EZ1® DNA Investigator Handbook - The Murder of Meredith Kercher

EZ1® DNA Investigator Handbook - The Murder of Meredith Kercher
Fourth Edition
April 2009
EZ1® DNA Investigator Handbook
For automated purification of DNA from
forensic and biosecurity samples using
EZ1 instruments
Sample & Assay Technologies
QIAGEN Sample and Assay Technologies
QIAGEN is the leading provider of innovative sample and assay technologies, enabling
the isolation and detection of contents of any biological sample. Our advanced,
high-quality products and services ensure success from sample to result.
QIAGEN sets standards in:
■
Purification of DNA, RNA, and proteins
■
Nucleic acid and protein assays
■
microRNA research and RNAi
■
Automation of sample and assay technologies
Our mission is to enable you to achieve outstanding success and breakthroughs. For
more information, visit www.qiagen.com.
Contents
Kit Contents
5
Storage
5
Quality Control
6
Product Use Limitations
6
Product Warranty and Satisfaction Guarantee
6
Technical Assistance
7
Safety Information
8
Introduction
9
Principle and procedure
9
Description of protocols
11
Equipment and Reagents to Be Supplied by User
13
Important Notes
15
Starting material
15
Working with EZ1 instruments
15
Yield of purified DNA
20
Precipitate in reagent cartridge
20
Equilibrating reagent cartridges
20
Lysis with proteinase K
21
Quantification of DNA
21
Pretreatment protocols
■
Pretreatment for Whole Blood
22
■
Pretreatment for Dried Blood
23
■
Pretreatment for Saliva
25
■
Pretreatment for Forensic Surface and Contact Swabs
26
■
Pretreatment for Nail Scrapings
28
■
Pretreatment for Chewing Gum
29
■
Pretreatment for Cigarette Butts
30
■
Pretreatment for Postage Stamps
32
■
Pretreatment for Stains on Fabric
34
■
Pretreatment for Human Tissues
36
■
Pretreatment for Epithelial Cells Mixed with Sperm Cells
37
■
Pretreatment for Hair
39
■
Pretreatment for Bones or Teeth
40
EZ1 DNA Investigator Handbook 04/2009
3
■
Pretreatment for Soil
41
■
Pretreatment for Other Forensic Samples
42
Purification protocols
■
DNA Purification (Trace Protocol)
44
■
DNA Purification (“Tip Dance” Protocol)
46
■
DNA Purification (Large-Volume Protocol)
49
Troubleshooting Guide
52
Appendix A: Purification of Low Amounts of DNA
54
Appendix B: Example of an EZ1 Advanced Report File
55
Ordering Information
57
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EZ1 DNA Investigator Handbook 04/2009
Kit Contents
EZ1 DNA Investigator Kit
Catalog no.
(48)
952034
Number of preps
48
Reagent Cartridge, DNA Investigator*
48
Disposable Tip Holders
50
Disposable Filter-Tips
50
Sample Tubes (2 ml)
50
Elution Tubes (1.5 ml)
50
Buffer G2
1 x 11 ml
Proteinase K
2 x 250 µl
Carrier RNA†
1 x 310 µg
Q-Card
‡
Handbook
1
1
* Contains a guanidine salt. Not compatible with disinfectants containing bleach. See page 8 for safety
information.
†
Use of carrier RNA is optional. See “Description of protocols”, page 12 and Appendix A for more
information.
‡
The information encoded in the bar code on the Q-Card is needed for reagent data tracking using the
EZ1 Advanced or EZI Advanced XL instrument.
Additional filter-tips and tip holders are available separately. Additional Buffer G2 and
QIAGEN Proteinase K, required for some protocols, are available separately. See
page 57 for ordering information.
Storage
The EZ1 DNA Investigator Kit is shipped at ambient temperature. All buffers and
reagents can be stored at room temperature (15–25°C). Do not freeze the reagent
cartridges. When stored properly, the reagent cartridges are stable until the expiration
date on the Q-Card. Lyophilized carrier RNA is stable until the expiration date on the
Q-Card when stored at room temperature.
The ready-to-use proteinase K solution is stable for up to one year after delivery when
stored at room temperature.
