Basics of Molecular Cloning
Basics of Molecular Cloning
Instructor’s Manual
1. Purpose and Concepts Covered .........................................................................1 This instructor’s
! manual is avaliable
2. Protocol for Cloning the Luciferase Gene into the pGEM® Vector...................2 online only.
A. Excising the Luciferase Gene from Surrounding DNA.....................................2 This teaching resource is
made available free of
B. Purifying the Gene Fragment...........................................................................4
charge by Promega
C. Ligating the Gene into the Vector ....................................................................6 Corporation. Reproduction
permitted for noncommer-
D. Transforming Bacteria with Your Clone ............................................................7 cial educational purposes
E. Expressing Luciferase in E. coli .......................................................................9 only. Copyright 2010
Promega Corporation. All
3. Composition of Buffers and Solutions .............................................................11 rights reserved.
This introductory cloning laboratory is for use in courses that cover basic topics in molec-
ular biology and genetics. Molecular cloning is a basic technique used in a molecular
biology labs. In this manual, we include a protocol for isolating the luciferase gene from
DNA using restriction digestion and cloning it into the multiple cloning region of a vector.
The cloned luciferase gene is then expressed in E. coli.
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2. Protocol for Cloning the Luciferase Gene into the pGEM® Vector
Materials Required
• pGEM®-luc DNA (Cat.# E1541)
• pGEM®-4Z Vector (Cat.# P2161)
• BamHI restriction enzyme (Cat.# R6021; 10u/µl)
• SacI restriction enzyme (Cat.# R6061; 10u/µl)
• Buffer E (supplied with BamHI enzyme)
Ethidium bromide
! is a carcinogen.
• Acetylated BSA (supplied with restriction enzymes)
• Agarose, LMP, Preparative Grade for Large Fragments (>1,000bp; Cat.# V2831)
Be sure to follow your
• TBE Buffer, 10X, Molecular Biology Grade (Cat.# V4251; or have students make
institution’s safety and
disposal instructions
their own buffer)
when working with • Ethidium Bromide Solution, Molecular Biology Grade (Cat.# H5041)
ethidium bromide. Note: The gel fragment cleanup system will not work with DNA that
has been stained with methylene blue.
• BenchTop pGEM® DNA Markers (Cat.# G7521)
• Wizard® SV Gel and PCR Clean-Up System (Cat.# A9281)
• Blue/Orange Loading Dye, 6X (Cat.# G1881)
• T4 DNA Ligase (Cat.# M1801)
• agarose gel electrophoresis apparatus and power supply
• 37°C water bath
• pipettors (0.5–10µl and 10–200µl) and appropriate sterile pipet tips
• long-wave UV light box and camera or scanner
• 1.5ml sterile tubes
• gloves
In this part of the protocol, you will be isolating the gene of interest, the firefly
luciferase gene, from surrounding DNA. To remove the luciferase gene, you will be
performing a restriction digest using BamHI and SacI. You also will need to perform
the same double digest on your target cloning vector (pGEM®-4Z Vector).
You will need to set up your restriction digest in a total volume of 20µl using the
guidelines below:
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1. Calculate the volume of Buffer E you will need in the reaction to achieve a
final concentration of 1X.
Note to the instructor: Buffer E is supplied as a 10X solution. The students will
need to dilute the Buffer E so that its final concentration in the reaction is 1X.
Using CV = CV,
(y µl) (10X Buffer E) = (20µl of 1X Buffer E)
10y = 20
y = 2µl of 10X Buffer E
2. Calculate the volume of DNA you will need to add to your reaction in order
to digest 1µg.
Note to the instructor: The concentration of the pGEM®-luc Vector is
provided on the lot-specific product information sheet that accompanies the
vector. Using that information, your students can calculate the volume of
DNA to add to their reaction.
They can do the same for the target vector (pGEM®-4Z Vector).
3. Calculate the volume of Acetylated BSA you will need to add to your reac-
tions, so that you have a total of 2µg of Acetylated BSA in your reaction. The
Acetylated BSA is supplied at a concentration of 10µg/µl.
Note: Pipetting volumes smaller than 0.5µl is very difficult. When determin-
ing how much Acetylated BSA to add, you may need to dilute the BSA to a
lower concentration so that you can pipette a larger volume into your reac-
tion (0.5 or 1.0µl).
4. Calculate the volume of water to add to bring the volume (without enzyme)
to a total of 19.0µl. Enter the volumes of each component into the table
below:
Nuclease-Free Water
(add to a total volume of 19.0µl) NA _______
Restriction Enzyme Buffer E 10X _______
5. Add the components, in the order listed, to a sterile 1.5ml tube. Mix them by
pipetting.
