Biotage PhyPrep User manual

Biotage®PhyPrep
User Manual

Biotage®PhyPrep User Manual | © Biotage 2021
Biotage® PhyPrep
Biotage®PhyPrep
User Manual
CONTENTS
4System Overview
 Quickstart Guide
 Hardware & Connections
 Instrument Safety
 Sample Filter Reservoir
 Biotage®PhyPrep Plasmid Kit Endotoxin-Free
 Instrument Deck
9Before You Begin
 Buffer Preparation
 Recommended Culture Conditions for Optimal Results
10 Sample Preparation Guide
 Resuspend Cells
 Lyse Cells
 Precipitate
 Filter
12 Maxiprep Sample Preparation
 Maxiprep  Sample Method
 Maxiprep  Sample Deck Layout
 Maxiprep Samples Method
 Maxiprep  Samples Deck Layout
 Maxiprep Samples Method
 Maxiprep  Samples Deck Layout
 Maxiprep Samples Method
 Maxiprep  Samples Deck Layout
20 Megaprep Sample Preparation
 Megaprep  Sample Method
 Megaprep  Sample Deck Layout
 Megaprep Samples Method
 Megaprep  Samples Deck Layout
 Megaprep Samples Method
 Megaprep  Samples Deck Layout
 Megaprep Samples Method
 Megaprep  Samples Deck Layout
28 Gigaprep Sample Preparation
 Gigaprep  Sample Method
 Gigaprep  Sample Deck Layout
 Gigaprep Samples Method
 Gigaprep  Samples Deck Layout
 Gigaprep Samples Method
 Gigaprep  Samples Deck Layout
 Gigaprep Samples Method
 Gigaprep  Samples Deck Layout
36 Software Overview
37 Recommended Alcohol Precipitation protocol
38 Maintenance
 Endotoxin Levels
 Using the endotoxin measuring instrument
 Wash Buffer Reservoir
 Carboys Set Up and Care
 Carboys Contents Disposal
40 Troubleshooting
 Low DNA yield
 Low DNA quality
42 General Information
 Consumables and Accessories


Biotage® PhyPrep

Biotage®PhyPrep User Manual | © Biotage 2021
System Overview
The Biotage®PhyPrep system is the only all-in-one instrument for automated endotoxin-free plasmid purification in maxi, mega, and
giga scales. This system offers a variety of user friendly protocols for endotoxin-free plasmid purification.
It is developed and supported by scientists and engineers to provide consistent high-quality endotoxin-free plasmids for transient
transfection.
System Overview
Prep Scale
Number
of Sample
Preps
Run Time
(Hour/Minutes)
Culture Volume
Per Sample
Pellet
Wet Weight
Per Sample
Optimal Pellet
Wet weight
Plasmid
Mass
Elution
Volume
Maxiprep
142 m
150–250 mL 3-5 g 3 g Up to
1 mg 5 mL
242 m
31 h 10 m
41 h 10 m
Megaprep
11 h 16 m
350–500 mL 6-8 g 7 g Up to
5 mg 18 mL
21 h 16 m
32 h 22 m
42 h 22 m
Gigaprep
12 h 31 m
60 0 –750 mL 14-16 g 15 g Up to
10 mg 28 mL
22 h 34 m
34 h 57 m
44 h 58 m
Quickstart Guide
Choose
your scale
Determine the culture volume and culture media needed for generating pellet wet weight of E-coli
cells for your prep scale . It is recommended to use TB or other high growth media for optimal yield.
Grow culture Grow overnight cultures and harvest the cell pellets by centrifugation.
Select
Sample Size
Choose the number of samples to purify. Power up the instrument and select your prep scale and
number of your samples in the PhyPrep software.
Set Up Deck Set up the deck with consumables as described in the protocols.
Prepare
Culture
Resuspend, lyse, and precipitate the sample(s) using the color-coded buffer system.
Pour the neutralized lysate into the Sample Filter Reservoirs on the instrument.
Run Method Start the method in the PhyPrep software to start the run.
Collect
Plasmids
When the run is complete, collect the elution tubes from the elution stand. Use immediately for
downstream assays or refrigerate or freeze for later use.



