, store the Competent Cells at
70C. All other components can be stored at 20C.


Part# TM042
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Printed in USA.
Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
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4.
Protocol for Ligations Using the pGEM-T and pGEM-T Easy Vectors
and the 2X Rapid Ligation Buffer
5.
1. Briefly centrifuge the pGEM-T or pGEM-T Easy Vector and Control

Insert DNA tubes to collect contents at the bottom of the tubes.
Use high-efficiency competent cells (1 108cfu/g DNA) for transformations.

The ligation of fragments with a single-base overhang can be inefficient, so it is
essential to use cells with a transformation efficiency of 1 108cfu/g DNA (or
higher) in order to obtain a reasonable number of colonies (see Section 6.E).
2. Set up ligation reactions as described below.
Note: Use 0.5ml tubes known to have low DNA-binding capacity (e.g.,
VWR Cat.# 20170-310).
Vortex the 2X Rapid Ligation Buffer vigorously before each use.
Standard Positive Background

Reaction Control
Control
2X Rapid Ligation Buffer, T4 DNA Ligase
5l
5l
5l
pGEM-T or pGEM-T Easy Vector (50ng)
1l
1l
1l
PCR product
Xl*
Control Insert DNA
2l
T4 DNA Ligase (3 Weiss units/l)

1l
1l
1l
deionized water to a final volume of
10l
10l
10l
*Molar ratio of PCR product:vector may require optimization (see Section 6.C).
3. Mix the reactions by pipetting. Incubate the reactions 1 hour at room

temperature.
Alternatively, if the maximum number of transformants is required,
incubate the reactions overnight at 4C.
Notes:
1. Use only Promega T4 DNA Ligase supplied with this system to perform
pGEM-T and pGEM-T Easy Vector ligations. Other commercial
preparations of T4 DNA ligase may contain exonuclease activities that may
remove the terminal deoxythymidines from the vector.
Protocol for Transformations Using the pGEM-T and pGEM-T Easy

Vector Ligation Reactions
We recommend using JM109 High Efficiency Competent Cells (Cat.# L2001);

these cells are provided with the pGEM-T and pGEM-T Easy Vector Systems II.
Other host strains may be used, but they should be compatible with blue/white
color screening and standard ampicillin selection.
JM109 cells should be maintained on M9 minimal medium plates supplemented
with thiamine hydrochloride prior to the preparation of competent cells. This
selects for the presence of the F episome, containing both the proAB genes,
which complement proline auxotrophy in a host with a (proAB) deletion, and
lacIqZM15, required for blue/white screening. If you are using competent cells
other than JM109 High Efficiency Competent Cells purchased from Promega, it
is important that the appropriate transformation protocol be followed. Selection
for transformants should be on LB/ampicillin/IPTG/X-Gal plates (see
Section 11.C). For best results, do not use plates that are more than 1 month old.
The genotype of JM109 is recA1, endA1, gyrA96, thi, hsdR17 (rK,mK+), relA1,
supE44, (lac-proAB), [F, traD36, proAB, lacIqZM15] (5).
Materials to Be Supplied by the User
(Solution compositions are provided in Section 11.C.)
LB plates with ampicillin/IPTG/X-Gal
SOC medium
2. 2X Rapid Ligation Buffer contains ATP, which degrades during temperature

fluctuations. Avoid multiple freeze-thaw cycles and exposure to frequent
temperature changes by making single-use aliquots of the buffer.
1. Prepare two LB/ampicillin/IPTG/X-Gal plates for each ligation reaction, plus

two plates for determining transformation efficiency (see Section 6.E). Equilibrate
the plates to room temperature prior to plating (Step 10).
3. It is important to vortex the 2X Rapid Ligation Buffer before each use.
2. Centrifuge the tubes containing the ligation reactions to collect contents at the
bottom of the tube. Add 2l of each ligation reaction to a sterile 1.5ml
microcentrifuge tube on ice (see Note 1). Set up another tube on ice with 0.1ng
uncut plasmid for determination of the transformation efficiency of the
competent cells (see Section 6.E).
4. Longer incubation times will increase the number of transformants.

Generally, incubation overnight at 4C will produce the maximum number
of transformants.
3. Remove tube(s) of frozen JM109 High Efficiency Competent Cells from storage
and place in an ice bath until just thawed (about 5 minutes). Mix the cells by
gently flicking the tube.
Note: Avoid excessive pipetting, as the competent cells are extremely fragile.


Part# TM042
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Revised 3/09
Part# TM042
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4. Carefully transfer 50l of cells into each tube prepared in Step 2 (100l cells
for determination of transformation efficiency).
5. Gently flick the tubes to mix and place them on ice for 20 minutes.
6. Heat-shock the cells for 4550 seconds in a water bath at exactly 42C (Do
not shake).
7. Immediately return the tubes to ice for 2 minutes.
8. Add 950l room temperature SOC medium to the tubes containing cells
transformed with ligation reactions and 900l to the tube containing cells
transformed with uncut plasmid (LB broth may be substituted, but colony
number may be lower).
9. Incubate for 1.5 hours at 37C with shaking (~150rpm).
10. Plate 100l of each transformation culture onto duplicate LB/ampicillin/
IPTG/X-Gal plates. For the transformation control, a 1:10 dilution with
SOC medium is recommended for plating. If a higher number of colonies is
desired, the cells may be pelleted by centrifugation at 1,000 g for 10
minutes, resuspended in 200l of SOC medium, and 100l plated on each
of two plates.
11. Incubate the plates overnight (1624 hours) at 37C. In our experience, if
100l is plated approximately 100 colonies per plate are routinely seen
when using competent cells that are 1 108cfu/g DNA. Longer
incubations or storage of plates at 4C (after 37C overnight incubation)
may be used to facilitate blue color development. White colonies generally
contain inserts; however, inserts may also be present in blue colonies.
Please see Section 6.D for more information.
Notes:
1. In our experience, the use of larger (17 100mm) polypropylene tubes (e.g.,
Falcon Cat.# 2059) has been observed to increase transformation efficiency.
Tubes from some manufacturers bind DNA, thereby decreasing the colony
number, and should be avoided.
2. Colonies containing -galactosidase activity may grow poorly relative to
cells lacking this activity. After overnight growth, the blue colonies may be
smaller than the white colonies, which are approximately one millimeter in
diameter.
6.
General Considerations
6.A. PCR Product Purity

