Gigapack III Gold Packaging Extract, Gigapack III
Plus Packaging Extract, and Gigapack III XL
Packaging Extract
Instruction Manual
Catalog #200201 (Gigapack III Gold-4), #200202 (Gigapack III Gold-7),
and #200203 (Gigapack III Gold-11)
Catalog #200204 (Gigapack III Plus-4), #200205 (Gigapack III Plus-7),
and #200206 (Gigapack III Plus-11)
Catalog #200207 (Gigapack III XL-4), #200208 (Gigapack III XL-7),
and #200209 (Gigapack III XL-11)
Revision B
Research Use Only. Not for Use in Diagnostic Procedures.
200201-12
LIMITED PRODUCT WARRANTY
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or implied, including without limitation, implied warranties of merchantability or fitness for a particular
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incidental damages arising out of the use, the results of use, or the inability to use this product.
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Gigapack III Gold Packaging Extract, Gigapack III Plus
Packaging Extract, and Gigapack III XL Packaging Extract
Gigapack III packaging extract is very sensitive to slight variations in temperature. Storing the packaging extracts at the
bottom of a –80°C freezer directly from the dry ice shipping container is required in order to prevent a loss of packaging
efficiency. Transferring tubes from one freezer to another may also result in a loss of efficiency. Do not allow the packaging extracts to thaw! Do not store the packaging extracts in liquid nitrogen as the tubes may explode.
b
The λcI857 Sam7 wild-type lambda control DNA is shipped frozen and should be stored at –80°C immediately on receipt.
c
The VCS257 host strain, included for plating the λcI857 Sam7 positive control, is shipped as a frozen bacterial glycerol
stock (see Preparation of Host Strains for additional storage instructions) and should also be stored at –80°C immediately
on receipt. This control host strain is a derivative of DP50 supF and should be used only when plating the packaged test
DNA. The control DNA used with Gigapack III Gold packaging extract requires a supF mutation in the bacterial host to
plate efficiently.
#200201
#200204
#200207
Catalog
#200202
Catalog
#200205
Catalog
#200208
Catalog
#200203
Catalog
#200206
Catalog
#200209
STORAGE CONDITIONS
Packaging Extracts: –80°C (Do not allow the packaging extracts thaw! Do not store the packaging
extracts in liquid nitrogen as the tubes may explode.)
Lambda Control DNA: –80°C (Store at 4°C after thawing.)
Packaging extracts are used to package recombinant lambda phage with
high efficiency. The single-tube format of Gigapack III packaging extract
simplifies the packaging procedure and increases the efficiency and
representation of libraries constructed from highly methylated DNA. Each
packaging extract is restriction minus (HsdR
–
McrA– McrBC– McrF– Mrr–)
to optimize packaging efficiency and library representation. When used in
conjunction with restriction-deficient plating cultures, Gigapack III
packaging extract improves the quality of DNA libraries constructed from
methylated DNA.
1-4
Because choice of an in vitro packaging extract designed to achieve specific
experimental goals is important, we offers three different packaging
extracts: Gigapack III Gold packaging extract, Gigapack III Plus packaging
extract, and Gigapack III XL packaging extract. Gigapack III Gold
packaging extract produces the highest packaging efficiency commercially
9
available (2 × 10
pfu/μg) and is designed for use in cDNA and genomic
library construction. Gigapack III Plus packaging extract is an economical
alternative to Gigapack III Gold packaging extract when the highest
packaging efficiency is not required. Gigapack III XL packaging extract
preferentially packages large inserts (i.e., 47–51-kb recombinants), which
eliminates the need for time-consuming size fractionation steps and the loss
associated with sizing columns or sucrose gradients. This packaging extract
is designed for use in genomic lambda and cosmid library construction.
Optimal packaging efficiencies are obtained with lambda DNAs that are
concatemeric. Ligations should be carried out at DNA concentrations of
0.2 μg/μl or greater, which favors concatemers and not circular DNA
molecules that only contain one cos site. DNA to be packaged should be
relatively free from contaminants. Polyethylene glycol (PEG), which is contained in some ligase buffers, can inhibit packaging. The volume of
DNA added to each extract should be between 1 and 4 μl. To obtain the
highest packaging efficiency [i.e., the number of plaque-forming units per
microgram (pfu/μg) of DNA], package 1 μl of the ligation reaction and
never more than 4 μl. Increased volume (i.e., >4 μl) yields more plaqueforming units per packaging reaction, but fewer plaque-forming units per
microgram of DNA.