Hardware & Connections
Parts
Instrument Side Panel
1. Power connector
2. Power switch
3. Vacuum power connector
4. Ethernet port
5. PC power connector
6. Vacuum port and red tubing
7. Waste port and blue tubing
Emergency Stop
Open the door for
emergency stop.
1
2
3
4
6
5
7
Panel PC
Leakage Tray
Waste
Carboy
Vacuum
pump
Vacuum
Carboy
Vacuum Waste
Vacuum
Carboy
Waste
Carboy
Sample
Filter
Reservoir
Elution Tube
Stand
Wash Buffer
Reservoir
Vacuum Växel
Column
Transfer
Tip
Elution
Tube
PhyPrep
Tube

Biotage®PhyPrep User Manual | © Biotage 2021
Instrument Safety
Open Section
Sample Filter Reservoir
Assembly
Assemble the Sample Filter Reservoirs with the correct orientation
before placing them on the deck. The reservoir consists of a filter
top and a reservoir bottom. The filter lid has an open section and
the reservoir has a large edge and a small edge for orientation.
To assemble the Sample Filter Reservoir, place the open section of
the filter top over the small edge of the reservoir bottom.
Placement on deck
Place the Sample Filter Reservoir on the deck with the filter
section closest to the front of the instrument.
Instrument Safety
Emergency Stop
The PhyPrep door works as an emergency stop. If the door is
opened at any time during system operation, the instrument
will stop operating immediately, and the current method will be
aborted. It is not possible to resume the stopped method again
after PhyPrep door is opened.
After an emergency stop, if the pipetting head has transfer tips
or Växel columns attached, eject these by using the “Initialize”
button in the software. There should not be any columns attached
to the pipetting head before starting a new run.
Important note
» Never try to take off attached transfer tips or Växel columns
manually as you may harm your hand.
The STOP Button
If the STOP button is pressed during a method run, you are asked
to confirm that the method should be stopped. If you confirm, the
system will stop, and the current method will be aborted. It is not
possible to resume the method after pressing STOP.
Vacuum Pump Voltage
Ensure the voltage on the vacuum pump is set correctly.
Elution Tube Stand
For each sample being purified, be sure
to place a  mL pyrogen-free elution
tube in the bottom level of the elution
stand.
Instrument Cleaning
Do not spray alcohol direclty onto the instrument robotics parts.
Doing so will lead to damages to your PhyPrep.
Ensure paper towels and or other materials are not placed in the
vacuum station.
Filter Reservoir
Filter
Reservoir
Open section
Small edge
Large edge
Open section
Small edgeLarge edge
 corresponds to
- volts
 corresponds to
- volts
Elution
stand
Elution
collection
tubes


Biotage® PhyPrep Plasmid Kit Endotoxin-Free
Biotage®PhyPrep Plasmid Kit Endotoxin-Free
Kit Contents
Maxiprep kit DPM-16-05-72-KIT
710-0001 900-0078 900-0081 900-0084 900-0091 900-0093 900-0087 900-0089 700-0030 DPM -16- 05-
72-RNA 417458SP DPM-00- 25-00
16 x 16 x 16 x 16 x 1 x 16 x 1 x 1 x 16 x 16 x 50 x 50 x
Växel
Maxiprep
Column
Resuspension
Buffer
Lysis
Buffer
Precipitation
Buffer
Wash
Buffer
Elution
Buffer
Endotoxin
Removal
Buffer
Equilibration
Buffer
Sample Filter
Reservoir
RNase A
Tubes
PhyPrep
Tube
20 mL
Transfer Tip
Megaprep kit DPM-16-10-72-KIT
710-0002 900-0079 900-0082 900-0085 900-0092 900-0094 900-0087 900-0089 700-0030 DPM -16-10 -
72-RNA 417458SP DPM-00- 25-00
16 x 16 x 16 x 16 x 1 x 16 x 1 x 1 x 16 x 16 x 100 x 50 x
Växel
Megaprep
Column
Resuspension
Buffer
Lysis
Buffer
Precipitation
Buffer
Wash
Buffer
Elution
Buffer
Endotoxin
Removal
Buffer
Equilibration
Buffer
Sample Filter
Reservoir
RNase A
Tubes
PhyPrep
Tube
20 mL
Transfer Tip
Gigaprep kit DPM-08-20-72-KIT
710-0003 900-0080 900-0083 900-0086 900-0092 900-0094 900-0088 900-0090 700-0030 DPM-08-20-
72-RNA 417458SP DPM-00- 25-00
8 x 8 x 8 x 8 x 1 x 8 x 1 x 1 x 8 x 8 x 50 x 25 x
Växel
Gigaprep
Column
Resuspension
Buffer
Lysis
Buffer
Precipitation
Buffer
Wash
Buffer
Elution
Buffer
Endotoxin
Removal
Buffer
Equilibration
Buffer
Sample Filter
Reservoir
RNase A
Tubes
PhyPrep
Tube
20 mL
Transfer Tip

