Zymo Research ZymoPURE Plasmid Miniprep User manual

ZYMO RESEARCH CORP.
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ZymoPURE™Plasmid Miniprep Kit
Catalog Nos. D4209, D4210, D4211 & D4212 (Patent Pending)
Highlights
•Fast and reliable purification of up to 100 µg of transfection-grade plasmid DNA using a spin-column.
•Innovative ZymoPURE™technology enables elution of ultra-pure endotoxin-free plasmid DNA in as little
as 25 µl.
Contents
Product Contents .................................................1
Product Specifications..........................................1
Product Description..............................................2
Procedure Overview.............................................3
Buffer Preparation................................................4
Protocol.............................................................4-6
Troubleshooting ...................................................7
Ordering Information............................................8
Related Products.............................................9-10
For Research Use Only Version 1.0.0
INSTRUCTION MANUAL

ZYMO RESEARCH CORP.
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Page 1
Product Contents:
ZymoPURE™Plasmid Miniprep
Kit Size
D4209
50 preps.
D4210
100 preps.
D4211
400 preps.
D4212
800 preps.
Storage
Temperature
ZymoPURE™P11(Red)
13 ml
2x 13 ml
100 ml
210 ml
4°C
ZymoPURE™P22,3 (Green)
13 ml
2x 13 ml
100 ml
210 ml
Room Temp.
ZymoPURE™P3 (Yellow)
13 ml
2x 13 ml
100 ml
210 ml
Room Temp.
ZymoPURE™Binding Buffer3
14 ml
2x 14 ml
110 ml
2x 110 ml
Room Temp.
ZymoPURE™Wash 1
2x 20 ml
4x 20 ml
320 ml
2x 320 ml
Room Temp.
ZymoPURE™Wash 24
12 ml
23 ml
3x 28 ml
6x 28 ml
Room Temp.
ZymoPURE™Elution Buffer
2x 1 ml
6 ml
12 ml
30 ml
Room Temp.
Zymo-Spin™II-P Columns
50
100
400
800
Room Temp.
Collection Tubes
50
100
400
800
Room Temp.
Instruction Manual
1
1
1
1
-
Note - Integrity of kit components is guaranteed for up to one year from date of purchase. Reagents are routinely
tested on a lot-to-lot basis to ensure they provide maximal performance and reliability.
1 ZymoPURE™P1 contains RNase A (100 µg/ml) and is stable at room temperature without loss in RNase activity,
however, for long-term storage the product should be stored at 4-8° C.
2 Caution: ZymoPURE™P2 Buffer contains NaOH. Please use proper safety precautions.
3The ZymoPURE™P2 and ZymoPURE™Binding Buffer may have precipitated. If this occurs, dissolve the precipitate
by incubating the bottles at 30-37 ºC for 10-20 minutes and mix by inversion. Do not microwave!
4 ZymoPURE™Wash 2 included with D4208S is supplied ready-to-use and does not require the addition of ethanol
prior to use. ZymoPURE™Wash 2 included with D4209, D4210, D4211, and D4212 are supplied as a concentrate and
require the addition of ethanol prior to use. See Buffer Preparation (page 4) for instructions.
Specifications:
•DNA Purity: Eluted DNA is ultrapure, endotoxin-free, and well suited for transfection,
transformation, sequencing, restriction endonuclease digestion, in vitro transcription, and
other sensitive applications.
oTypical Abs260/280 ≥ 1.8 and Abs260/230 ≥ 2.0
•Plasmid DNA Yield: Up to 100 µg per preparation (Actual yield is dependent on the plasmid
copy number, culture growth conditions, and strain of E. coli utilized)
•Plasmid DNA Size: Up to 25 kb
•Recovery Volume: ≥25 µl of ZymoPURE™Elution Buffer or DNase free water
•Required Equipment: Microcentrifuge and/or vacuum manifold (recommended).
•Processing Time: 15 min
Satisfaction of all Zymo
Research products is
guaranteed. If you are
dissatisfied with this product,
please call 1-888-882-9682.
Notes:
This product is for research use
only and should only be used by
trained professionals. It is not for
use in diagnostic procedures.
Some reagents included with this
kit are irritants. Wear protective
gloves and eye protection.
Follow the safety guidelines and
rules enacted by your research
institution or facility.
™ Trademarks of Zymo Research
Corporation.
Several ZymoPURE™product
technologies are subject to U.S.
and foreign patents or are patent
pending.
pGL3™is a registered trademark
of Promega Corporation.