EZ1 DNA Investigator Handbook 04/2009
5
Quality Control
In accordance with QIAGEN’s ISO-certified Quality Management System, each lot of
EZ1 DNA Investigator Kits is tested against predetermined specifications to ensure
consistent product quality. Functional QC testing ensures that the EZ1 DNA Investigator
Kit meets the high standards required by forensic scientists.
Product Use Limitations
The EZ1 DNA Investigator Kit is intended for molecular biology applications. This
product is neither intended for the diagnosis, prevention, or treatment of a disease, nor
has it been validated for such use either alone or in combination with other products.
All due care and attention should be exercised in the handling of the products. We
recommend all users of QIAGEN® products to adhere to the NIH guidelines that have
been developed for recombinant DNA experiments, or to other applicable guidelines.
Product Warranty and Satisfaction Guarantee
QIAGEN guarantees the performance of all products in the manner described in our
product literature. The purchaser must determine the suitability of the product for its
particular use. Should any product fail to perform satisfactorily due to any reason other
than misuse, QIAGEN will replace it free of charge or refund the purchase price. We
reserve the right to change, alter, or modify any product to enhance its performance
and design. If a QIAGEN product does not meet your expectations, simply call your
local Technical Service Department or distributor. We will credit your account or
exchange the product — as you wish. Separate conditions apply to QIAGEN scientific
instruments, service products, and to products shipped on dry ice. Please inquire for
more information.
A copy of QIAGEN terms and conditions can be obtained on request, and is also
provided on the back of our invoices. If you have questions about product specifications
or performance, please call QIAGEN Technical Services or your local distributor (see
back cover or visit www.qiagen.com).
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EZ1 DNA Investigator Handbook 04/2009
Technical Assistance
At QIAGEN we pride ourselves on the quality and availability of our technical support.
Our Technical Service Departments are staffed by experienced scientists with extensive
practical and theoretical expertise in sample and assay technologies and the use of
QIAGEN products. If you have any questions or experience any difficulties regarding
the EZ1 DNA Investigator Kit or QIAGEN products in general, please do not hesitate
to contact us.
QIAGEN customers are a major source of information regarding advanced or
specialized uses of our products. This information is helpful to other scientists as well as
to the researchers at QIAGEN. We therefore encourage you to contact us if you have
any suggestions about product performance or new applications and techniques.
For technical assistance and more information, please see our Technical Support Center
at www.qiagen.com/goto/TechSupportCenter or call one of the QIAGEN Technical
Service Departments or local distributors (see back cover or visit www.qiagen.com).
EZ1 DNA Investigator Handbook 04/2009
7
Safety Information
When working with chemicals, always wear a suitable lab coat, disposable gloves,
and protective goggles. For more information, please consult the appropriate material
safety data sheets (MSDSs). These are available online in convenient and compact PDF
format at www.qiagen.com/Support/MSDS.aspx where you can find, view, and print
the MSDS for each QIAGEN kit and kit component.
CAUTION: DO NOT add bleach or acidic solutions directly to the
sample-preparation waste.
Buffers in the reagent cartridges contain guanidine salts, which can form highly reactive
compounds when combined with bleach. If liquid containing these buffers is spilt, clean
with suitable laboratory detergent and water. If the spilt liquid contains potentially
infectious agents, clean the affected area first with laboratory detergent and water, and
then with 1% (v/v) sodium hypochlorite.
If liquid containing potentially infectious agents is spilt on the EZ1 Advanced XL, EZ1
Advanced, or BioRobot® EZ1, clean the affected area first with laboratory detergent
and water, and then with 1% (v/v) sodium hypochlorite, followed by water.
The following risk and safety phrases apply to components of the EZ1 DNA Investigator
Kit.