6. Calculate the amount of each enzyme to add to your reaction. You will need
to add a total of 5 units of each enzyme. Using the concentration of each of
the enzymes provided to you by your instructor, determine what dilution (if
any) you need to make so that 0.5µl of the enzyme contains 5 units.
Note: High concentrations of either glycerol or enzyme can interfere with
your restriction digestion. Therefore, be sure that you do not add more than
1.0µl total of enzymes to your digest.
7. Add 5 units of BamHI and 5 units of SacI to your restriction digest. Mix
gently by pipetting.
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8. Close the tube and centrifuge for a few seconds in a microcentrifuge to pull
all of the liquid to the bottom of the tube.
9. Incubate at 37°C for 1 hour.
Note to the students: You should have performed two restriction diges-
tions: one of pGEM®-luc DNA to remove the luciferase gene insert, and one
of the pGEM®-4Z Vector to prepare it to receive the insert.
After your restriction digest is complete, you will separate the luciferase gene frag-
ment (~1,740bp) from the remainder of the DNA using agarose gel electrophoresis.
The luciferase gene DNA can be purified from the gel using a commercially available
DNA cleanup system. You also will need to gel purify your restricted target vector
(pGEM®-4Z Vector), which will be a fragment of ~2,733bp.
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2.B. Purifying the Gene Fragment (continued)
You will need to provide detailed instructions (volume, inserting comb, etc.)
for gel preparation based on the particular gel aparatus you are using.
We recommend adding ethidium bromide (final concentration 5µg/ml) to the
gel before it is poured rather than using it in the gel running buffer. Although
the sizing is more accurate when the gel is stained after running, confining
the ethidum bromide to the gel itself helps manage disposal.
4. When the gel has solidified, remove the comb, being careful not to tear the
wells. Place the gel in the gel box and cover with 1X TBE buffer.
5. Remove 5µl from each of your restriction digests. Add 1µl of 6X blue/orange
loading dye. Add 1µl of dye to 5µl of the uncut DNA.
6. Load digests and run the gel until the markers in the loading dye have
migrated to the appropriate point in the gel to have separated the fragments
in which you are interested. (See reference material at:
www.promega.com/techserv/techref/agarose_polyacryl.htm for help
determining this).
7. Turn off the electricity flowing to the gel box. Remove the gel, and place it on
a long-wave UV box. (Short wave UV can damage the DNA.) Using a
scalpel or razor blade, cut the 1,740bp gene fragment from the gel, and
place it in a preweighed 1.5ml microcentrifuge tube.
8. Weigh the tube with the gel slice, and determine the weight of your gel slice.
Note: At this point you will use the Wizard® SV Gel and PCR Clean-Up
System (Cat.# A9281) to extract your insert DNA from the gel slice. Detailed
instructions are available in Technical Bulletin #TB308, available at:
www.promega.com/tbs/
9. Add 10µl of Membrane Binding Solution per 10mg of gel slice. Vortex and
incubate at 50–65°C for 10 minutes or until gel slice is completely dissolved.
10. Insert the SV Minicolumn into a Collection Tube from the Wizard® SV Gel
and PCR Clean-Up System.
11. Transfer the dissolved gel mixture to the Minicolumn assembly. Incubate at
room temperature for 1 minute.
12. Centrifuge at 16,000 × g for 1 minute. Discard flowthrough and reinsert
Minicolumn into Collection Tube.
13. Add 700µl of Membrane Wash Solution (ethanol added). Centrifuge at
16,000 × g for 1 minute. Discard flowthrough and reinsert Minicolumn into
Collection Tube.
Note: You can have students calculate the RPM of the centrifuge to achieve
a target RCF (in this case the target is 16,000 × g) for your
particular microcentrifuge using the radius of the rotor. There is an online
calculator at: www.sciencegateway.org/tools/rotor.htm, but if you
prefer, your students can use this equation:
g = (1.118 × 10-5) RS2
Where g is the relative centrifugal force, R is the radius of the rotor in cen-
timeters, and S is the speed of the centrifuge in revolutions per minute.
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Note: The Wizard® SV 14. Repeat Step 13 with of 500µl Membrane Wash Solution. Centrifuge at
Gel and PCR Clean-Up 16,000 × g for 5 minutes.
System recommends
spinning down the mini- 15. Empty the Collection Tube, place the open column in a stand on the lab
column for one minute bench to evaporate the ethanol. There should be no longer an odor of the
to help with ethanol Column Wash buffer.
evaporation. We elimi-
nated this direction from
16. Carefully transfer Minicolumn to a clean 1.5ml microcentrifuge tube.
Step 15 because of 17. Add 50µl of Nuclease-Free Water to the Minicolumn. Incubate at room
safety concerns. temperature for 1 minute. Centrifuge at 16,000 × g for 1 minute.