ZYMO RESEARCH CORP.
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Page 2
Product Description
The ZymoPURE™Plasmid Miniprep Kit features a spin column-based
method for the purification of up to 100 µg of ultra-pure endotoxin-free plasmid DNA in
less than 15 minutes. The unique spin-column design also provides zero buffer
retention and a low elution volume.
ZymoPURE™technology uses a modified alkaline lysis method and features
novel binding chemistry that yields highly concentrated plasmid DNA (up to 3 µg/µl).
In addition, the wash regimen has been optimized to ensure the plasmid DNA is free of
endotoxins, salt, protein, and RNA. The result is plasmid DNA suitable for transfection,
restriction endonuclease digestion, bacterial transformation, PCR amplification, DNA
sequencing, and other sensitive downstream applications.
As an added convenience, the ZymoPURE™Plasmid Miniprep Kit contains
colored buffers that permit error-free visualization and identification of complete
bacterial cell lysis and neutralization.
Plasmid DNA yield and concentration from the ZymoPure™ Miniprep Kit compared to other major suppliers.
Plasmid DNA (pGL3®) was isolated from 5 ml of JM109 E. coli culture grown overnight following the manufacturer’s
suggested protocol (in duplicate). One (1) µl of eluted plasmid DNA was visualized post agarose gel electrophoresis.
M, ZR 1 kb DNA Marker (Zymo Research).

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Page 3
Procedure Overview:

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Page 4
Buffer Preparation:
✓Add 46 ml of 95% ethanol to the 12 ml ZymoPURE™ Wash 2 (Concentrate) (D4209), 88
ml of 95% ethanol to the 23 ml ZymoPURE™ Wash 2 (Concentrate) (D4210), or 107 ml of
95% ethanol to the 28 ml ZymoPURE™ Wash 2 (Concentrate) (D4211 & D4212) before
use.
✓The ZymoPURE™P2 and ZymoPURE™Binding Buffer may have precipitated. If this
occurs, dissolve the precipitate by incubating the bottles at 30-37 ºC for 10-20 minutes and
mix by inversion. Do not microwave!
✓Before Starting: Incubate ZymoPURE™P3 on ice for 30 minutes before use.
Protocol:
The following procedure should be performed at room temperature (15-30°C).
1. Centrifuge 0.5-5 ml1of bacterial culture in a clear 1.5 ml tube at full speed for 15-
20 seconds in a microcentrifuge. Discard supernatant.
2. Add 250 µl of ZymoPURE™P1 (Red) to the bacterial cell pellet and resuspend
completely by vortexing or pipetting.
3. Add 250 µl of ZymoPURE™P2 (Green) and immediately mix by gently inverting
the tube 6-8 times. Do not vortex! Let sit at room temperature for 2-3 minutes2.
Cells are completely lysed when the solution appears clear, purple, and viscous.
4. Add 250 µl of ice cold ZymoPURE™P3 (Yellow) and mix thoroughly by inversion.
Do not vortex! Invert the tube an additional 3-4 times after the sample turns
completely yellow. The sample will turn yellow when the neutralization is complete
and a yellowish precipitate will form.
5. Incubate the neutralized lysate on ice for 5 minutes.
6. Centrifuge the neutralized lysate for 5 minutes at 16,000 x g.
7. Transfer 600 µl of supernatant from step 6 into a clean 1.5 ml microcentrifuge tube.
Be careful not to disturb the yellow pellet and avoid transferring any cellular debris
to the new tube.
8. Add 275 µl of ZymoPURE™Binding Buffer to the cleared lysate from step 7 and
mix thoroughly by inverting the capped tube 8 times.
To continue processing the lysate using the recommended vacuum protocol,
proceed to the next page. If a vacuum is not available, proceed to page 6 for an
alternative centrifugation method.
For Technical Assistance,
please contact us at
1-888-882-9682 or E-mail
[e-mail].
Notes:
1Depending on the volume
of bacterial culture it may be
necessary to repeat Step 1
several times.
2Do not allow the lysis
reaction to proceed for more
than 3 minutes. Excessive
lysis can result in denatured
plasmid DNA. When
processing a large number
of samples, work with
groups of ≤ 10 at a time.