Reagent cartridge
Contains ethanol, guanidine hydrochloride, and guanidine thiocyanate: highly
flammable, harmful, and irritant. Risk and safety phrases:* R11-20/21/22-32-36/38,
S13-26-36/37/39-46
QIAGEN proteinase K
Contains proteinase K: sensitizer, irritant. Risk and safety phrases:* R36/37/3842/43, S23-24-26-36/37
24-hour emergency information
Emergency medical information in English, French, and German can be obtained
24 hours a day from:
Poison Information Center Mainz, Germany
Tel: +49-6131-19240
* R11: Highly flammable; R20/21/22: Harmful by inhalation, in contact with skin, and if swallowed; R32:
Contact with acids liberates very toxic gas; R36/38: Irritating to eyes and skin; R36/37/38: Irritating
to eyes, respiratory system, and skin; R42/43: May cause sensitization by inhalation and skin contact.
S13: Keep away from food, drink, and animal feedingstuffs; S23: Do not breathe spray; S24: Avoid
contact with skin; S26: In case of contact with eyes, rinse immediately with plenty of water and seek
medical advice; S36/37: Wear suitable protective clothing and gloves; S36/37/39: Wear suitable
protective clothing, gloves, and eye/face protection; S46: If swallowed, seek medical advice immediately
and show container or label.
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EZ1 DNA Investigator Handbook 04/2009
Introduction
EZ1 instruments and the EZ1 DNA Investigator Kit reproducibly automate purification of
genomic DNA from 1–6 samples (EZ1 Advanced and BioRobot EZ1) or 1–14
samples (EZ1 Advanced XL) encountered in forensic, human-identity, and biosecurity
applications. Purification is efficient and purified DNA performs well in downstream
analyses, such as quantitative PCR and STR analysis, with high signal-to-noise ratios.
Magnetic-particle technology provides high-quality DNA that is suitable for direct use
in downstream applications such as STR analysis or other enzymatic reactions. EZ1
instruments perform all steps of the sample preparation procedure, and the user can
choose sample input volumes of 200 µl or 500 µl, allowing purification from varying
amounts of starting material. Up to 6 samples (BioRobot EZ1, EZ1 Advanced) or up to
14 samples (EZ1 Advanced XL) are processed in a single run.
Principle and procedure
Magnetic-particle technology combines the speed and efficiency of silica-based DNA
purification with the convenient handling of magnetic particles (see flowchart,
page 10). DNA is isolated from lysates in one step through its binding to the silica
surface of the particles in the presence of a chaotropic salt. The particles are separated
from the lysates using a magnet. The DNA is then efficiently washed and eluted in the
user’s choice of either water or TE buffer. The user can choose elution volumes of 40 µl
(EZ1 Advanced XL only), 50 µl, 100 µl, or 200 µl.
EZ1 DNA Investigator Handbook 04/2009
9
EZ1 DNA Investigator Procedure
Blood or pretreated sample
Lysis
Magnetic particles
added to samples
DNA binds
to magnetic
particles
Magnetic
separation
Magnet
Wash
Magnetic
separation
Magnet
Elute
Pure, high-quality DNA
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EZ1 DNA Investigator Handbook 04/2009
Description of protocols
This handbook contains two types of protocols.
■
Pretreatment protocols detail the preliminary steps, such as proteinase K digestion,
prior to processing on the EZ1 instrument.
■
DNA purification protocols describe setting up the EZ1 instrument and starting
a fully automated run.
Pretreatment protocols
Since the type of samples that can be processed using the EZ1 DNA Investigator Kit
can vary greatly, there is also a variety of different pretreatments, optimized for specific
sample types. For sample types not specifically included in this handbook, the Protocol:
Pretreatment for Other Forensic Samples, page 42, provides a generic protocol that can
serve as a starting point for optimizing pretreatment for other sample types.
DNA purification protocols
There are 3 DNA purification protocols, which can be used in conjunction with the pretreatment protocols. Within each protocol, the user can specify elution in water or TE
buffer, with elution volumes of 40 µl (EZ1 Advanced XL only), 50 µl, 100 µl, or 200 µl.
The standard Protocol: DNA Purification (Trace Protocol), page 44, can be used with all
sample types.
In the Protocol: DNA Purification (“Tip Dance” Protocol), page 46, the filter-tip moves
back-and-forth relative to the worktable platform while pipetting. This enables
processing of solid materials, such as swabs, fabrics, blood discs, or cigarette butts,
directly in the sample tube. There is generally no need for prior centrifugation to remove
solid materials that could clog the tip. However, when processing fluffy sample material
such as cotton wool, we recommend removing solid material if you cannot process a
replicate sample or the sample material is precious.