Instructors should use
their discretion about 18. Discard Minicolumn and store DNA at 4°C or –20°C.
recommending this pro-
cedure for students. 2.C. Ligating the Insert into the Vector
Example: How much 500bp insert DNA needs to be added to 100ng of 3.0kb vector
in a ligation reaction for a desired vector:insert ratio of 1:3?
1. Briefly centrifuge the pGEM®-4Z Vector and the DNA insert tubes to collect
contents at the bottom of the tube. (Note: Detailed information about the
vector is provided in Technical Bulletin #TB033, available at:
www.promega.com/tbs .)
2. Set up ligation reactions as described below. Vortex the T4 DNA Ligase 10X
Buffer vigorously before each use. Use 0.5ml tubes known to have low DNA-
binding capacity.
! Note: If digest yields are low, it may be necessary to increase the overall
volume of the reaction. Remember to maintain rations of volume is
increased.
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2.C. Ligating the Insert into the Vector (continued)
3. Mix the reactions by pipetting. Incubate the reactions for 1 hour at room
temperature. Alternatively, incubate the reactions overnight at 4°C for the
maximum number of transformants.
Note to the Instructor: Because the target vector was cut with two different
enzymes that do not generate compatible ends, the vector should not spon-
taneously religate. You might discuss with the students what precautions
they would have to take if the enzymes produced “compatible ends” or if
they were only cutting the vector with a single enzyme (i.e., removing phos-
phate groups from the end of the vector so that the ligation reaction could
not be catalyzed between the two ends).
Materials Required
• Single-Step KRX Competent Cells (Cat.# L3002; three tubes per lab group)
• vector with ligated insert
• uncut vector positive transformation control
• cut vector negative transformation control
• 17 × 100mm polypropylene tubes (BD Falcon Cat.# 352059) or
1.5ml microcentrifuge tubes
• ice bath
• 42°C water bath
• 37°C shaking water bath or incubator
• pipettors (0.5–10µl and 10–200µl) and appropriate sterile pipet tips
• LB/ampicillin/IPTG/X-Gal plates
• SOC medium
• glass “hockey stick” for plating cells on selective plates
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2.D. Transforming Bacteria with Your Clone (continued)
Example:
Note to the Instructor: If you have your students plate 10µl, 100µl, 500µl of the
uncut positive transformation control, they can practice calculating the transforma-
tion frequency for their experiment using the above equation.
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2.E. Expressing Luciferase in E. coli
White colonies should have the luciferase gene cloned in the correct orientation in
the pGEM®-4Z Vector to be expressed from the T7 promoter on the vector. Since the
KRX strain of E. coli contains the necessary information to express a gene from the
T7 promoter, your students should be able to see “glowing” cells when the cells are
provided with the appropriate substrates for the luciferase reaction.
1. From your transformation plates, use a sterile innoculating loop to pick four
or five white colonies into indivdual 5ml liquid cultures of LB Broth + Amp
using aseptic technique and grow overnight at 37°C with shaking*. (Seal
your original plates and store them, inverted at 4°C.)
Note: Better growth was observed when culture tubes were incubated at an
angle during overnight shaking.
2. Dilute your overnight cultures 1:100 into new, labeled tubes of Terrific Broth
+ Ampicillin. Grow cultures at 37°C with shaking at 275rpm until they reach
an O.D.600 of 0.8–1.0.
3. Shift cultures to a second incubator shaker set at 15–25°C and continue
shaking until cells reach an O.D.600 of 1.0–1.5.
4. Induce protein expression by adding rhamnose to a concentration of 0.1%.
(1:200 dilution of a 20% rhamnose solution).
5. Grow cultures overnight at 15–25°C with shaking at 275rpm.
6. Transfer 500µl of each your cultures to labeled 1.5ml centrifuge tubes. Pellet
the cells by centrifugation at 10,000 × g for 3 minutes in a microcentrifuge.
7. Aspirate the supernatant and resuspend the cell pellet in 450µl 100mM
sodium citrate + 50µl Luciferase Assay Reagent.
7. Take the tube into a dark room. Vigorously shake the tube to break up the
clumps of cells and to introduce oxygen into the reaction.
8. Are any of the cells in your tubes “glowing”?
Note: The luminescence will be very faint to the naked eye. Comparison to
blank tubes helps with visual dectection of luminescence.
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3. Composition of Buffers and Solutions
sodium citrate
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