Biotage®PhyPrep User Manual | © Biotage 2021

Instrument Deck
The Biotage PhyPrep has specific deck layouts for all of the
pre-programmed methods.
Section 1: Transfer tips
Tips are placed in the upper left corner.
Section 2: Vacuum and waste station
Section 3: Wash Buffer Reservoir
The Wash Buffer Reservoir is located in the upper
right corner. It should be removed from the deck prior
to filling it with wash buffer to minimize the risk of
spilling. Empty remaining volume after each run and
clean with % alcohol.
Section 4: PhyPrep Tubes and Växel columns
This section contains space for  Växel columns
and  PhyPrep Tubes.
Section 5: Supplemental buffer section
The supplemental buffer section contains  rows of
PhyPrep Tube spots. Each row contains space for 
tubes.
Figure 1. The PhyPrep deck layout 1) Transfer tubes 2) Vacuum station 3) Wash Buffer Reservoir 4) Biotage Växel columns and PhyPrep Tubes
5) Supplemental buffers 6) Biotage Växel columns and PhyPrep Tubes 7) Elution Tube Stand 8) Sample Filter Reservoirs
Section 6: PhyPrep Tubes and Växel columns
This section contains space for  Biotage Växel
columns and  PhyPrep Tubes.
Section 7: Elution Tube Stand
The Elution Tube Stand is located near
the front center. For each sample being
purified, a  mL pyrogen-free elution
tube must be placed in the bottom level
of the elution stand. Before collecting
the purified sample, carefully remove
the Växel columns from the Elution
Tube Stand. There may be a residual
drop attached to the bottom of each tip.
Lightly tap the drop onto the elution tube
you would like to collect.
Section 8: Sample Filter Reservoirs
The Sample Filter Reservoirs are located in the
frontmost portion of the deck. For each sample
being purified, one sample reservoir should be
used. Place the Filter Reservoirs in the correct
orientation with the filter closest to the front of
the deck.
1
23
4
5
6
7
8
Elution
collection
tube
Wash Buffer
Reservoir
Sample Filter
Reservoir
Transfer
Tip
PhyPrep
Tube
Elution
tube
stand
PhyPrep
Tube
PhyPrep
Tube


Before You Begin
Before You Begin
Buffer Preparation
» Add the provided lyophilized RNase A to
Resuspension Buffer before use. Once RNase A is
added to Resuspension Buffer, the solution should
be stored at –˚C if not immediately used.
» Check Lysis Buffer for precipitation due to low
storage temperature. In the case of precipitation,
dissolve by warming bottle(s) in water bath at
–˚C for – minutes and mix by inversion.
» Store these buffers at ˚C overnight before use
for optimal yield:
» Resuspension Buffer
» Precipitation Buffer
» Endotoxin Removal Buffer
» Equilibration Buffer
» To maintain the sterility of the equilibration buffer,
endotoxin removal buffer, and wash buffer when
aliquoting, use the fume hood and a flame. With the flame
and fume hood on, pass the buffer container lid and neck
through the flame and open the bottle while hovering
near the flame.
When pouring out the specified amount of buffer,
pour the buffer from the bulk bottle into the
specified container for the deck while hovering
near the flame. After aliquoting, flame through the
cap and opening of the bottle before closing.
Preparing Resuspension Buffer
You can add the RNase A to Resuspension Buffer when you
receive your kit. Once RNase A has been added to
Resuspension Buffer , store at –˚C.
Recommended Culture Conditions
for Optimal Results
The Biotage PhyPrep’s robust instrumentation and chemistry
allows for dense sample processing without the worry for
clogging or contamination. Because of the instrument’s
flexibility and scale, Biotage recommends growing denser
cultures compared to traditional manual preps.
Please follow the outlined recommendations for optimizing
culture growth:
Growth Medias
The use of rich medias has the highest impact on cell growth
density.
We recommend the following:
» Terrific Broth (TB)
» Thomson Plasmid+®
» Agencourt Ale
Ratio of Media to Flask Size
Use a : ratio of media to flask size. The volume of media
should not exceed % of the flask volume. This is to allow
proper aeration of the culture during incubation and maximize
cell division.
Incubator Temperature and Shaking Frequency
We recommend incubating at °C and  RPM. Larger
cultures require faster shaking speeds to properly aerate the
whole volume of cells. Certain plasmids (for example pUC)
will increase in copy number when grown at slightly higher
temperatures.
Starter and Overnight Culture Times
A smaller culture grown for – hours to inoculate the overnight
culture at a dilution of : is recommended. In rich media,
cultures may grow slightly longer for about  hours overnight.
Growth Flask and Air Permeable Seal
Cell density in cultures can be further optimized using Thomson
flasks and seals.
» Thomson Optimal Growth Flasks
» Thomson AirOtop™Enhanced Seals
Harvest Cells
  g pellet wet weight is needed for Maxiprep, achieved
by growing  mL of an overnight bacterial culture.
  g pellet wet weight is needed for Megaprep, achieved
by growing  mL of an overnight bacterial culture.
  g pellet wet weight is needed for Gigaprep, achieved
by growing  mL of an overnight bacterial culture.
» Centrifuge at ≥  x g for  minutes. Discard supernatant.
» The PhyPrep deck can be set up while waiting for cells to
pellet. See appropriate deck layout per desired method
for further instructions.