The Protocol: DNA Purification (Large-Volume Protocol), page 49, enables fully
automated processing of starting volumes up to 500 µl. This not only allows efficient
DNA purification from dilute samples with low concentrations of DNA, such as diffuse
stains, but also enables purification from samples that require larger volumes for
thorough lysis. The ability to process larger sample volumes — with the same elution
volume as the standard trace protocol — enables higher yields of more concentrated
DNA for greater sensitivity in downstream applications.
EZ1 DNA Investigator Handbook 04/2009
11
The protocol for purification of low amounts of DNA in Appendix A, describes the
optional use of carrier RNA in the purification procedure. Carrier RNA enhances
binding of DNA to the silica surface of the magnetic particles, especially if the sample
contains low amounts of DNA (<100 ng). Recently published data suggest that addition
of carrier RNA enables more efficient isolation of low amounts of DNA from forensic
samples and may, for some sample types, provide improved DNA yields. Addition of
carrier RNA to sample lysates did not interfere with downstream STR analyses. This
protocol has not been thoroughly tested and optimized by QIAGEN.
12
EZ1 DNA Investigator Handbook 04/2009
Equipment and Reagents to Be Supplied by User
When working with chemicals, always wear a suitable lab coat, disposable gloves,
and protective goggles. For more information, consult the appropriate material safety
data sheets (MSDSs), available from the product supplier.
All protocols
■
Thermomixer, heating block, or water bath
■
Vortexer
■
Pipets and pipet tips (to prevent cross-contamination, we strongly recommend the
use of pipet tips with aerosol barriers)
■
Distilled water
For BioRobot EZ1 users
■
BioRobot EZ1 instrument (cat. no. 9000705) and disposables
■
EZ1 DNA Investigator Card (cat. no. 9016387)
For EZ1 Advanced users
■
EZ1 Advanced instrument (cat. no. 9001410)
■
EZ1 Advanced DNA Investigator Card (cat. no. 9018302)
For EZ1 Advanced XL users
■
EZ1 Advanced XL instrument (cat. no. 9001492)
■
EZ1 Advanced XL DNA Investigator Card (cat. no. 9018699)
For EZ1 Advanced and EZ1 Advanced XL users
For documentation purposes, one of the following is required:
■
EZ1 Advanced Communicator Software (supplied with the EZ1 Advanced and EZ1
Advanced XL instruments), PC (can be connected with up to 4 EZ1 Advanced and EZ1
Advanced XL instruments), and monitor (cat. no. for PC and monitor 9016643)
■
EZ1 Advanced Communicator Software (supplied with the EZ1 Advanced and
EZ1 Advanced XL instruments) and your own PC and monitor (connection with up
to 4 EZ1 Advanced and EZ1 Advanced XL instruments not recommended)
■
Printer (cat. no. 9018464) and accessory package for printer (cat. no. 9018465)
For purification of DNA from dried blood
■
Filter paper (e.g., QIAcard® FTA® Spots, see “Ordering Information”, page 57)
■
Manual paper punch, 3 mm (e.g., Harris UNI-CORE 3.00 mm Punch Kit (4),
cat. no. 159331, or equivalent punch with cutting mat)
EZ1 DNA Investigator Handbook 04/2009
13
For purification of DNA from forensic surface and contact swabs
■
Plastic swabs with cotton or Dacron® tips (Puritan® applicators with plastic shafts
and cotton or Dacron tips are available from: Hardwood Products Company,
www.hwppuritan.com, item nos. 25-806 1PC and 25-806 1PD; and from
Daigger, www.daigger.com, cat. nos. EF22008D and EF22008DA). Nylon
cytology brushes and other swab types may also be used.*
For purification of DNA from chewing gum
■
Forceps
For purification of DNA from human tissues
■
1.5 ml screw-capped tubes
For purification of DNA from epithelial cells mixed with sperm cells
■
■
■
■
Buffer G2, cat. no. 1014636
1 M dithiothreitol (DTT)
Microcentrifuge
Forceps
For purification of DNA from hair
■
■
QIAGEN Proteinase K, cat. no. 19131 or 19133
DTT solution (1 M dithiothreitol, 10 mM sodium acetate, pH 5.2)
For purification of DNA from bones or teeth
■
■
■
■
■
■
QIAGEN Proteinase K, cat. no. 19131 or 19133
0.5 M EDTA, pH 8.3
Liquid nitrogen
2 ml microcentrifuge tubes
Microcentrifuge
TissueLyser II, cat. no. 85300, with the Grinding Jar Set, S. Steel, cat. no. 69985,
or an equivalent bead mill
For purification of DNA from soil
■
■
InhibitEX® tablets (contact QIAGEN Technical Services, see back cover)
Microcentrifuge
For DNA purification, large-volume protocol
■
Buffer MTL (contact QIAGEN Technical Services, see back cover)
* This is not a complete list of suppliers and does not include many important vendors of biological supplies.