An aliquot of the PCR reaction should be analyzed on an agarose gel before use
in the ligation reaction. The PCR product to be ligated can be gel-purified or
purified directly from the PCR amplification using the Wizard SV Gel and PCR
Clean-Up System (Cat.# A9281). Exposure to shortwave ultraviolet light should
be minimized in order to avoid the formation of pyrimidine dimers. If smearing
of the PCR product or inappropriate banding is observed on the gel, excise the
bands to be cloned and purify the DNA with Wizard SV Gel and PCR CleanUp System. Even if distinct bands of the expected size are observed, primerdimers should be removed by gel purification or by using the Wizard SV Gel
and PCR Clean-Up System. Use of crude PCR product may produce successful
ligation in some cases; however, the number of white colonies containing the
relevant insert may be reduced due to preferential incorporation of primerdimers or other extraneous reaction products. Therefore, it may be necessary to
screen numerous colonies in order to identify clones that contain the PCR
product of interest.
6.B. Blunt-Ended PCR Products
Thermostable DNA polymerases with proofreading activity, such as Pfu DNA
Polymerase (Cat.# M7741), Pwo DNA polymerase and Tli DNA Polymerase
(Cat.# M7101) generate blunt-ended fragments during PCR amplification.
Nevertheless, PCR fragments generated using these polymerases can be
modified using the A-tailing procedure outlined in Figure 4 and ligated into
the pGEM-T and pGEM-T Easy Vectors (6). Using this method, only one
insert will be ligated into the vector as opposed to multiple insertions that can
occur with blunt-ended cloning. In addition, with T-vector cloning there is no
need to dephosphorylate the vector, and there is a low background of
religated vector.
Using this procedure with optimized insert:vector ratios, 5595% recombinants
were obtained when Pfu and Tli DNA Polymerases were used to generate the
insert DNA (Table 2). It is critical that the PCR fragments are purified using
the Wizard SV Gel and PCR Clean-Up System (Cat.# A9281) or by direct
isolation from a gel by other means. In the absence of purification, the
proofreading activity of the Pfu, Pwo and Tli DNA Polymerases will degrade
the PCR fragments, or remove the 3-terminal deoxyadenosine added during
tailing or the 3-terminal deoxythymidine from the vector during the A-tailing
reaction or ligation.
To optimize cloning efficiency, the amount of DNA in the A-tailing reaction
and the ligation volumes must be adjusted depending on the molar yield of
the purified PCR product. When molar concentrations are high due to small
fragment size and/or good amplification, small volumes of the PCR fragment
are needed for the A-tailing and ligation reactions. However, when molar
concentration is low due to large fragment size and/or poor amplification,


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Revised 3/09
Part# TM042
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Start with 17l of purified PCR fragment generated by a

proofreading polymerase (e.g., Pfu DNA Polymerase).
Add 1l Taq DNA Polymerase 10X Reaction Buffer with MgCl2.
Add dATP to a final concentration of 0.2mM.
Add 5 units of Taq DNA Polymerase.
Table 2. Comparison of A-Tailing Procedures Used With Different DNA

Polymerases.
Polymerase
Pfu DNA Polymerase
Tli DNA Polymerase
% Recombinants1
1-Hour Ligation at 24C 16-Hour Ligation at 4C
(Standard)
(Alternative)
542bp
1.8kb
542bp
1.8kb
6584%2
3155%3
8195%2
5075%3
6877%4
3765%5
8593%4
6081%5
PCR fragments generated by Pfu and Tli DNA Polymerase were A-tailed and ligated into
pGEM-T Easy Vector for 1 hour at 24C or for 16 hours at 4C. Two microliters of ligation
mix was transformed into JM109 Competent Cells and plated on LB/amp/IPTG/X-gal
plates.
1% Recombinants = % white and/or pale blue colonies. PCR fragments were purified
with the Wizard PCR Preps DNA Purification System prior to A-tailing.
2Insert:vector ratios tested: 5:1, 3:1, 1:1. Volume of PCR amplification product used in Atailing: 12l.
5Insert:vector ratios tested: 2:1, 1:1. Volume of PCR amplification product used in Atailing: 47l.
Add deionized water to a final reaction volume of 10l.

Incubate at 70C for 1530 minutes.
Use 12l in a ligation reaction with
Promegas pGEM-T and pGEM-T Easy Vector.
2357MA02_9A
large volumes of the PCR fragment are needed for the A-tailing and ligation
reactions. We have successfully used 17l of purified PCR fragment in Atailing reactions to optimize the insert:vector ratio. (See Section 6.C for further
discussion of optimizing the insert:vector ratio.) Recombinants were identified
by blue/white screening, and 70100% were shown to have the correct size
insert by PCR. Few recombinants were observed in control reactions in which
the PCR fragment was not tailed. These control results confirm that the
majority of the pGEM-T Easy Vector used contained 3-terminal
deoxythymidine and that, during the A-tailing, Taq DNA Polymerase added a
3-terminal deoxyadenosine to a significant proportion of the PCR fragments.
Figure 4. An A-tailing procedure for blunt-ended PCR fragments purified with the
Wizard SV Gel and PCR Clean-Up System (Cat.# A9281) and used in T-vector
cloning.
6.C. Optimizing Insert:Vector Molar Ratios
The pGEM-T and pGEM-T Easy Vector Systems have been optimized using
a 1:1 molar ratio of the Control Insert DNA to the vectors. However, ratios of
8:1 to 1:8 have been used successfully. If initial experiments with your PCR
product are suboptimal, ratio optimization may be necessary. Ratios from 3:1
to 1:3 provide good initial parameters. The concentration of PCR product
should be estimated by comparison to DNA mass standards on a gel or by
using a fluorescent assay (7). The pGEM-T and pGEM-T Easy Vectors are
approximately 3kb and are supplied at 50ng/l. To calculate the appropriate
amount of PCR product (insert) to include in the ligation reaction, use the
following equation.
ng of vector kb size of insert
insert:vector molar ratio = ng of insert
kb size of vector
Example of insert:vector ratio calculation:
How much 0.5kb PCR product should be added to a ligation in which 50ng of
3.0kb vector will be used if a 3:1 insert:vector molar ratio is desired?
50ng vector 0.5kb insert 3
= 25ng insert
3.0kb vector
1
Using the same parameters for a 1:1 insert:vector molar ratio, 8.3ng of a 0.5kb
insert would be required.