DNA that is digested with restriction enzymes and religated packages less
efficiently (by a factor of 10–100) than uncut lambda DNA. For example,
uncut wild-type lambda DNA packages with efficiencies exceeding
9
1 × 10
pfu/μg of vector when using a Gigapack III packaging extract.
However, predigested arms, when ligated to a test insert, yield
6
~5 × 10
– 1 × 107 recombinant plaques/μg of vector.
2 Gigapack III Packaging Extract
PREPARATION OF HOST STRAINS
NoteThe appendix is included as a convenient reference for preparing
host strains other than the VCS257 control host strain provided
with the packaging extracts (see Appendix: Host Strain
Preparation).
The host strain is shipped as a bacterial glycerol stock. For the appropriate
media, please refer to the following table:
Host strain
VCS257
strain
a
NZY medium (see Preparation of Media and Reagents) may be substituted for LB
medium in all cases.
b
See Preparation of Media and Reagents.
On arrival, prepare the following from the bacterial glycerol stock using the
appropriate media as indicated in the previous table:
Agar plates for
bacterial
streak
LBb LBb LB with 0.2% (w/v) maltose–
Medium for
a
bacterial
glycerol stock
Medium for bacterial
cultures for titering phage
a
(final concentration)
10 mM MgSO
4
a
1. Revive the stored cells by scraping off splinters of solid ice with a
sterile wire loop.
2. Streak the splinters onto an LB agar plate.
3. Incubate the plate overnight at 37°C.
®
4. Seal the plate with Parafilm
laboratory film and store the plate at 4°C
for up to 1 week.
5. Restreak the cells onto a fresh plate every week.
Preparation of a –80°C Bacterial Glycerol Stock
1. In a sterile 50-ml conical tube, inoculate 10 ml of appropriate liquid
medium containing the appropriate antibiotic, if one is necessary, with
one colony from the plate. Grow the cells to an OD
2.0.
2. Add 4.5 ml of a sterile glycerol–liquid medium solution (5 ml of
glycerol + 5 ml of appropriate medium) to the bacterial culture from
step 1. Mix well.
3. Aliquot into sterile centrifuge tubes (1 ml/tube).
This preparation may be stored at –20°C for 1–2 years or at –80°C for more
than 2 years.
between ~1.0 and
600
Gigapack
III Packaging Extract 3
Preparation of Host Bacteria
NotePrepare an overnight culture of the VCS257 strain (see the table
in Preparation of Host Strains) prior to performing the protocol for
the positive wild-type lambda DNA control (see Positive Wild-
Type Lambda DNA Control for the Gigapack III Packaging
Extract).
1. Streak the bacterial glycerol stock onto the appropriate agar plates (see
Appendix: Host Strain Preparation). Incubate the plates overnight at
37°C.
NoteDo not add antibiotic to the medium in the following step.
The antibiotic will bind to the bacterial cell wall and will
inhibit the ability of the phage to infect the cell.
2. Inoculate an appropriate medium, supplemented with 10 mM MgSO
and 0.2% (w/v) maltose (see Appendix: Host Strain Preparation), with
a single colony.
3. Grow at 37°C, shaking for 4–6 hours (do not grow past an OD
1.0). Alternatively, grow overnight at 30°C, shaking at 200 rpm.
Note The lower temperature keeps the bacteria from overgrowing,
4. Pellet the bacteria at 500 × g for 10 minutes.
5. Gently resuspend the cells in half the original volume with sterile
10 mM MgSO
6. Dilute the cells to an OD
Note The bacteria should be used immediately following dilution.
PACKAGING PROTOCOL
NotePolyethylene glycol, which is contained in some ligase buffers, can
thus reducing the number of nonviable cells. Phage can
adhere to nonviable cells resulting in a decreased titer.
.
4
of 0.5 with sterile 10 mM MgSO4.
600
inhibit packaging.
600
of
4
1. Remove the appropriate number of packaging extracts from a –80°C
freezer and place the extracts on dry ice.
2. Quickly thaw the packaging extract by holding the tube between your
fingers until the contents of the tube just begins to thaw.
3. Add the experimental DNA immediately (1–4 μl containing
0.1–1.0 μg of ligated DNA) to the packaging extract.
4 Gigapack III Packaging Extract
4. Stir the tube with a pipet tip to mix well. Gentle pipetting is allowable
provided that air bubbles are not introduced.
5. Spin the tube quickly (for 3–5 seconds), if desired, to ensure that all
contents are at the bottom of the tube.
6. Incubate the tube at room temperature (22°C) for 2 hours.
7. Add 500 μl of SM buffer (see Preparation of Media and Reagents) to
the tube.