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EZ1 DNA Investigator Handbook 04/2009
Important Notes
Starting material
The amount of starting material for use in EZ1 DNA Investigator procedures can vary
greatly, depending on the amount of DNA in the sample. Specific guidance for starting
amounts is given in the individual protocols. EZ1 instruments can process 200 µl
pretreated samples using the trace protocol (page 44) or the “tip dance” protocol (page
46) for DNA purification. With the large-volume protocol (page 49), up to 500 µl
pretreated samples can be processed.
Working with EZ1 instruments
The main features of the EZ1 instruments include:
■
Purification of high-quality nucleic acids from 1–6 or 1–14 samples per run
■
Small footprint to save laboratory space
■
Preprogrammed EZ1 Cards containing ready-to-use protocols for nucleic acid
purification
■
Prefilled, sealed reagent cartridges for easy, safe, and fast setup of EZ1 instruments
■
Complete automation of nucleic acid purification, from opening of reagent
cartridges to elution of nucleic acids, with no manual centrifugation steps
Additional features of the EZ1 Advanced and EZ1 Advanced XL include:
■
Bar code reading and sample tracking
■
Kit data tracking with the Q-Card provided in the kit
■
UV lamp to help eliminate sample carryover from run-to-run and to allow pathogen
decontamination on the worktable surfaces
Note: UV decontamination helps to reduce possible pathogen contamination of the EZ1
Advanced and EZ1 Advanced XL worktable surfaces. The efficiency of inactivation has
to be determined for each specific organism and depends, for example, on layer thickness and sample type. QIAGEN cannot guarantee complete eradication of specific
pathogens.
EZ1 Cards, EZ1 Advanced Cards, and EZ1 Advanced XL Cards
Protocols for nucleic acid purification are stored on preprogrammed EZ1 Cards
(integrated circuit cards). The user simply inserts an EZ1 Advanced XL Card into the EZ1
Advanced XL, an EZ1 Advanced Card into the EZ1 Advanced, or an EZ1 Card into the
BioRobot EZ1, and the instrument is then ready to run a protocol (Figure 1). The
availability of various protocols increases the flexibility of EZ1 instruments.
EZ1 DNA Investigator Handbook 04/2009
15
Figure 1. Ease of protocol setup using EZ1 Cards. Inserting an EZ1 Card, containing a protocol, into an EZ1
instrument. The instrument should only be switched on after an EZ1 Card is inserted. EZ1 Cards should not be
exchanged while the instrument is switched on.
The EZ1 DNA Investigator Kit requires use of the EZ1 Advanced XL DNA Investigator
Card with the EZ1 Advanced XL, or use of the EZ1 Advanced DNA Investigator Card
with the EZ1 Advanced, or use of the EZ1 DNA Investigator Card with the BioRobot
EZ1. These EZ1 Cards contain protocols for purification of DNA from forensic and
human-identity samples.
EZ1 instruments should only be switched on after an EZ1 Card is inserted. Make sure
that the EZ1 Card is completely inserted (Figure 2), otherwise essential instrument data
could be lost, leading to a memory error. EZ1 Cards should not be exchanged while
the instrument is switched on.
Figure 2. Complete insertion of EZ1 Card. The EZ1 Card must be completely inserted before the EZ1 instrument
is switched on.