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Revised 3/09
Part# TM042
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6.D. Screening Transformants for Inserts
Background Control
pGEM-T
Set up a ligation reaction with 50ng of pGEM-T or pGEM-T Easy Vector and
no insert as described in Section 4 and use it for transformations as described
in Section 5. This control allows determination of the number of background
blue colonies resulting from non-T-tailed or undigested pGEM-T or pGEM-T
Easy Vector alone. If the recommendations in Section 5 are followed, 1030
blue colonies will typically be observed if the transformation efficiency of the
competent cells is 1 108cfu/g DNA. (Under these conditions, cells that have
an efficiency of 1 107cfu/g DNA would yield 13 blue colonies and cells
with a transformation efficiency of 1 109cfu/g DNA would yield 100300
blue colonies). Compare the number of blue colonies obtained with this
background control to the number of blue colonies obtained in the standard
reaction using the PCR product. If ligation of the PCR product yields
dramatically more blue colonies than the background control reaction, then
recombinants are probably among these blue colonies (see Section 6.D).
pGEM-T
and
Easy Vectors
Successful cloning of an insert into the
interrupts the coding sequence of -galactosidase; recombinant clones can
usually be identified by color screening on indicator plates. However, the
characteristics of PCR products cloned into the pGEM-T and pGEM-T Easy
Vectors can significantly affect the ratio of blue:white colonies obtained
following transformation of competent cells. Clones that contain PCR products,
in most cases, produce white colonies, but blue colonies can result from PCR
fragments that are cloned in-frame with the lacZ gene. Such fragments are
usually a multiple of 3 base pairs long (including the 3-A overhangs), and do
not contain in-frame stop codons. There have been reports of DNA fragments of
up to 2kb that have been cloned in-frame and have produced blue colonies.
Even if your PCR product is not a multiple of 3 bases long, the amplification
process can introduce mutations (e.g., deletions or point mutations) that may
result in blue colonies when competent cells are transformed with the
fragment inserted into the pGEM-T or pGEM-T Easy Vectors.
Transformation Control
Check the transformation efficiency of the competent cells by transforming
them with an uncut plasmid (not pGEM-T or pGEM-T Easy since these
vectors are linearized) and calculating cfu/g DNA. If the transformation
efficiency is lower than 1 108cfu/g DNA, prepare fresh cells. (Competent
cells are available from Promega. See Section 11.D.) If you are not using JM109
High Efficiency Competent Cells (provided with pGEM-T and pGEM-T Easy
Vector Systems II; Cat.# A3610 and A1380, respectively), be sure the cells are
compatible with blue/white screening and standard ampicillin selection and
have a transformation efficiency of at least 1 108cfu/g DNA.
The Control Insert DNA supplied with the pGEM-T and pGEM-T Easy
Systems is a 542bp fragment from pGEM-luc Vector DNA (Cat.# E1541). This
sequence has been mutated to contain multiple stop codons in all six reading
frames, which ensures a low background of blue colonies for the control
reaction. Results obtained with the Control Insert DNA may not be
representative of those achieved with your PCR product.
6.E. Experimental Controls
Promega strongly recommends performing the controls described below.
These are necessary to accurately assess the performance of the pGEM-T and
pGEM-T Easy Vector Systems.
Example of Transformation Efficiency Calculation

After 100l competent cells are transformed with 0.1ng uncut plasmid DNA, the
transformation reaction is added to 900l of SOC medium (0.1ng DNA/ml).
From that volume, a 1:10 dilution with SOC medium (0.01ng DNA/ml) is made
and 100l plated on two plates (0.001ng DNA/100l). If 200 colonies are
obtained (average of two plates), what is the transformation efficiency?
Positive Control
Set up a ligation reaction with the Control Insert DNA as described in Section 4
and use it for transformations as described in Section 5. This control will allow
you to determine whether the ligation is proceeding efficiently. Typically,
approximately 100 colonies should be observed, 1040% of which are blue,
when competent cells that have a transformation efficiency of 1 108cfu/g
DNA are transformed. Greater than 60% of the colonies should be white. The
Control Insert DNA is designed to produce white colonies; however, other insert
DNA may not yield white colonies (see Section 6.D). Background blue colonies
from the positive control ligation reaction arise from non-T-tailed or undigested
pGEM-T or pGEM-T Easy Vector. These blue colonies are a useful internal
transformation control; if no colonies are obtained, the transformation has failed.
If blue colonies are obtained, but no whites, the ligation reaction may have
failed. If <50% white colonies are seen in the positive control reaction, then the
ligation conditions were probably suboptimal.
200cfu
= 2 105cfu/ng = 2 108cfu/g DNA
0.001ng
7.
Isolation of Recombinant Plasmid DNA
Standard plasmid miniprep procedures may be used to isolate the recombinant

plasmid DNA. The DNA Purification Chapter of the Promega Protocols and
Applications Guide provides an overview of plasmid DNA purification methods
(8). A convenient and reliable method is the Wizard Plus SV Minipreps DNA
Purification System (Cat.# A1330).
The concentration of the Control Insert DNA is such that 2l (4ng/l) can be
used in a 10l ligation reaction to achieve a 1:1 molar ratio with 50ng of the
pGEM-T or pGEM-T Easy Vectors.