 Biotage®PhyPrep User Manual | © Biotage 2021
Sample Preparation Guide
Sample Preparation Guide
All steps are carried out at room temperature. Please review the section “Before You Begin” on page 9 prior to
proceeding with sample preparation.
. Resuspend Cells
» Add contents of RNase A tube to the RESUSPENSION BUFFER. Uncap the centrifuge bottle and add the entire contents
of RESUSPENSION BUFFER. To aid in pellet resuspension, agitation beads are included in RESUSPENSION BUFFER.
Recap the centrifuge bottle and shake vigorously until the bacterial pellet is completely resuspended.
Important reminder
» Use 1 Resuspension Buffer bottle per sample. Verify that RNase A is added to Resuspension Buffer.
Important notes
» Incomplete resuspension can result in poor recovery of plasmid DNA.
. Lyse Cells
» Uncap the centrifuge bottle and add the entire contents of LYSIS BUFFER. Recap the centrifuge bottle and mix by
inverting gently – times. To aid in the lysis step, a blue indicator dye is present in LYSIS BUFFER. Ensure the
solution turns completely blue. If nonblue portions are observed after  inversions, continue mixing gently.
Let the lysis step occur for at least  minutes. Do not let the lysis step exceed  minutes.
Important reminder
» Use 1 Lysis Buffer bottle per sample. Verify that Lysis Buffer has not precipitated.
Important notes
» Do not shake or vortex during this step. Harsh mixing will shear genomic DNA and may contaminate the
final recovered plasmid DNA.
» Do not allow lysis to proceed longer than 5 minutes. Prolonged alkaline lysis may permanently denature
the supercoiled plasmid DNA and may render it unsuitable for use in downstream applications.
» If the buffer contents have precipitated due to low temperatures, warm bottle to 30–37°C for 10–20 min
and shake to dissolve potential precipitation.
. Precipitate
» Uncap the centrifuge bottle and add the entire contents of PRECIPITATION BUFFER. Recap the centrifuge bottle and mix by
inverting - times. A white precipitate containing cell debris, proteins, lipids, SDS, and chromosomal DNA will form.
Upon complete neutralization, the solution will turn from blue to clear. If blue portions are observed after  inversions,
continue mixing gently.
Important reminder Use 1 Preciptation Buffer bottle per sample.
Important notes
» Mixing during this step should be gentle but thorough. Although it is important to completely mix the
solution to ensure complete precipitation of cellular debris, do not shake or vortex during this step. Harsh
mixing can cause break up of precipitated debris and may contaminate the final recovered plasmid DNA.
» For increased yield, use cold Preciptation Buffer, Equilibration Buffer, Endotoxin Removal Buffer, and
Resuspension Buffer that have been stored at 4°C.
. Filter
» Place Sample Filter Reservoir on the PhyPrep deck. Then slowly pour entire contents of the centrifuge bottle into the middle
of the Sample Filter Reservoir to allow the supernatant to go through the filter first. This will prevent the precipitated
particulates clogging the filter.