8. Add 20 μl of chloroform and mix the contents of the tube gently.
9. Spin the tube briefly to sediment the debris.
10. The supernatant containing the phage is ready for titering. The
supernatant may be stored at 4°C for up to 1 month.
Positive Wild-Type Lambda DNA Control for the Gigapack III Packaging
Extract
Use the following procedure to test the efficiency of the Gigapack III
packaging extract with the λcI857 Sam7 wild-type lambda control DNA.
1. Thaw the frozen wild-type lambda control DNA on ice and gently mix
the control after thawing.
2. Using 1 μl of the wild-type lambda control DNA (~0.2 μg), proceed
with steps 1–10 in the Packaging Protocol.
NoteBecause of the high titer achieved with the wild-type lambda
control DNA, stop the control packaging reaction with 1 ml
of SM buffer. This should make the plaques easier to count.
3. Prepare two consecutive 10
step 10 in the Packaging Protocol in SM buffer. (The final dilution is
–4
.)
10
4. Add 10 μl of the 10
(This strain is recommended for plating the wild-type lambda control
DNA only.) Incubate at 37°C for 15 minutes. Add 3 ml of LB top agar
(see Preparation of Media and Reagents), melted and cooled to ~48°C,
and quickly pour the dilution onto dry, prewarmed LB agar plates.
–2
dilutions of the packaging reaction from
–4
dilution to 200 μl of the VCS257 host strain.
Gigapack
5. Incubate the plates for at least 12 hours at 37°C.
6. Count the plaques. Approximately 400 plaques should be obtained on
–4
the 10
dilution plate when the reaction is stopped with 1 ml of
SM buffer.
III Packaging Extract 5
TITERING THE PACKAGING REACTION
NoteFor titering cosmid libraries, see Titering the Cosmid Packaging
Reaction.
1. Streak the bacterial glycerol stock onto the appropriate agar plates
(see Appendix: Host Strain Preparation). Incubate the plates overnight
at 37°C.
NoteDo not add antibiotic to the medium in the following step.
The antibiotic will bind to the bacterial cell wall and will
inhibit the ability of the phage to infect the cell.
2. Inoculate an appropriate medium, supplemented with 10 mM MgSO
4
and 0.2% (w/v) maltose (see Appendix: Host Strain Preparation), with
a single colony.
3. Grow at 37°C, shaking for 4–6 hours (do not grow past an OD
600
of
1.0). Alternatively, grow overnight at 30°C, shaking at 200 rpm.
NoteThe lower temperature keeps the bacteria from overgrowing,
thus reducing the number of nonviable cells. Phage can
adhere to nonviable cells resulting in a decreased titer.
4. Pellet the bacteria at 500 × g for 10 minutes.
5. Gently resuspend the cells in half the original volume with sterile
10 mM MgSO
6. Dilute the cells to an OD
.
4
of 0.5 with sterile 10 mM MgSO4.
600
Note The bacteria should be used immediately following dilution.
7. Prepare dilutions of the final packaged reaction in SM buffer. Add 1 μl
of the final packaged reaction to 200 μl of host cells diluted in
10 mM MgSO
to an OD
4
of 0.5. If desired, also add 1 μl of a
600
1:10 dilution of the packaged reaction in SM buffer to 200 μl of host
cells.
8. Incubate the phage and the bacteria at 37°C for 15 minutes to allow the
phage to attach to the cells.
9. Add 3 ml of LB top agar (48°C) and plate immediately on prewarmed
LB agar plates.
10. Incubate the plates at 37°C for 12 hours.
11. Count the plaques and determine the titer in plaque-forming units per
milliliter (pfu/ml).
6 Gigapack III Packaging Extract
TITERING THE COSMID PACKAGING REACTION
1. Streak the bacterial glycerol stock onto the appropriate agar plates
(see Appendix: Host Strain Preparation). Incubate the plates overnight
at 37°C.
NoteDo not add antibiotic to the medium in the following step.
The antibiotic will bind to the bacterial cell wall and will
inhibit the ability of the phage to infect the cell.
2. Inoculate an appropriate medium, supplemented with 10 mM MgSO
4
and 0.2% (w/v) maltose (see Appendix: Host Strain Preparation), with
a single colony.
3. Grow at 37°C, shaking for 4–6 hours (do not grow past an OD
600
of
1.0). Alternatively, grow overnight at 30°C, shaking at 200 rpm.
NoteThe lower temperature keeps the bacteria from overgrowing,
thus reducing the number of nonviable cells. Phage can
adhere to nonviable cells resulting in a decreased titer.
4. Pellet the bacteria at 500 × g for 10 minutes.
5. Gently resuspend the cells in half the original volume with sterile
10 mM MgSO
6. Dilute the cells to an OD
.