Part# TM042
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Revised 3/09
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Revised 3/09
Part# TM042
Page 15
8.
9.
Generation of Single-Stranded DNA from the pGEM-T

and pGEM-T Easy Vectors
For induction of ssDNA production, bacterial cells containing either the

pGEM-T or pGEM-T Easy Vector are infected with an appropriate helper
phage (e.g., R408 Helper Phage, Cat.# P2291). The plasmid then enters the f1
replication mode, and the resulting ssDNA is exported as an encapsulated
virus-like particle. The ssDNA is purified from the supernatant by simple
precipitation and extraction procedures (9). For further information, please
contact your local Promega Branch Office or Distributor. In the U.S., contact
Technical Services at 1-800-356-9526.
9.
Troubleshooting (continued)
Symptoms
Causes and Comments
Less than 10% white colonies

with Control Insert DNA
(continued)
Ligation reaction has failed. Ligase buffer may

have low activity. The 2X Rapid Ligation Buffer
contains ATP, which degrades during
temperature fluctuations. Avoid multiple freezethaw cycles by making single-use aliquots of the
buffer. Use a fresh vial of buffer. To test the
activity of the ligase and buffer, set up a ligation
with ~20ng of DNA markers (e.g., Lambda
DNA/Hind III Markers, Cat.# G1711). Compare
ligated and nonligated DNA on a gel and check
that the fragments have been religated into highmolecular-weight material.
Troubleshooting
For questions not addressed here, please contact your local Promega Branch Office or Distributor.
Contact information available at: www.promega.com. E-mail: techserv@promega.com
Symptom
Causes and Comments
No colonies
A problem has occurred with the transformation

reaction or the cells have lost competence. Background undigested vector and religated non-Ttailed vector should yield 1030 blue colonies
independent of the presence of insert DNA.
Check the background control (Section 6.E).
T-overhangs have been removed, allowing bluntended ligation of vector and giving rise to more
blue than white colonies. Avoid introduction of
nucleases, which may degrade the T-overhangs.
Use only the T4 DNA Ligase provided with the
system, which has been tested for minimal
exonuclease activity.
Use high-efficiency competent cells (1 108cfu/

g DNA). Test the efficiency by transforming the
cells with an uncut plasmid that allows for
antibiotic selection, such as the pGEM-5Zf(+)
Vector. If the guidelines in Section 5.A are
followed, cells at 1 108cfu/g DNA typically
yield 100 colonies. Therefore, you would not see
any colonies from cells that are <1 107cfu/g
DNA (Section 6.E).
Improper dilution of the 2X Rapid Ligation

Buffer. The T4 DNA ligase buffer is provided at
a concentration of 2X. Use 5l in a 10l reaction.
If the total number of colonies is high, but there
are few/no white colonies, competent cells may
be high efficiency (1 109cfu/g) but there may
be a ligation problem. Approximately 1,000
colonies can be obtained from the positive
control ligation using cells that are 109cfu/g
DNA, with 7090% white colonies. If ligation is
suboptimal or fails, the total number of colonies
will be high (up to 300 cells at 1 109cfu/g),
but the amount of white colonies will be low or
zero. See comments below on ligation failure.
Improper dilution of the Rapid Ligation Buffer.

The Rapid Ligation Buffer is provided at a 2X
concentration. Use 5l in a 10l reaction.
T-overhangs have been removed, allowing bluntended ligation of vector and giving rise to more
blue than white colonies. Avoid introduction of
nucleases, which may degrade the T-overhangs.
Use only the T4 DNA Ligase provided with the
system, which has been tested for minimal
exonuclease activity.
Ligation temperature is too high. Higher
temperatures (>28C) give rise to increased
background and fewer recombinants.
Low number or no
white colonies containing
PCR product
Improper dilution of the Rapid Ligation Buffer.

The Rapid Ligation Buffer is provided at a 2X
concentration. Use 5l in a 10l reaction.
Ligation incubation is not long enough. Optimal
results are seen with an overnight ligation.
Failed ligation due to an inhibitory component in
the PCR product. Mix some of the PCR product
with the positive control ligation to determine
whether an inhibitor is present. If an inhibitor is
indicated, repurify the PCR fragment.


Part# TM042
Page 16
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Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
Page 17
9.
9.
Symptoms
Causes and Comments
Symptom
Causes and Comments
Low number or no white

colonies containing PCR product
(continued)
PCR product is not ligating because there are no

3-A overhangs. As summarized in Table 1, not
all thermostable DNA polymerases create a 3-A
overhang (3,4). Blunt-ended fragments may be
subsequently A-tailed by treatment with an
appropriate polymerase and dATP (1012).
Low number or no white

colonies with PCR product
(continued)
DNA has rearranged. Check a number of clones

to see whether the rearrangement is random.
If so, the clone of interest should be present and
can be identified by screening several clones.
If the same rearrangement is found in all of the
clones, use of a repair-deficient bacterial strain
(e.g., SURE cells) may reduce recombination
events.
PCR product ligation

reaction produces
white colonies only
(no blue colonies)
Ampicillin is inactive, allowing ampicillinsensitive cells to grow. Check that ampicillin

plates are made properly and used within one
month. Test ampicillin activity by streaking
plates, with and without ampicillin, using an
ampicillin-sensitive clone.
PCR product cannot be ligated due to

pyrimidine dimers formed from UV overexposure. This is a common problem with gelpurified DNA. There is no way to fix this; the
DNA must be remade. Exposure to shortwave
UV should be limited as much as possible. Use a
glass plate between the gel and UV source to
decrease UV overexposure. If possible, only
visualize the PCR product using a longwave UV
source.
The bacterial strain (e.g., JM109) has lost its F

episome. Check the background control. If these
colonies are not blue, the cells may have lost the
F episome (assuming lacIqZM15 is located on
the F in the transformed strain and appropriate
plates were used). Be sure that the cells are
prepared properly for use with this system (see
Section 5).
The PCR fragment is inserted, but it is not

disrupting the lacZ gene. If there are a higher
number of blue colonies resulting from the PCR
fragment ligation than with the background
control, some of these blue colonies may contain
insert. Screen blue and pale blue colonies (see
Section 6.D).
Plates are incompatible with blue/white