Sample Preparation Guide
Sample Preparation Guide
Required Kit
RNase A Resuspension Buffer Lysis Buffer Precipitation Buffer Thawed Cell Pellet
4. Filter
2. Lyse Cells
1. Resuspend Cells
3. Precipitate
Precipitated
Sample
Sample
Reservoir
Lysis
Buffer
RNase A
ADD TO
ADD TO
ADD TO
POUR INTO
THEN ADD TO
THEN
THEN
Resuspension
Buffer
Precipitation
Buffer
Resuspended
Cell Pellet
Thawed or Fresh
Cell Pellet
Gently invert bottle 20-30 times.
Solution turns blue when fully mixed.
Do not exceed 5 minutes during Lysis.
Shake until pellet is
completely resuspended
(20-30 seconds)
Gently invert bottle 20-30 times.
Solution turns clear when fully mixed.
Place Sample Filter Reservoir on deck. Then pour
precipitated sample into Sample Filter Reservoir.
Lysed
Cells
THEN

 Biotage®PhyPrep User Manual | © Biotage 2021
Maxiprep  Sample Method
This protocol is designed for the preparation of up to  mg of
high-copy plasmid DNA per sample using the Biotage PhyPrep
Maxiprep kit. While setting up the deck, place the appropriate
consumables in the corresponding numbered sections of the
deck.
Required
Parts
20 mL
Transfer Tip
Växel
Maxiprep
Column
Wash
Buffer
Elution
Buffer
Endotoxin
Removal
Buffer
Equilibration
Buffer
50 mL
Pyrogen-free
Elution Tube
Sample Filter
Reservoir
PhyPrep
Tube
Quantity 3 1 1 1 1 1 1 1 3
Part # DPM-00-
25-00 710-0001 900-0091 900-0093 900-0087 900-0089 DPM-00-
10-01 700-0030 417458SP
Section
1
» Place  x Transfer Tips in A, E, and I.
Section
3
» Add  mL of WASH BUFFER to the Wash Buffer Reservoir.
Section
4
» Place  x PhyPrep Tube into A.
» Place  x PhyPrep Tube into I.
Add  mL of EQUILIBRATION BUFFER to this tube.
» Place x Biotage®Växel Maxiprep column into K.
Section
5
» Uncap and place  x ELUTION BUFFER tube into C.
» Place  x PhyPrep Tube into E.
Add  mL of ENDOTOXIN REMOVAL BUFFER to this tube.
Section
7
» Remove the Elution Tube Stand from the PhyPrep deck.
» Uncap and place  x  mL pyrogen-free conical tubes into position A.
» Elution collection tube should rest in the bottom portion of the elution stand.
» Place the Elution Tube Stand back onto the PhyPrep deck.
Section
8
» Place  x Sample Filter Reservoir into A.
» Ensure the filter part is towards the front of the deck.
Recommended cell wet weight
 3-5 g per sample from culture volume range of 150–250 mL
Maxiprep 1 Sample Method
Important notes
» Ensure correct volume of Wash Buffer is added to the Wash
Buffer Reservoir in Section 3. Ensure correct volumes of
Equilibration Buffer and Endotoxin Removal Buffer are added to
PhyPrep Tubes in sections 4 and 5.


Maxiprep  Sample Deck Layout
Maxiprep 1 Sample Deck Layout
1
4
5
6
7
8
3
2
Wash Buffer
130 mL
Elution
Buffer Elution Buffer
25 mL
EQ
Buffer
25 mL
EQ
Buffer
Sample
Tube Sample
Tube
20 mL
ER
Buffer
20 mL
ER
Buffer
Elution
Tube
Sample 1
Sample 1 Sample 2 Sample 3 Sample 4
Växel
column
PhyPrep
Tube
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
I
M
E
A
A
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
J
N
F
B
C
B
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
C
G
K
O
D
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
D
H
L
P
A
B
C
D
E
F
G
A
B
C
D
E
F
H
J
I
K
A
B
A
B
C
D
C
D
E
F
G
H
J
I
N
M
K
L
O
P
L
A
B
C
D
25 mL
EQ
Buffer
Sample
Tube
Sample
Tube
25 mL
EQ
Buffer
Sample
Tube
Sample
Tube
PhyTip
Sample
Tube
Sample
Tube
PhyTip
Sample
Tube
Sample
Tube
Elution
Tube
Elution
Tube Elution Tube
Sample
Tube
Sample
Tube Sample Tube
Sample
Tube
Sample 2
Sample 3 Sample 4
Elution
Buffer Elution Buffer