4
of 0.5 with sterile 10 mM MgSO4.
600
Note The bacteria should be used immediately following dilution.
7. Prepare a 1:10 and a 1:50 dilution of the cosmid packaging reaction in
SM buffer.
8. Mix 25 μl of each dilution with 25 μl of the appropriate bacterial cells
at an OD
of 0.5 in a microcentrifuge tube and incubate the tube at
600
room temperature for 30 minutes.
Gigapack
9. Add 200 μl of LB broth to each sample and incubate for 1 hour at
37°C, shaking the tube gently once every 15 minutes. This incubation
will allow time for expression of the antibiotic resistance.
10. Spin the microcentrifuge tube for 1 minute and resuspend the pellet in
50 μl of fresh LB broth.
11. Using a sterile spreader, plate the cells on LB agar plates with the
required amount of the appropriate antibiotic. Incubate the plates
overnight at 37°C.
III Packaging Extract 7
APPENDIX:HOST STRAIN PREPARATION
Host strain
Agar plate for
bacterial streak
Medium for
glycerol stock
Medium for bacterial cultures for titering
phage (final concentration)
a
AG-1 strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
BB4 strain LB–tetracyclineb LB–tetracyclineb LB with 0.2% (w/v) maltose–10 mM MgSO4
C600 strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
JM101 strainc M9d M9b LB with 0.2% (w/v) maltose–10 mM MgSO4
JM109 strainc M9 M9 LB with 0.2% (w/v) maltose–10 mM MgSO4
JM110 straind M9 M9 LB with 0.2% (w/v) maltose–10 mM MgSO4
LE392 strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
NM514 strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
NM522 strainc M9 M9 LB with 0.2% (w/v) maltose–10 mM MgSO4
NM554 strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
P2392 strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
SCS110 straind M9 M9 LB with 0.2% (w/v) maltose–10 mM MgSO4
SURE straine LB–tetracycline LB–tetracycline LB with 0.2% (w/v) maltose–10 mM MgSO4
VCS257 strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
XL1-Blue strain LB–tetracycline LB–tetracycline LB with 0.2% (w/v) maltose–10 mM MgSO4
XL1-Blue MR strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
XL1-Blue MRF´ strain LB–tetracycline LB–tetracycline LB with 0.2% (w/v) maltose–10 mM MgSO4
XL1-Blue MRF´ Kan strain LB–kanamycin LB–kanamycin LB with 0.2% (w/v) maltose–10 mM MgSO4
XL1-Blue MRA strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
XL1-Blue MRA (P2) strain LB LB LB with 0.2% (w/v) maltose–10 mM MgSO4
Y1088 strain LB–ampicillinb LB–ampicillinb LB with 0.2% (w/v) maltose–10 mM MgSO4
Y1089r– strain LB–ampicillin LB–ampicillin LB with 0.2% (w/v) maltose–10 mM MgSO4
Y1090r– strain LB–ampicillin LB–ampicillin LB with 0.2% (w/v) maltose–10 mM MgSO4
a
NZY medium (see Preparation of Media and Reagents) may be substituted for LB medium in all cases.
b
See Preparation of Media and Reagents.
c
Will grow two times slower on M9 medium.
d
The amino acids—threonine, leucine, valine, and isoleucine—must be added to the M9 medium and plated at a
concentration of 50 mg/liter for proper growth. Filter-sterilize the amino acids with the glucose and add as instructed.
e
When growing lambda phage for plaque formation, incubate plates at 39°C.
8 Gigapack III Packaging Extract
TROUBLESHOOTING
–
A
Observation Suggestion(s)
Packaging efficiency is too low Gigapack III packaging extract is very sensitive to slight variations in temperature;
therefore, store the packaging extracts at the bottom of a –80°C freezer and avoid
transferring tubes from one freezer to another
Do not allow the packaging extracts to thaw
Avoid use of ligase buffers containing PEG, which can inhibit packaging
Ligate at DNA concentrations of 0.2 μg/μl or greater and package between
1 and 4 μl of the ligation reaction
Never package >4 μl of the ligation reaction, which causes dilution of the
proteins contained within the packaging extract
Neither a bacterial lawn nor
plaques is observed on the plate
Be sure to spin down the chloroform completely prior to removing an aliquot for
titering
PREPARATION OF MEDIA AND REAGENTS
Note All media must be autoclaved before use.
