Powersoil Dna Isolation Kit: Catalog No. 12888-50 Catalog No. 12888-100
Powersoil Dna Isolation Kit: Catalog No. 12888-50 Catalog No. 12888-100
Powersoil Dna Isolation Kit: Catalog No. 12888-50 Catalog No. 12888-100
INSTRUCTION MANUAL
Version 07272016
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Introduction 5
Protocol Overview 5
Equipment Required 8
Precautions 9
Detailed Protocol 13
Technical Support 21
Trademarks 21
Contact Information 24
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INTRODUCTION
The PowerSoil® DNA Isolation Kit is comprised of a novel and proprietary method
for isolating genomic DNA from environmental samples utilizing our patented
Inhibitor Removal Technology® (IRT). The kit is intended for use with environmental
samples containing a high humic acid content including difficult soil types such as
compost, sediment, and manure. Other more common soil types have also been
used successfully with this kit. The isolated DNA has a high level of purity allowing
for more successful PCR amplification of organisms from the sample. PCR analysis
has been performed to detect a variety of organisms including bacteria (e.g. Bacillus
subtilis, Bacillus anthracis), fungi (e.g. yeasts, molds), algae and Actinomycetes
(e.g. Streptomyces).
PROTOCOL OVERVIEW
The PowerSoil® DNA Isolation Kit is effective at removing PCR inhibitors from even
the most difficult soil types. Environmental samples are added to a bead beating
tube for rapid and thorough homogenization. Cell lysis occurs by mechanical and
chemical methods. Total genomic DNA is captured on a silica membrane in a spin
column format. DNA is then washed and eluted from the membrane. DNA is then
ready for PCR analysis and other downstream applications.
https://mobio.com/blog/cat/technical-tips/post/Molecular_Biology_of_Soil_an_
introduction/
https://mobio.com/blog/cat/technical-tips/post/Molecular_Biology_of_Soil_
DNA_Isolation_Part_I/
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PowerLyzer® 24 Bench Top Bead-Based Homogenizer
The PowerLyzer® 24 Bench Top Bead-Based Homogenizer is a bead beating instrument
uniquely designed for the most efficient and complete lysis and homogenization of
any biological sample. In as little as 30 seconds, the PowerLyzer® 24 homogenizer
is capable of processing up to 24 samples in 2 ml tubes. With true “hands-free”
operation, the downtime associated with manipulating samples through multiple
cycles is eliminated. Even the toughest and most difficult samples such as pine
needles, seeds, spores, fungal mats, and clay soils are easily and effectively lysed.
For more information and protocols, call technical service.
PowerLyzer® 24
Bench Top Bead-Based Homogenizer
Catalog#13155
www.mobio.com/powerlyzer
This kit is for research purposes only. Not for diagnostic use.
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EQUIPMENT REQUIRED
FF Microcentrifuge (10,000 x g)
FF Pipettors (50 μl - 500 μl)
FF Vortex-Genie® 2 Vortex (MO BIO Catalog# 13111-V or 13111-V-220)
FF Vortex Adapter (MO BIO Catalog # 13000-V1-24)
KIT CONTENTS
KIT STORAGE
Kit reagents and components should be stored at room temperature (15-30°C).
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PRECAUTIONS
Please wear gloves when using this product. Avoid all skin contact with
reagents in this kit. In case of contact, wash thoroughly with water. Do not
ingest. See Material Safety Data Sheets for emergency procedures in case
of accidental ingestion or contact. All SDS information is available upon
request (760-929-9911) or on our web site at www.mobio.com. Reagents
labeled flammable should be kept away from open flames and sparks.
IMPORTANT NOTE FOR USE: Make sure the 2 ml PowerBead Tubes rotate freely in
your centrifuge without rubbing. Shake to mix Solution C4 before use.
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EXPERIENCED USER PROTOCOL
PowerSoil® DNA Isolation Kit
Catalog No. 12888-50 & 12888-100
Note
If you are using the 24 place Vortex Adapter for more than
12 preps, increase the vortex time by 5-10 minutes.
6. Make sure the PowerBead Tubes rotate freely in your centrifuge without
rubbing. Centrifuge tubes at 10,000 x g for 30 seconds at room temperature.