 Biotage®PhyPrep User Manual | © Biotage 2021
Maxiprep  Samples Method
This protocol is designed for the preparation of up to  mg of
high-copy plasmid DNA per sample using the Biotage PhyPrep
Maxiprep kit. While setting up the deck, place the appropriate
consumables in the corresponding numbered sections of the
deck.
Required
Parts
20 mL
Transfer Tip
Växel
Maxiprep
Column
Wash
Buffer
Elution
Buffer
Endotoxin
Removal
Buffer
Equilibration
Buffer
50 mL
Pyrogen-free
Elution Tube
Sample Filter
Reservoir
PhyPrep
Tube
Quantity 6 21211226
Part # DPM-00-
25-00 710-0001 900-0091 900-0093 900-0087 900-0089 DPM-00-
10-01 700-0030 417458SP
Section
1
» Place  x Transfer Tips in A, C, E, G, I, and K.
Section
3
» Add  mL of WASH BUFFER to the Wash Buffer Reservoir.
Section
4
» Place  x PhyPrep Tubes into A and B.
» Place  x PhyPrep Tubes into I and J.
Add  mL of EQUILIBRATION BUFFER to these tubes.
» Place x Biotage®Växel Maxiprep columns into K and L.
Section
5
» Uncap and place  x ELUTION BUFFER tubes into C and D.
» Place  x PhyPrep Tubes into E and F.
Add  mL of ENDOTOXIN REMOVAL BUFFER to these tubes.
Section
7
» Remove the Elution Tube Stand from the PhyPrep deck.
» Uncap and place  x  mL pyrogen-free conical tubes into positions A and B.
» Elution collection tubes should rest in the bottom portion of the elution stand.
» Place the Elution Tube Stand back onto the PhyPrep deck.
Section
8
» Place  x Sample Filter Reservoirs into A and B.
» Ensure the filter part is towards the front of the deck.
Recommended cell wet weight
 3-5 g per sample from culture volume range of 150–250 mL
Maxiprep 2 Samples Method
Important notes
» Ensure correct volume of Wash Buffer is added to the Wash
Buffer Reservoir in Section 3. Ensure correct volumes of
Equilibration Buffer and Endotoxin Removal Buffer are added to
PhyPrep Tubes in sections 4 and 5.


Maxiprep  Samples Deck Layout
1
4
5
6
7
8
3
2
Wash Buffer
190 mL
Elution
Buffer Elution Buffer
25 mL
EQ
Buffer
25 mL
EQ
Buffer
Sample
Tube Sample
Tube
20 mL
ER
Buffer
20 mL
ER
Buffer
Elution
Tube
Sample 1
Sample 1 Sample 2 Sample 3 Sample 4
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
I
M
E
A
A
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
J
N
F
B
C
B
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
C
G
K
O
D
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
D
H
L
P
A
B
C
D
E
F
G
A
B
C
D
E
F
H
J
I
K
A
B
A
B
C
D
C
D
E
F
G
H
J
I
N
M
K
L
O
P
L
A
B
C
D
25 mL
EQ
Buffer
Sample
Tube
Sample
Tube
25 mL
EQ
Buffer
Sample
Tube
Sample
Tube
PhyTip
Sample
Tube
Sample
Tube
PhyTip
Sample
Tube
Sample
Tube
Elution
Tube
Elution
Tube Elution Tube
Sample
Tube
Sample
Tube Sample Tube
Sample
Tube
Sample 2
Sample 3 Sample 4
Elution
Buffer Elution Buffer
Växel
column
PhyPrep
Tube
Växel
column
PhyPrep
Tube
Maxiprep 2 Samples Deck Layout