LB Broth (per Liter)
10 g of NaCl
10 g of tryptone
5 g of yeast extract
Add deionized H
O to a final volume of
2
1 liter
Adjust to pH 7.0 with 5 N NaOH
Autoclave
LB–Ampicillin Broth (per Liter)
1 liter of LB broth, autoclaved
Cool to 55°C
Add 10 ml of 10-mg/ml filter-sterilized
ampicillin
LB–Kanamycin Broth (per Liter)
1 liter of LB broth
Autoclave
Cool to 55°C
Add 50 mg of filter-sterilized kanamycin
LB Agar (per Liter)
10 g of NaCl
10 g of tryptone
5 g of yeast extract
20 g of agar
Add deionized H
O to a final volume of
2
1 liter
Adjust pH to 7.0 with 5 N NaOH
Autoclave
Pour into petri dishes
(~25 ml/100-mm plate)
LB
mpicillin Agar (per Liter)
1 liter of LB agar, autoclaved
Cool to 55°C
Add 10 ml of 10-mg/ml filter-sterilized
ampicillin
Pour into petri dishes
(~25 ml/100-mm plate)
LB–Kanamycin Agar (per Liter)
1 liter of LB agar
Autoclave
Cool to 55°C
Add 50 mg of filter-sterilized kanamycin
Pour into petri dishes
(~25 ml/100-mm plate)
Gigapack
III Packaging Extract 9
LB–Tetracycline Broth (per Liter)
1 liter of LB broth
Autoclave
Cool to 55°C
Add 12.5 mg of filter-sterilized tetracycline
Store broth in a dark, cool place as
tetracycline is light-sensitive
LB Top Agar (per Liter)
1 liter of LB broth
Add 0.7% (w/v) agarose
Autoclave
M9 Medium (per Liter)
6.0 g of dibasic sodium
phosphate (Na
3.0 g of monobasic potassium
phosphate (KH
1.0 g of ammonium chloride (NH
0.5 g of NaCl
Add deionized H
1 liter
Autoclave
While autoclaving, prepare the following
solution:
1.0 ml of 1 M MgSO
2.0 g of glucose
0.1 ml of 1 M CaCl
1.0 ml of 1 M thiamine-HCl
Add deionized H
of 10 ml and filter sterilize
Add the above solution to the cooled
M9 media
HPO4)
2
)
2PO4
Cl)
4
O to a final volume of
2
4
2
O to a final volume
2
LB–Tetracycline Agar (per Liter)
1 liter of LB agar
Autoclave
Cool to 55°C
Add 12.5 mg of filter-sterilized tetracycline
Pour into petri dishes
(~25 ml/100-mm plate)
Store plates in a dark, cool place or cover
plates with foil if left out at room
temperature for extended time periods
as tetracycline is light-sensitive
NZY Top Agar (per Liter)
1 liter of NZY broth
Add 0.7% (w/v) agarose
Autoclave
NZY Agar (per Liter)
5 g of NaCl
2 g of MgSO
. 7H2O
4
5 g of yeast extract
10 g of NZ amine (casein hydrolysate)
15 g of agar
Add deionized H
O to a final volume of
2
1 liter
Adjust the pH to 7.5 with NaOH
Autoclave
Pour into petri dishes
(~80 ml/150-mm plate)
NZY Broth (per Liter)
5 g of NaCl
2 g of MgSO
5 g of yeast extract
10 g of NZ amine (casein hydrolysate)
Add deionized H
1 liter
Adjust the pH to 7.5 with NaOH
Autoclave
. 7H2O
4
O to a final volume of
2
SM Buffer (per Liter)
5.8 g of NaCl
2.0 g of MgSO
50.0 ml of 1 M Tris-HCl (pH 7.5)
5.0 ml of 2% (w/v) gelatin
Add deionized H
1 liter
Autoclave
10 Gigapack III Packaging Extract
· 7H2O
4
O to a final volume of
2
REFERENCES
1. Kretz, P. L., Reid, C. H., Greener, A. and Short, J. M. (1989) Nucleic Acids Res
17(13):5409.
2. Kretz, P. L. and Short, J. M. (1989) Strategies in Molecular Biology 2(2):25-26.
3. Kohler, S. W., Provost, G. S., Kretz, P. L., Dycaico, M. J., Sorge, J. A. et al. (1990)
Nucleic Acids Res 18(10):3007-13.
4. Kretz, P. L., Kohler, S. W. and Short, J. M. (1991) J Bacteriol 173(15):4707-16.
ENDNOTES
Parafilm® is a registered trademark of American Can Company.
MSDSINFORMATION
Material Safety Data Sheets (MSDSs) are provided online at http://www.genomics.agilent.com. MSDS
documents are not included with product shipments.
Gigapack
III Packaging Extract 11
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