screening. Check the background control. If these
colonies are not blue, check that the plates have
ampicillin/IPTG/X-Gal and are fresh. If there is
any question about the quality of the plates,
repeat plating with fresh plates.
Insert:vector ratio is not optimal. Check the

integrity and quantity of your PCR fragment by
gel analysis. Optimize the insert:vector ratio (see
Section 6.C).
There may be primer-dimers present in PCR
fragment preparation. Primer-dimers will ligate
into the pGEM-T or pGEM-T Easy Vector but
may not be seen after restriction digestion and
gel analysis because of their small size. The
vector will appear to contain no insert. More
blue colonies may be seen with the ligation than
on the background control plates. The PCR
fragment should be gel-purified.
Not enough clones contain

the PCR product of interest
Insufficient A-tailing of the PCR fragment. After

purification of the PCR fragment, set up an Atailing reaction (1012). Clean up the sample and
proceed with the protocol.
Insert:vector ratio is not optimal. Check the
integrity and quality of your PCR fragment by
gel analysis. Optimize the insert:vector ratio (see
Section 6.C).
Multiple PCR products may have been generated

and cloned into the pGEM-T or pGEM-T Easy
Vector. Gel-purify the PCR fragment of interest.
Multiple PCR products are generated and cloned

into the pGEM-T or pGEM-T Easy Vector. Gel
purify the PCR fragment of interest.


Part# TM042
Page 18
Printed in USA.
Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
Page 19
10. References
Table 3. Restriction Enzymes That Cut the pGEM-T Vector 15 Times.
1. Mezei, L.M. and Storts, D.R. (1994) Purification of PCR products. In: PCR Technology:
Current Innovations, Griffin, H.G. and Griffin, A.M., eds., CRC Press, Boca Raton, FL,
21.
2. Robles, J. and Doers, M. (1994) pGEM-T Vector Systems troubleshooting guide.
Promega Notes 45, 1920.
3. Clark, J.M. (1988) Novel non-templated nucleotide addition reactions catalyzed by
procaryotic and eucaryotic DNA polymerases. Nucl. Acids Res. 16, 967786.
4. Newton, C.R. and Graham, A. (1994) In: PCR, BIOS Scientific Publishers, Ltd.,
Oxford, UK, 13.
5. Messing, J. et al. (1981) A system for shotgun DNA sequencing. Nucl. Acids Res. 9,
30921.
6. Knoche, K. and Kephart, D. (1999) Cloning blunt-end Pfu DNA Polymerase-generated
PCR fragments into pGEM-T Vector Systems. Promega Notes 71, 1013.
7. Haff, L. and Mezei, L. (1989) Amplifications 1, 8.
8. Protocols and Applications Guide, Online Edition (2005) Promega Corporation.
(www.promega.com/paguide/)
9. eNotes online FAQ #fq0024 (2000) How does one generate single-stranded DNA
(ssDNA) from the pGEM-T Vector? Promega Corporation.
(www.promega.com/enotes/faqspeak/0006/fq0024.htm)
10. Kobs, G. (1995) pGEM-T Vector: Cloning of modified blunt-ended DNA fragments.
Promega Notes 55, 2829.
11. Kobs, G. (1997) Cloning blunt-end DNA fragments into the pGEM-T Vector
Systems. Promega Notes 62, 1518.
12. Zhou, M.-Y., Clark, S.E. and Gomez-Sanchez, C.E. (1995) Universal cloning method
by TA strategy. BioTechniques 19, 3435.
11. Appendix
11.A. pGEM-T Vector Restriction Enzyme Sites
The pGEM-T Vector is derived from the circular pGEM-5Zf(+) Vector
(GenBank Accession No. X65308). The pGEM-5Zf(+) Vector sequence is
available on the Internet at: www.promega.com/vectors/
The following restriction enzyme tables are based on those of the circular
pGEM-5Zf(+) Vector. The pGEM-T Vector has been created by linearizing the
pGEM-5Zf(+) Vector with EcoRV at base 51 and adding a T to both 3-ends.
This site will not be recovered upon ligation of the vector and insert. The tables
below were constructed using DNASTAR sequence analysis software. Please
note that we have not verified this information by restriction digestion with each
enzyme listed. The location given specifies the 3-end of the cut DNA (the base
to the left of the cut site). Please contact your local Promega Branch Office or
Distributor if you identify a discrepancy. In the U.S., contact Technical Services
at 1-800-356-9526.
Enzyme # of Sites
AatII
1
AccI
1
AcyI
2
AflIII
2
Alw26I
2
Alw44I
2
AlwNI
1
ApaI
1
AspHI
4
AvaII
2
BanI
3
BanII
3
BbuI
1
BglI
3
BsaI
1
BsaAI
1
BsaHI
2
BsaJI
5
Bsp120I
BspHI
BspMI
BssSI
BstOI
1
2
1
2
5
BstXI
BstZI
Cfr10I
DdeI
1
2
2
4
DraI
DraIII
DrdI
DsaI
EagI
EarI
EclHKI
Eco52I
EcoICRI
EcoRV
3
1
2
2
2
3
1
2
1
1
Location
20
76
17, 1932
99, 502
1456, 2232
816, 2062
918
14
94, 820, 1981, 2066
1533, 1755
246, 1343, 2626
14, 94, 2664
26
39, 1515, 2833
1456
2589
17, 1932
37, 43, 241, 662,
2936
10
1222, 2230
62
675, 2059
242, 530, 651,
664, 2937
103
31, 62
1475, 2690
777, 1186, 1352,
1892
1261, 1280, 1972
2589
610, 2544
37, 43
31, 62
386, 2190, 2878
1395
31, 62
92
51*
Enzyme # of Sites Location