 Biotage®PhyPrep User Manual | © Biotage 2021
Maxiprep  Samples Method
This protocol is designed for the preparation of up to  mg of
high-copy plasmid DNA per sample using the Biotage PhyPrep
Maxiprep kit. While setting up the deck, place the appropriate
consumables in the corresponding numbered sections of the
deck.
Required
Parts
20 mL
Transfer Tip
Växel
Maxiprep
Column
Wash
Buffer
Elution
Buffer
Endotoxin
Removal
Buffer
Equilibration
Buffer
50 mL
pyrogen-free
Elution Tube
Sample Filter
Reservoir
PhyPrep
Tube
Quantity 9 31311338
Part # DPM-00-
25-00 710-0001 900-0091 900-0093 900-0087 900-0089 DPM-00-
10-01 700-0030 417458SP
Section
1
» Place  x Transfer Tips in A, B, C, E, F, G, I, J, and K.
Section
3
» Add  mL of WASH BUFFER to the Wash Buffer Reservoir.
Section
4
» Place  x PhyPrep Tubes into A and B.
» Place  x PhyPrep Tubes into I and J.
Add  mL of EQUILIBRATION BUFFER to these tubes.
» Place x Biotage®Växel Maxiprep columns into K and L.
Section
5
» Uncap and place  x ELUTION BUFFER tubes into A, C and D.
» Place  x PhyPrep Tubes into E and F.
Add ENDOTOXIN REMOVAL BUFFER as follows:  mL into E and  mL to F.
Section
6
» Place  x PhyPrep Tube into A.
» Place  x PhyPrep Tube into I.
Add  mL of EQUILIBRATION BUFFER to this tube.
» Place x Biotage®Växel Maxiprep column into K.
Section
7
» Remove the Elution Tube Stand from the PhyPrep deck.
» Uncap and place  x  mL pyrogen-free conical tubes in position A, B, and C.
» Elution collection tubes should rest in the bottom portion of the elution stand.
» Place the Elution Tube Stand back onto the PhyPrep deck.
Section
8
» Place  x Sample Filter Reservoirs into A, B, and C.
» Ensure the filter part is towards the front of the deck.
Recommended cell wet weight
 3-5 g per sample from culture volume range of 150–250 mL
Maxiprep 3 Samples Method
Important notes
» Ensure correct volume of Wash Buffer is added to the Wash
Buffer Reservoir in Section 3. Ensure correct volumes of
Equilibration Buffer and Endotoxin Removal Buffer are added to
PhyPrep Tubes in sections 4, 5, and 6.


Maxiprep  Samples Deck Layout
1
4
5
6
7
8
3
2
Wash Buffer
250 mL
Elution
Buffer Elution Buffer
25 mL
EQ
Buffer
25 mL
EQ
Buffer
Sample
Tube Sample
Tube
40 mL
ER
Buffer
20 mL
ER
Buffer
Elution
Tube
Sample 1
Sample 1 Sample 2 Sample 3 Sample 4
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
I
M
E
A
A
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
J
N
F
B
C
B
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
C
G
K
O
D
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
D
H
L
P
A
B
C
D
E
F
G
A
B
C
D
E
F
H
J
I
K
A
B
A
B
C
D
C
D
E
F
G
H
J
I
N
M
K
L
O
P
L
A
B
C
D
25 mL
EQ
Buffer
Sample
Tube
25 mL
EQ
Buffer
Sample
Tube
Sample
Tube
Sample
Tube
Sample
Tube
PhyTip
Sample
Tube
Sample
Tube
Elution
Tube
Elution
Tube Elution Tube
Sample
Tube
Sample
Tube Sample Tube
Sample
Tube
Sample 2
Sample 3 Sample 4
Elution
Buffer Elution Buffer
Växel
column
PhyPrep
Tube
Växel
column
PhyPrep
Tube
PhyPrep
Tube
Växel
column
Maxiprep 3 Samples Deck Layout

 Biotage®PhyPrep User Manual | © Biotage 2021
Maxiprep  Samples Method
This protocol is designed for the preparation of up to  mg of
high-copy plasmid DNA per sample using the Biotage PhyPrep
Maxiprep kit. While setting up the deck, place the appropriate
consumables in the corresponding numbered sections of the
deck.
Required
Parts
20 mL
Transfer Tip
Växel
Maxiprep
Column
Wash
Buffer
Elution
Buffer
Endotoxin
Removal
Buffer
Equilibration
Buffer
50 mL
pyrogen-free
Elution Tube
Sample Filter
Reservoir
PhyPrep
Tube
Quantity 12 414114410
Part # DPM-00-
25-00 710-0001 900-0091 900-0093 900-0087 900-0089 DPM-00-
10-01 700-0030 417458SP
Section
1
» Place  x Transfer Tips in A, B , C, D, E, F, G, H, I, J, K, and L.
Section
3
» Add  mL of WASH BUFFER to the Wash Buffer Reservoir.
Section
4
» Place  x PhyPrep Tubes into A and B.
» Place  x PhyPrep Tubes into I and J.
Add  mL of EQUILIBRATION BUFFER to these tubes.
» Place x Biotage®Växel Maxiprep columns into K and L.
Section
5
» Uncap and place  x ELUTION BUFFER tubes into A, B, C and D.
» Place  x PhyPrep Tubes into E and F. Add  mL of
ENDOTOXIN REMOVAL BUFFER to these tubes.
Section
6
» Place  x PhyPrep Tubes into A and B.
» Place  x PhyPrep Tubes into I and J.
Add mL of EQUILIBRATION BUFFER to these tubes.
» Place x Biotage®Växel Maxiprep columns into K and L.
Section
7
» Remove the Elution Tube Stand from the PhyPrep deck.
» Uncap and place  x  mL pyrogen-free conical tubes in position A, B, C, and D.
» Elution collection tubes should rest in the bottom portion of the elution stand.
» Place the Elution Tube Stand back onto the PhyPrep deck.
Section
8
» Place  x Sample Filter Reservoirs into A, B, C, and D.
» Ensure the filter part is towards the front of the deck.
Recommended cell wet weight
 3-5 g per sample from culture volume range of 150–250 mL
Maxiprep 4 Samples Method
Important notes
» Ensure correct volume of Wash Buffer is added to the Wash
Buffer Reservoir in Section 3. Ensure correct volumes of
Equilibration Buffer and Endotoxin Removal Buffer are added to
PhyPrep Tubes in sections 4, 5, and 6.