CAUTION: Be sure not to exceed 10,000 x g or tubes may break.
7. Transfer the supernatant to a clean 2 ml Collection Tube (provided).
Note
Expect between 400 to 500 μl of supernatant. Supernatant
may still contain some soil particles.
8. Add 250 μl of Solution C2 and vortex for 5 seconds. Incubate at 4°C for 5
minutes.
9. Centrifuge the tubes at room temperature for 1 minute at 10,000 x g.
10. Avoiding the pellet, transfer up to, but no more than, 600 μl of supernatant
to a clean 2 ml Collection Tube (provided).
11. Add 200 μl of Solution C3 and vortex briefly. Incubate at 4°C for 5 minutes.
12. Centrifuge the tubes at room temperature for 1 minute at 10,000 x g.
13. Avoiding the pellet, transfer up to, but no more than, 750 μl of supernatant
into a clean 2 ml Collection Tube (provided).
14. Shake to mix Solution C4 before use. Add 1200 μl of Solution C4 to the
supernatant and vortex for 5 seconds.
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15. Load approximately 675 μl onto a Spin Filter and centrifuge at 10,000
x g for 1 minute at room temperature. Discard the flow through and add an
additional 675 μl of supernatant to the Spin Filter and centrifuge at 10,000 x g
for 1 minute at room temperature. Load the remaining supernatant onto the Spin
Filter and centrifuge at 10,000 x g for 1 minute at room temperature.
Note
A total of three loads for each sample processed are
required.
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DETAILED USER PROTOCOL (DESCRIBES WHAT IS HAPPENING AT EACH STEP)
PowerSoil® DNA Isolation Kit
Catalog No. 12888-50 & 12888-100
Note
Note: If you are using the 24 place Vortex Adapter for more
than 12 preps, increase the vortex time by 5-10 minutes.
Note
The vortexing step is critical for complete homogenization
and cell lysis. Cells are lysed by a combination of chemical
agents from steps 1-4 and mechanical shaking introduced
at this step. By randomly shaking the beads in the presence
of disruption agents, collision of the beads with microbial
cells will cause the cells to break open.
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What’s happening: The MO BIO Vortex Adapter is designed to be a simple
platform to facilitate keeping the tubes tightly attached to the vortex. It
should be noted that although you can attach tubes with tape, often the tape
becomes loose and not all tubes will shake evenly or efficiently. This may
lead to inconsistent results or lower yields. Therefore, the use of the MO BIO
Vortex Adapter is a highly recommended and cost effective way to obtain
maximum DNA yields.
6. Make sure the PowerBead Tubes rotate freely in your centrifuge without
rubbing. Centrifuge tubes at 10,000 x g for 30 seconds at room temperature.
CAUTION: Be sure not to exceed 10,000 x g or tubes may break.
7. Transfer the supernatant to a clean 2 ml Collection Tube (provided).
Note
Expect between 400 to 500 μl of supernatant at this step.
The exact recovered volume depends on the absorbency of
your starting material and is not critical for the procedure to
be effective. The supernatant may be dark in appearance
and still contain some soil particles. The presence of carry
over soil or a dark color in the mixture is expected in many
soil types at this step. Subsequent steps in the protocol will
remove both carry over soil and coloration of the mixture.
8. Add 250 μl of Solution C2 and vortex for 5 seconds. Incubate at 4°C for 5
minutes.
What’s happening: Solution C2 is patented Inhibitor Removal Technology®
(IRT). It contains a reagent to precipitate non-DNA organic and inorganic
material including humic substances, cell debris, and proteins. It is important
to remove contaminating organic and inorganic matter that may reduce
DNA purity and inhibit downstream DNA applications.
9. Centrifuge the tubes at room temperature for 1 minute at 10,000 x g.
10. Avoiding the pellet, transfer up to 600 μl of supernatant to a clean 2 ml
Collection Tube (provided).
What’s happening: The pellet at this point contains non-DNA organic and
inorganic material including humic acid, cell debris, and proteins. For the
best DNA yields, and quality, avoid transferring any of the pellet.