FokI
5
119, 1361, 1542,
1829, 2919
FspI
2
1617, 2840
HaeII
4
380, 750, 2740,
2748
HgaI
4
613, 1191, 1921,
2806
HincII
1
77
HindII
1
77
Hsp92I
2
17, 1932
MaeI
5
56, 997, 1250,
1585, 2740
MluI
1
99
NaeI
1
2692
NciI
4
30, 882, 1578, 1929
NcoI
1
37
NdeI
1
82
NgoMIV
1
2690
NotI
1
62
NsiI
1
112
NspI
2
26, 506
Ppu10I
1
108
PstI
1
73
PvuI
2
1765, 2861
PvuII
2
326, 2890
RsaI
1
1875
SacI
1
94
SacII
1
46
SalI
1
75
ScaI
1
1875
SfiI
1
39
SinI
2
1533, 1755
SpeI
1
55
SphI
1
26
Sse8387I
1
73
SspI
2
2199, 2381
StyI
1
37
TaqI
4
76, 602, 2046, 2622
TfiI
2
337, 477
VspI
3
273, 332, 1567
XmnI
1
1994
*The pGEM-T Vector has been created by linearizing the pGEM-5Zf(+) Vector with EcoRV at
base 51 and adding a T to both 3-ends. This site will not be recovered upon ligation of the vector
and insert.
Note: The enzymes listed in boldface type are available from Promega.


Part# TM042
Page 20
Printed in USA.
Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
Page 21
Table 4. Restriction Enzymes That Do Not Cut the pGEM-T Vector.

AccB7I
AccIII
Acc65I
AflII
AgeI
AscI
AvaI
AvrII
BalI
BamHI
BbeI
BbrPI
BbsI
BclI
BglII
BlpI
Bpu1102I
BsaBI
BsaMI
BsmI
BsrGI
BssHII
Bst1107I
Bst98I
BstEII
Bsu36I
ClaI
CspI
Csp45I
DraII
Eco47III
Eco72I
Eco81I
EcoNI
EcoRI
EheI
Table 5. Restriction Enzymes that Cut the

AciI
AluI
BbvI
BsaOI
Bsp1286I
BsrI
BsrSI
Bst71I
BstUI
CfoI
DpnI
DpnII
EaeI
Fnu4HI
HaeIII
HhaI
HinfI
HpaII
HphI
Hsp92II
MaeII
PinAI
PmeI
PmlI
PpuMI
PshAI
Psp5II
PspAI
RsrII
SgfI
SgrAI
SmaI
SnaBI
FseI
HindIII
HpaI
I-PpoI
KasI
KpnI
NarI
NheI
NruI
PacI
PaeR7I
PflMI
pGEM-T
Table 6. Restriction Enzymes that Cut the pGEM-T Easy Vector 15 Times.
SplI
SrfI
StuI
SwaI
Tth111I
XbaI
XcmI
XhoI
XmaI
Vector 6 or More Times.
MaeIII
MboI
MboII
MnlI
MseI
MspI
MspA1I
NdeII
NlaIII
NlaIV
PleI
Sau3AI
Sau96I
ScrFI
SfaNI
Tru9I
XhoII
11.B. pGEM-T Easy Vector Restriction Enzyme Sites

The sequence of the pGEM-T Easy Vector is available on the Internet at:
www.promega.com/vectors/
The pGEM-T Easy Vector has been linearized at base 60 with EcoRV and a T
added to both 3-ends. This site will not be recovered upon ligation of the
vector and insert. The tables below were constructed using DNASTAR
sequence analysis software. Please note that we have not verified this
information by restriction digestion with each enzyme listed. The location
given specifies the 3-end of the cut DNA (the base to the left of the cut site).
Please contact your local Promega Branch Office or Distributor if you identify
a discrepancy. In the U.S., contact Technical Services at 1-800-356-9526.
Enzyme # of Sites
AatII
1
AccI
1
AcyI
2
AflIII
2
Alw26I
2
Alw44I
2
AlwNI
1
ApaI
1
AspHI
4
AvaII
BanI
BanII
BbuI
BglI
BsaI
BsaAI
BsaHI
BsaJI
2
3
3
1
4
1
1
2
5
Bsp120I
BspHI
BspMI
BssSI
BstOI
1
2
1
2
5
BstXI
BstZI
Cfr10I
DdeI
1
3
2
4
DraI
DraIII
DrdI
DsaI
EagI
EarI
EclHKI
Eco52I
EcoICRI
EcoRI
EcoRV
3
1
2
2
3
3
1
3
1
2
1
Location
20
91
17, 1947
114, 517
1471, 2247
831, 2077
933
14
109, 835, 1996,
2081
1548, 1770
261, 1358, 2641
14, 109, 2679
26
39, 42, 1530, 2848
1471
2604
17, 1947
37, 46, 256, 677,
2951
10
1237, 2245
77
690, 2074
257, 545, 666, 679,
2952
118
31, 43, 77
1490, 2705
792, 1201, 1367,
1907
1276, 1295, 1987
2604
625, 2559
37, 46
31, 43, 77
401, 2205, 2893
1410
31, 43, 77
107
52, 70
60*
Enzyme # of Sites Location

FokI
5
134, 1376, 1557,
1844, 2931
FspI
2
1632, 2855
HaeII
4
395, 765, 2755,
2763
HgaI
4
628, 1206, 1936,
2821
HincII
1
92
HindII
1
92
Hsp92I
2
17, 1947
MaeI
5
65, 1012, 1265,
1600, 2755
MluI
1
114
NaeI
1
2707
NciI
4
30, 897, 1593,
1944
NcoI
1
37
NdeI
1
97
NgoMIV
1
2705
NotI
2
43, 77
NsiI
1
127
NspI
2
26, 521
Ppu10I
1
123
PstI
1
88
PvuI
2
1780, 2876
PvuII
2
341, 2905
RsaI
1
1890
SacI
1
109
SacII
1
49
SalI
1
90
ScaI
1
1890
SinI
2
1548, 1770
SpeI
1
64
SphI
1
26
Sse8387I
1
88
SspI
2
2214, 2396
StyI
1
37
TaqI
5
56, 91, 617, 2061,
2637
TfiI
2
352, 492
VspI
3
288, 347, 1582
XmnI
1
2009
*The pGEM-T Easy Vector has been linearized at base 60 with EcoRV and a T added to both
3-ends. This site will not be recovered upon ligation of the vector and insert.