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Page 5
Vacuum Protocol: (Recommended)
This product is compatible with any conventional vacuum-based manifold. The vacuum pump should be a
single or double-staged unit capable of producing up to 400 mm Hg pressure at the vacuum manifold1.
9. Place the Zymo-Spin™II-P Column onto a vacuum manifold. (If vacuum is not
available, see page 6 for the centrifugation protocol.)
10. With the vacuum off, add the entire mixture from step 8 into the Zymo-Spin™II-P
Column. Turn on the vacuum until all of the liquid has passed completely through
the column.
11. With the vacuum off, add 800 µl of ZymoPURE™Wash 1 to the Zymo-Spin™II-P
Column.Turn on the vacuum until all of the liquid has passed completely through
the column.
12. With the vacuum off, add 800 µl of ZymoPURE™Wash 2 to the Zymo-Spin™II-P
Column. Turn on the vacuum until all of the liquid has passed completely through
the column.
13. With the vacuum off, add 200 µl of ZymoPURE™Wash 2 to the Zymo-Spin™II-P
Column. Turn on the vacuum until all of the liquid has passed completely through
the column.
14. Place the Zymo-Spin™II-P Column in a Collection Tube and transfer to a
microcentrifuge. Centrifuge at ≥10,000 x gfor 1 minute in order to remove any
residual wash buffer.
15. Transfer the Zymo-Spin™II-P Column into a clean 1.5 ml tube and add 25 µl of
ZymoPURE™Elution Buffer2,3 directly to the column matrix. Incubate at room
temperature for 2 minutes, and then centrifuge at ≥ 10,000 x gfor 1 minute in a
microcentrifuge. Store the eluted plasmid DNA at ≤ -20°C.
Notes:
1 To achieve optimal
performance, the vacuum
pump should be able to
apply at least 400 mm Hg
pressure. If less pressure is
applied, centrifuge the
column prior to washing to
remove any residual lysate
remaining in the matrix.
2 The ZymoPURE™Elution
Buffer contains 10 mM Tris-
HCl, pH 8.5, 0.1 mM EDTA.
If required, pure water can
also be used to elute the
DNA.
3 The DNA yield can be
increased by pre-warming the
Zymo PURE™Elution Buffer
to 50 ºC and/or increasing the
incubation period up to 5
minutes prior to centrifugation.

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Page 6
Centrifugation Protocol: (Alternative)
Perform steps 1-8 as indicated in the general protocol, see page 4.
9. Place a Zymo-Spin™II-P Column in a Collection Tube and transfer the entire
mixture from step 8 into the Zymo-Spin™II-P Column.
10. Incubate the Zymo-Spin™II-P/Collection Tube assembly at room temperature for
2 minutes and then centrifuge at 5,000 x g for 1 min. Discard the flow through1.
11. Add 800 µl of ZymoPURE™Wash 1 to the Zymo-Spin™II-P Column and centrifuge
at 5,000 x g for 1 min. Discard the flow through.
12. Add 800 µl of ZymoPURE™Wash 2 to the Zymo-Spin™II-P Column and centrifuge
at 5,000 x g for 1 min. Discard the flow through.
13. Add 200 µl of ZymoPURE™Wash 2 to the Zymo-Spin™II-P Column and centrifuge
at 5,000 x g for 1 min. Discard the flow through.
14. Centrifuge the Zymo-Spin™II-P Column at ≥ 10,000 x gfor 1 minute in order to
remove any residual wash buffer.
15. Transfer the Zymo-Spin™II-P Column into a clean 1.5 ml tube and add 25 µl of
ZymoPURE™Elution Buffer2,3 directly to the column matrix. Incubate at room
temperature for 2 minutes, and then centrifuge at ≥ 10,000 x gfor 1 minute in a
microcentrifuge. Store the eluted plasmid DNA at ≤ -20°C.
Notes:
1 The capacity of the
collection tube with the
column inserted is 900 µl.
Empty the collection tube
whenever necessary to
prevent contamination of the
spin-column with the flow
through.
2 The ZymoPURE™Elution
Buffer contains 10 mM Tris-
HCl, pH 8.5, 0.1 mM EDTA.
If required, pure water can
also be used to elute the
DNA.
3 The DNA yield can be
increased by pre-warming the
Zymo PURE™Elution Buffer
to 50 ºC and/or increasing the
incubation period up to 5
minutes prior to centrifugation.