Maxiprep  Samples Deck Layout
1
4
5
6
7
8
3
2
Wash buffer
310 mL
Växel
column
PhyPrep
Tube
Elution
buffer Elution buffer
25 mL
EQ
buffer
25 mL
EQ
buffer
Sample
Tube Sample
Tube
40 mL
ER
buffer
40 mL
ER
buffer
Elution
Tube
Sample 1
Sample 1 Sample 2 Sample 3 Sample 4
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
I
M
E
A
A
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
J
N
F
B
C
B
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
C
G
K
O
D
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
20 mL
T Tip
D
H
L
P
A
B
C
D
E
F
G
A
B
C
D
E
F
H
J
I
K
A
B
A
B
C
D
C
D
E
F
G
H
J
I
N
M
K
L
O
P
L
A
B
C
D
25 mL
EQ
buffer
Sample
Tube
PhyPrep
Tube
25 mL
EQ
buffer
Sample
Tube
PhyPrep
Tube
Växel
column
Sample
Tube
Sample
Tube
Växel
column
Sample
Tube
Sample
Tube
Elution
Tube
Elution
Tube Elution Tube
Sample
Tube
Sample
Tube
Växel
column
Sample
Tube
Sample
Tube
PhyPrep
Tube
Sample 2
Sample 3 Sample 4
Elution
buffer Elution buffer
Maxiprep 4 Samples Deck Layout

 Biotage®PhyPrep User Manual | © Biotage 2021
Megaprep  Sample Method
This protocol is designed for the preparation of up to  mg of
high-copy plasmid DNA per sample using the Biotage PhyPrep
Megaprep kit. While setting up the deck, place the appropriate
consumables in the corresponding numbered sections of the
deck.
Required
Parts
20 mL
Transfer Tip
Växel
Megaprep
Column
Wash
Buffer
Elution
Buffer
Endotoxin
Removal
Buffer
Equilibration
Buffer
50 mL
Pyrogen-free
Elution Tube
Sample Filter
Reservoir
PhyPrep
Tube
Quantity 3 11111115
Part # DPM-00-
25-00 710-0002 900-0092 900-0094 900-0087 900-0089 DPM-00-
10-01 700-0030
Section
1
» Place  x transfer tips in A, E, and I.
Section
3
» Add  mL of WASH BUFFER to the Wash Buffer Reservoir.
Section
4
» Place  x PhyPrep Tubes in A, C, and E.
» Place  x PhyPrep Tube into I.
Add  mL of EQUILIBRATION BUFFER to this tube.
» Place x Biotage®Växel Megaprep column in K.
Section
5
» Uncap and place  x ELUTION BUFFER tube into C.
» Place  x PhyPrep Tube into E.
Add  mL of ENDOTOXIN REMOVAL BUFFER to this tube.
Section
7
» Remove the Elution Tube Stand from the PhyPrep deck.
» Uncap and place  x  mL pyrogen-free conical tube in position A.
» Elution collection tubes should rest in the bottom portion of the elution stand.
» Place the Elution Tube Stand back onto the PhyPrep deck.
Section
8
» Place  x Sample Filter Reservoir into A.
» Ensure the filter part is towards the front of the deck.
Recommended cell wet weight
 6-8 g per sample from culture volume range of 350–500 mL
Megaprep 1 Sample Method
Important notes
» Ensure correct volume of Wash Buffer is added to the Wash
Buffer Reservoir in Section 3. Ensure correct volumes of
Equilibration Buffer and Endotoxin Removal Buffer are added to
PhyPrep Tubes in sections 4 and 5.