Part# TM042
Page 22
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Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
Page 23
Table 7. Restriction Enzymes That Do Not Cut the pGEM-T Easy Vector.
AccB7I
AccIII
Acc65I
AflII
AgeI
AscI
AvaI
AvrII
BalI
BamHI
BbeI
BbrPI
BbsI
BclI
BglII
BlpI
Bpu1102I
BsaBI
BsaMI
BsmI
BsrGI
BssHII
Bst1107I
Bst98I
BstEII
Bsu36I
ClaI
CspI
Csp45I
DraII
Eco47III
Eco72I
Eco81I
EcoNI
EheI
FseI
HindIII
HpaI
I-PpoI
KasI
KpnI
NarI
NheI
NruI
PacI
PaeR7I
PflMI
PinAI
PmeI
PmlI
PpuMI
PshAI
Psp5II
PspAI
RsrII
SfiI
SgfI
SgrAI
SmaI
SnaBI
SplI
SrfI
StuI
SwaI
Tth111I
XbaI
XcmI
XhoI
XmaI
Bst71I
BstUI
CfoI
DpnI
DpnII
EaeI
Fnu4HI
HaeIII
HhaI
HinfI
HpaII
HphI
Hsp92II
MaeII
MaeIII
MboI
MboII
MnlI
MseI
MspI
MspA1I
NdeII
NlaIII
NlaIV
PleI
Sau3AI
Sau96I
ScrFI
IPTG stock solution (0.1M)

1.2g IPTG
Add water to 50ml final volume.
Filter-sterilize and store at 4C.
X-Gal (2ml)
100mg 5-bromo-4-chloro-3indolyl--D-galactoside
Dissolve in 2ml N,N-dimethylformamide. Cover with aluminum
foil and store at 20C.
Table 8. Restriction Enzymes that Cut the pGEM-T Easy Vector 6 or More Times.
AciI
AluI
BbvI
BsaOI
Bsp1286I
BsrI
BsrSI
11.C. Composition of Buffers and Solutions
SfaNI
Tru9I
XhoII
LB medium (per liter)

10g Bacto-tryptone
5g Bacto-yeast extract
5g NaCl
Adjust pH to 7.0 with NaOH.
LB plates with ampicillin
Add 15g agar to 1 liter of LB
medium. Autoclave. Allow the
medium to cool to 50C before
adding ampicillin to a final
concentration of 100g/ml. Pour
3035ml of medium into 85mm petri
dishes. Let the agar harden. Store at
4C for up to 1 month or at room
temperature for up to 1 week.
LB plates with ampicillin/IPTG/XGal

Make the LB plates with ampicillin
as above; then supplement with
0.5mM IPTG and 80g/ml X-Gal
and pour the plates. Alternatively,
100l of 100mM IPTG and 20l of
50mg/ml X-Gal may be spread over
the surface of an LB-ampicillin plate
and allowed to absorb for 30
minutes at 37C prior to use.
SOC medium (100ml)

2.0g
0.5g
1ml
0.25ml
1ml
Bacto-tryptone
Bacto-yeast extract
1M NaCl
1M KCl
2M Mg2+ stock, filtersterilized
1ml 2M glucose, filtersterilized
Add Bacto-tryptone, Bacto-yeast
extract, NaCl and KCl to 97ml
distilled water. Stir to dissolve.
Autoclave and cool to room
temperature. Add 2M Mg2+ stock
and 2M glucose, each to a final
concentration of 20mM. Bring to
100ml with sterile, distilled water.
The final pH should be 7.0.
2M Mg2+ stock
20.33g MgCl2 6H2O
24.65g MgSO4 7H2O
Add distilled water to 100ml. Filter
sterilize.
2X Rapid Ligation Buffer, T4 DNA
Ligase (provided)
60mM
20mM
20mM
2mM
10%
Tris-HCl (pH 7.8)

MgCl2
DTT
ATP
polyethylene glycol
(MW8000, ACS Grade)
Store in single-use aliquots at 20C.

Avoid multiple freeze-thaw cycles.
TYP broth (per liter)
16g
16g
5g
2.5g
Bacto-tryptone
Bacto-yeast extract
NaCl
K2HPO4


Part# TM042
Page 24
Printed in USA.
Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
Page 25
11.D. Related Products
PCR Purification Systems
PCR Cloning Systems
Product
Wizard SV Gel and PCR Clean-Up System
Product
pTARGET Mammalian Expression Vector System
Direct mammalian expression from a T-Vector.
Size
20 reactions
Cat.#
A1410
Wizard SV 96 PCR Clean-Up System
Amplification Products
Please request our Amplification Products Brochure #BR139 or visit our Web site at
www.promega.com/applications/pcr/ to see a complete listing of our amplification
products.
Thermostable DNA Polymerases

Product
GoTaq Green Master Mix
GoTaq Colorless Master Mix
Size
100 reactions
1,000 reactions
100 reactions
1,000 reactions
Cat.#
M71121, M71222
M71131, M71232
M71421, M71322
M71431, M71332
GoTaq Master Mixes are premixed solutions containing GoTaq DNA Polymerase, GoTaq
Reaction Buffer (Green or Colorless), dNTPs and Mg2+.
1Cat.#s M7112, M7113, M7142 & M7143 are available in Europe or through Distributors
supported by Promega European Branch Offices.
2Cat.#s M7122, M7123, M7132 & M7133 are available in all other countries, including the
United States. For Laboratory Use.
Product
GoTaq DNA Polymerase
Size
Cat.#
100u M31711, M30012
Product
PCR Nucleotide Mix (10mM each)
dATP, dCTP, dGTP, dTTP, each at 100mM
ImProm-II Reverse Transcription System*
Size
2g
2g
2g
2g
Cat.#
Q5011
Q5021
Q5601
Q5421
Size
5 200l
5 200l
Cat.#
L2001
L3001
Size
100mg (50mg/ml)
1g
5g
Cat.#
V3941
V3955
V3951
Sequencing Primers
Product
SP6 Promoter Primer
T7 Promoter Primer
pUC/M13 Primer, Forward (24mer)
pUC/M13 Primer, Reverse (22mer)
*For Laboratory Use.
AccessQuick RT-PCR System
Cat.#
C1141
C1145
U1330
U1240
U1410
For Laboratory Use.
RT-PCR Systems
Cat.#
A1260
A1250
A1280
A1701
A1702
A1703
A3800
Size
200l
1,000l
10mol of each
40mol of each
200mol of each
dNTPs
Competent Cells
Size
20 reactions
100 reactions
500 reactions
20 reactions
100 reactions
500 reactions
100 reactions
Cat.#
A9281
A9282
A9340
A9341
A9342
For Laboratory Use.
Available in additional sizes.