11. Add 200 μl of Solution C3 and vortex briefly. Incubate at 4°C for 5 minutes.
What’s happening: Solution C3 is patented Inhibitor Removal Technology®
(IRT) and is a second reagent to precipitate additional non-DNA organic
and inorganic material including humic acid, cell debris, and proteins. It is
important to remove contaminating organic and inorganic matter that may
reduce DNA purity and inhibit downstream DNA applications.
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12. Centrifuge the tubes at room temperature for 1 minute at 10,000 x g.
13. Transfer up to 750 μl of supernatant to a clean 2 ml Collection Tube
(provided).
What’s happening: The pellet at this point contains additional non-DNA
organic and inorganic material including humic acid, cell debris, and
proteins. For the best DNA yields, and quality, avoid transferring any of
the pellet.
14. Shake to mix Solution C4 before use. Add 1.2 ml of Solution C4 to the
supernatant (be careful solution doesn’t exceed rim of tube) and vortex for 5
seconds.
What’s happening: Solution C4 is a high concentration salt solution. Since
DNA binds tightly to silica at high salt concentrations, this will adjust the
DNA solution salt concentrations to allow binding of DNA, but not non-DNA
organic and inorganic material that may still be present at low levels, to the
Spin Filters.
15. Load approximately 675 μl onto a Spin Filter and centrifuge at 10,000
x g for 1 minute at room temperature. Discard the flow through and add an
additional 675 μl of supernatant to the Spin Filter and centrifuge at 10,000 x g
for 1 minute at room temperature. Load the remaining supernatant onto the Spin
Filter and centrifuge at 10,000 x g for 1 minute at room temperature.
Note
A total of three loads for each sample processed are
required.
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18. Centrifuge at room temperature for 1 minute at 10,000 x g.
What’s happening: This second spin removes residual Solution C5
(ethanol wash solution). It is critical to remove all traces of wash
solution because the ethanol in Solution C5 can interfere with many
downstream DNA applications such as PCR, restriction digests, and
gel electrophoresis.
19. Carefully place Spin Filter in a clean 2 ml Collection Tube (provided).
Avoid splashing any Solution C5 onto the Spin Filter.
Note
It is important to avoid any traces of the ethanol based wash
solution.
20. Add 100 μl of Solution C6 to the center of the white filter membrane.
Note
Placing the Solution C6 (sterile elution buffer) in the
center of the small white membrane will make sure the
entire membrane is wetted. This will result in a more
efficient and complete release of the DNA from the
silica Spin Filter membrane. As Solution C6 (elution
buffer) passes through the silica membrane, DNA that
was bound in the presence of high salt is selectively
released by Solution C6 (10 mM Tris) which lacks salt.
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VACUUM PROTOCOL USING THE POWERVAC™ MANIFOLD
Please wear gloves at all times
For each sample lysate, use one Spin Filter column. Keep the Spin Filter in the
attached 2 ml Collection Tube and continue using the Collection Tube as a
Spin Filter holder until needed for the Vacuum Manifold Protocol. Label each
Collection Tube top and Spin Filter column to maintain sample identity. If the
Spin Filter becomes clogged during the vacuum procedure, you can switch to the
procedure for purification of the DNA by centrifugation.
You will need to provide 100% ethanol for step 4 of this protocol.
1. For each prep, attach one aluminum PowerVac™ Mini Spin Filter Adapter
(MO BIO Catalog# 11992-20) into the Luer-Lok® fitting of one port in the
manifold. Gently press a Spin Filter column into the PowerVac™ Mini Spin Filter
Adapter until snugly in place. Ensure that all unused ports of the vacuum manifold
are closed.
Note
Aluminum PowerVac™ Mini Spin Filter Adapters are
reusable.
2. Transfer 650 μl of prepared sample lysate (from step 14) to the Spin Filter
column.
3. Turn on the vacuum source and open the stopcock of the port. Hold the
tube in place when opening the stopcock to keep the spin filter steady. Allow the
lysate to pass through the Spin Filter column. After the lysate has passed through
the column completely, load again with the next 650 μl of lysate. Continue until
all of the lysate has been loaded onto the Spin Filter column. Close the one-way
Luer-Lok® stopcock of that port.