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Page 7
Troubleshooting Guide:
Problem
Possible Causes and Suggested Solutions
Low DNA Yield
Culture growth conditions
•Poor aeration of culture. The optimal culture volume to air volume ratio is 1:5 or
less. For best aeration, use baffled culture flasks, or a vented or gas-permeable seal
on the culture vessel.
•The culture was overgrown, undergrown, contaminated, or antibiotics were
omitted from the growth medium. Use a fresh culture for optimal performance. An
OD600 of 0.2-0.35 is the optimal optical density of a tenfold dilution of the culture.
Cell density is too high
•Too much culture used. Lysis and neutralization will be incomplete resulting in
poor lysate clarification. More culture does not always equal more plasmid.
Incomplete lysis and neutralization are two of the most common causes of failed
plasmid preps and both are caused by too much culture being used.
•Incomplete lysis: After addition of ZymoPURE™P2, the solution should change
from opaque pink to a clear viscous purple, indicating complete lysis. Different
E. coli strains often require different growth conditions and may vary in their
susceptibility to alkaline lysis.
•Incomplete neutralization: The solution should not be viscous following
neutralization and the yellowish precipitate should appear fluffy and readily float to
the surface. Make sure the neutralization is complete prior to centrifugation. Invert
the tube an additional 3-4 times after the sample turns yellow following the addition
of ZymoPURE™P3.
Lysate clarification
•Less than 600 µl of supernatant was recovered after pelleting the lysate debris.
For optimal performance, add 275 µl of ZymoPURE™Binding Buffer to 600 µl of
clarified lysate.
ZymoPURE P2 and
ZymoPURE Binding Buffer
precipitated
•Both buffers may have precipitated during shipping. To completely resuspend
the buffers, incubate the bottles at 30-37 ºC for 10 minutes and mix by inversion. DO
NOT MICROWAVE.
Wash buffer
•Ensure that the correct volume of ethanol was added to the ZymoPURE™Wash 2.
•Ensure that the bottle cap is screwed on tightly after each use to prevent
evaporation of the ethanol.
DNA elution
•Incomplete elution: For large size plasmids (> 10 kb), add ZymoPURE™Elution
Buffer and incubate the column for 5-10 minutes before centrifugation. Also, pre-
warm the ZymoPURE™Elution Buffer to 50 ºC prior to elution.
Low DNA Quality
DNA does not perform well
•Incomplete neutralization: Incomplete neutralization generates poor quality
supernatant. Ensure that neutralization is complete by inverting the sample an
additional 3-4 times after the sample turns yellow following the addition of
ZymoPURE™P3.
•Insufficient centrifugation: Make sure that all centrifugation steps are performed at
the indicated speed and time. If a lower centrifuge speed is used, then extend the
centrifugation time to compensate.
RNA in eluate
•Ensure that ZymoPURE™P1 has been stored at 4°C. RNase A can be purchased
separately if necessary.
Genomic DNA in eluate
•Improper handling (Sample was vortexed or handled too roughly). Genomic DNA
contamination is usually caused by excessive mechanical shearing during the lysis
and neutralization steps. Also, prolonged lysis or incomplete mixing of lysis or
neutralization buffers may contribute to genomic DNA contamination in your sample.
•Overgrown culture. Overgrown or old cultures may contain more genomic DNA
contamination than fresh cultures.

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Page 8
Ordering Information
Product Description
Kit Size
Catalog No.
ZymoPURE™Plasmid Miniprep Kit
50 preps.
D4209
ZymoPURE™Plasmid Miniprep Kit
100 preps.
D4210
ZymoPURE™Plasmid Miniprep Kit
400 preps.
D4211
ZymoPURE™Plasmid Miniprep Kit
800 preps.
D4212
For Individual Sale
Amount
Catalog No.
ZymoPURE™P1 (Red)
3 ml
13 ml
100 ml
210 ml
D4200-1-3
D4200-1-13
D4200-1-100
D4200-1-210
ZymoPURE™P2 (Green)
3 ml
13 ml
100 ml
210 ml
D4200-2-3
D4200-2-13
D4200-2-100
D4200-2-210
ZymoPURE™P3 (Yellow)
3 ml
13 ml
100 ml
210 ml
D4200-3-3
D4200-3-13
D4200-3-100
D4200-3-210
ZymoPURE™Binding Buffer
3 ml
14 ml
110 ml
D4200-4-3
D4200-4-14
D4200-4-110
ZymoPURE™Wash 1
12 ml
20 ml
320 ml
D4200-5-12-S
D4200-5-20
D4200-5-320
ZymoPURE™Wash 2 (Concentrate)
12 ml
23 ml
28 ml
D4200-6-12
D4200-6-23
D4200-6-28
ZymoPURE™Elution Buffer
1 ml
6 ml
12 ml
30 ml
D4200-7-1
D4200-7-6
D4200-7-12
D4200-7-30
Zymo-Spin™II-P
10
50
C1055-10
C1055-50
Collection Tubes
50
500
1000
C1001-50
C1001-500
C1001-1000

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Page 9

ZYMO RESEARCH CORP.
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Page 10

ZYMO RESEARCH CORP.
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