1Cat.# M3171 is available in Europe or through Distributors supported by Promega
European Branch Offices.
2Cat.# M3001 is available in all other countries, including the United States. For Laboratory
Use.
Product
Access RT-PCR System
Size
50 preps
250 preps
1 96 preps
4 96 preps
8 96 preps
Product
JM109 Competent Cells*, >108cfu/g
Single Step (KRX) Competent Cells
Accessory Products
Product
X-Gal
IPTG, Dioxane-Free
For Laboratory Use.
*For Laboratory Use.


Part# TM042
Page 26
Printed in USA.
Revised 3/09
Printed in USA.
Revised 3/09
Part# TM042
Page 27
(a)Licensed under one or more of U.S. Pat. Nos. 5,487,993 and 5,827,657 and European Pat. Nos. 0 550 693 and 0 738 779.
(b)Licensed under U.S. Pat. No. 5,075,430.
19962009 Promega Corporation. All Rights Reserved.

Erase-a-Base, GoTaq, pGEM, Riboprobe and Wizard are registered trademarks of Promega Corporation. AccessQuick,
ImProm-II and pTARGET are trademarks of Promega Corporation.
AmpliTaq is a registered trademark of Roche Molecular Systems, Inc. Bacto is a registered trademark of Difco Laboratories.
DNASTAR is a registered trademark of DNASTAR, Inc. GenBank is a registered trademark of the U.S. Dept. of Health and
Human Services. Luer-Lok is a registered trademark of Becton, Dickinson and Company. SURE is a registered trademark of
Stratagene. Vent and Deep Vent are registered trademarks of New England Biolabs, Inc.
Products may be covered by pending or issued patents or may have certain limitations. Please visit our Web site for more
information.
All prices and specifications are subject to change without prior notice.
Product claims are subject to change. Please contact Promega Technical Services or access the Promega online catalog for the
most up-to-date information on Promega products.

Part# TM042
Page 28
Printed in USA.
Revised 3/09

pGEM-T Easy

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Technical Manual

pGEM-T and pGEM-T

pGEM-T and pGEM-T Easy

3. Product Components and Storage Conditions ............................................7

PCR Product Purity............................................................................................11

7. Isolation of Recombinant Plasmid DNA....................................................15

pGEM-T Vector Restriction Enzyme Sites....................................................20

Promega Corporation 2800 Woods Hollow Road Madison, WI 53711-5399 USA

Table 1. Comparison of PCR Product Properties for Thermostable DNA Polymerases.

Thermostable DNA Polymerase

Specialized Applications of the pGEM-T and pGEM-T Easy Vectors:

Cloning PCR products.

Promega Corporation 2800 Woods Hollow Road Madison, WI 53711-5399 USA

Promega Corporation 2800 Woods Hollow Road Madison, WI 53711-5399 USA

2.B. pGEM-T Vector Map and Sequence Reference Points

2.A. Multiple Cloning Sequences

SP6 Transcription Start

T7 RNA polymerase transcription initiation site

GCGGC CGCGG GAATT CGATT3

SP6 Transcription Start

pGEM-T Vector sequence reference points:

Figure 2. pGEM-T Vector circle map and sequence reference points.

pGEM-T Easy Vector

Promega Corporation 2800 Woods Hollow Road Madison, WI 53711-5399 USA

Promega Corporation 2800 Woods Hollow Road Madison, WI 53711-5399 USA

2.C. pGEM-T Easy Vector Map and Sequence Reference Points

Product Components and Storage Conditions

1.2g pGEM-T Vector (50ng/l)

12l Control Insert DNA (4ng/l)

100u T4 DNA Ligase

200l 2X Rapid Ligation Buffer, T4 DNA Ligase

1.2g pGEM-T Vector (50ng/l)

12l Control Insert DNA (4ng/l)

100u T4 DNA Ligase

200l 2X Rapid Ligation Buffer, T4 DNA Ligase

1.2ml JM109 Competent Cells, High Efficiency (6 200l)

1.2g pGEM-T Easy Vector (50ng/l)

12l Control Insert DNA (4ng/l)

100u T4 DNA Ligase

200l 2X Rapid Ligation Buffer, T4 DNA Ligase

1.2g pGEM-T Easy Vector (50ng/l)

12l Control Insert DNA (4ng/l)

100u T4 DNA Ligase

200l 2X Rapid Ligation Buffer, T4 DNA Ligase

1.2ml JM109 Competent Cells, High Efficiency (6 200l)

Promega Corporation 2800 Woods Hollow Road Madison, WI 53711-5399 USA

Promega Corporation 2800 Woods Hollow Road Madison, WI 53711-5399 USA

1. Briefly centrifuge the pGEM-T or pGEM-T Easy Vector and Control

Use high-efficiency competent cells (1 108cfu/g DNA) for transformations.

2. Set up ligation reactions as described below.

Standard Positive Background

Control Insert DNA

T4 DNA Ligase (3 Weiss units/l)

3. Mix the reactions by pipetting. Incubate the reactions 1 hour at room

Protocol for Transformations Using the pGEM-T and pGEM-T Easy

We recommend using JM109 High Efficiency Competent Cells (Cat.# L2001);

LB plates with ampicillin/IPTG/X-Gal

2. 2X Rapid Ligation Buffer contains ATP, which degrades during temperature

1. Prepare two LB/ampicillin/IPTG/X-Gal plates for each ligation reaction, plus

3. It is important to vortex the 2X Rapid Ligation Buffer before each use.