Note
If Spin Filter Columns are filtering slowly, close the ports
to samples that have completed filtering to increase the
pressure to the other columns.
4. Load 800 μl of 100% ethanol into the Spin Filter so that it completely fills the
column. Open the stopcock while holding the column steady. Allow the ethanol
to pass through the column completely. Close the stopcock.
5. Add 500 μl of Solution C5 to each Spin Filter. Open the Luer-Lok® stopcock
and apply a vacuum until Solution C5 has passed through the Spin Filter
completely. Continue to pull a vacuum for another minute to dry the membrane.
Close each port.
6. Turn off the vacuum source and open an unused port to vent the manifold.
If all 20 ports are in use, break the vacuum at the source. Make certain that all
vacuum pressure is released before performing the next step. It is important to
turn off the vacuum at the source to prevent backflow into the columns.
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7. Remove the Spin Filter column and place in the original labeled 2 ml
Collection Tube. Place into the centrifuge and spin at 13,000 × g for 1 minute to
completely dry the membrane.
8. Transfer the Spin Filter column to a new 2 ml Collection Tube and add 100
μl of Solution C6 to the center of the white filter membrane. Alternatively, sterile
DNA-Free PCR Grade Water may be used for elution from the silica Spin Filter
membrane at this step (MO BIO Catalog # 17000-10).
9. Centrifuge at room temperature for 30 seconds at 10,000 x g.
10. Discard the Spin Filter column. The DNA in the tube is now ready for any
downstream application. No further steps are required.
We recommend storing DNA frozen (-20° to -80°C). Solution C6 contains no
EDTA. To concentrate the DNA see the Hints & Troubleshooting Guide.
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HINTS AND TROUBLESHOOTING GUIDE
Amount of Soil to Process
This kit is designed to process 0.25 grams of soil. For inquiries regarding the use
of larger sample amounts, please contact technical support for suggestions. For wet
soils, see information under “Wet Soil Sample” below.
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DNA Floats Out of Well When Loaded on a Gel
This usually occurs because residual Solution C5 remains in the final sample. Prevent
this by being careful in step 19 not to transfer liquid onto the bottom of the spin filter
basket. Ethanol precipitation (described in “Concentrating the DNA”) is the best
way to remove residual Solution C5.
Storing DNA
DNA is eluted in Solution C6 (10 mM Tris) and must be stored at -20° to -80°C to
prevent degradation. DNA can be eluted in TE without loss, but the EDTA may inhibit
downstream reactions such as PCR and automated sequencing. DNA may also be
eluted with sterile DNA-Free PCR Grade Water (MO BIO Catalog# 17000-10).
Do not use bleach to clean the PowerVac™ Mini Spin Filter Adapters while attached
to the PowerVac™ Manifold. Bleach should never be mixed with solutions containing
guanidine and should not be used to clean the PowerVac™ Manifold. For more
information on cleaning the PowerVac™ Manifold, please refer to the PowerVac™
Manifold manual.
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TECHNICAL SUPPORT Committed to resolving your technical
Phone: Toll Free 800-606-6246, questions promptly, our technical support
team is trained to work with you to rapidly
or 760-929-9911
and effectively trouble shoots any issues.
Email: technical@mobio.com We commit to providing you with relevant
Mail: MO BIO Laboratories, Inc., online support resources that help you
complete your research projects.
2746 Loker Ave West, Carlsbad,
CA 92010
Trademarks
Inhibitor Removal Technology® (IRT) is a registered trademark of MO BIO Laboratories, Inc. and
is covered by patents.
For other Trademarks and Limited Use Label License information go to:
www.mobio.com/lull-tm
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Corporate Headquarters
MO BIO Laboratories, Inc.
2746 Loker Avenue West
Carlsbad, CA 92010
Technical Support:
Toll Free 800-606-6246, or 760-929-9911
Email: technical@mobio.com
Ordering Information:
Toll Free 800-606-6246, or 760-929-9911
Fax: 760-929-0109
Email: orders@mobio.com
World Leader in Soil DNA & RNA Isolation®. © 2014 MO BIO Laboratories, Inc. All Rights Reserved
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