16
EZ1 DNA Investigator Handbook 04/2009
Reagent cartridges
Reagents for the purification of nucleic acids from a single sample are contained in a
single reagent cartridge (Figure 3). Each well of the cartridge contains a particular
reagent, such as magnetic particles, lysis buffer, wash buffer, or elution buffer. Since
each well contains only the required amount of reagent, generation of waste due to
leftover reagent at the end of the purification procedure is avoided.
A
B
Figure 3. Ease of setup using reagent cartridges. A A sealed, prefilled reagent cartridge. Fill levels vary,
depending on the type of reagent cartridge. B Loading reagent cartridges into the cartridge rack. The
cartridge rack itself is labeled with an arrow to indicate the direction in which reagent cartridges must be
loaded.
Worktable
The worktable of EZ1 instruments is where the user loads samples and the components
of the EZ1 DNA Investigator Kit (Figure 4).
Details on worktable setup are provided in the protocols in this handbook and are
also displayed in the vacuum fluorescent display (VFD) of the EZ1 Advanced and EZ1
Advanced XL or the liquid-crystal display (LCD) of the BioRobot EZ1 control panel when
the user starts worktable setup.
The display also shows protocol status during the automated purification procedure.
EZ1 DNA Investigator Handbook 04/2009
17
6
5
4
3
2
1
Figure 4. Typical EZ1 worktable.
1.First row: Elution tubes (1.5 ml) are loaded here.
2.Second row: Tip holders containing filter-tips are loaded here.
3.Third row: Tip holders containing filter-tips are loaded here. (In some protocols, this row is empty or loaded
with 2 ml Sarstedt tubes.)
4.Fourth row: Sample tubes (2 ml) are loaded here.
5.Reagent cartridges are loaded into the cartridge rack.
6.Heating block with 2 ml tubes in the reagent cartridges for lysis.
Data tracking with the EZ1 Advanced and EZ1 Advanced XL
The EZ1 Advanced and EZ1 Advanced XL enable complete tracking of a variety of data
for increased process control and reliability. The EZ1 Kit lot number and expiration date
are entered at the start of the protocol using the Q-Card bar code. A user ID and the
Q-Card bar code can be entered manually via the keypad or by scanning bar codes
using the handheld bar code reader. Sample and assay information can also be optionally
entered at the start of the protocol. At the end of the protocol run, a report file is
automatically generated. The EZ1 Advanced and EZ1 Advanced XL can store up to 10
result files, and the data can be transferred to a PC or directly printed on a printer (for
ordering information, see “Equipment and Reagents to Be Supplied by User” on page 13).
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EZ1 DNA Investigator Handbook 04/2009
To receive report files on a PC, the EZ1 Advanced Communicator software needs to be
installed. The software receives the report file and stores it in a folder that you define.
After the PC has received the report file, you can use and process the file with a LIMS
(Laboratory Information Management System) or other programs. An example of a
report file is shown in Appendix B (page 55). In report files, the 6 pipetting channels
of the EZ1 Advanced are named, from left to right, channels A to F or the 14 pipetting
channels of the EZ1 Advanced XL are named, from left to right, channels 1–14.
When scanning a user ID or Q-Card bar code with the bar code reader, a beep
confirms data input. After the information is displayed for 2 seconds, it is automatically
stored, and the next display message is shown. When scanning sample ID, assay
kit ID, or notes, a beep confirms data input, the information is displayed, and a message
prompts you to enter the next item of information. After scanning sample ID, assay
kit ID, and notes, press “ENT” once to confirm that the information entered is correct.
If, for example, a wrong bar code was scanned for one of the samples, press “ESC”
and then rescan all sample bar codes according to the onscreen instructions. For user
ID and notes, you can enter the numbers using the keypad, or you can easily generate
your own bar codes to encode these numbers.
For details about data tracking and using EZ1 Advanced Communicator software, see
the EZ1 Advanced User Manual or the EZ1 Advanced XL User Manual.
Workflow of EZ1 operation
Insert EZ1 Card into the EZ1 Card slot
↓
Switch on the EZ1 instrument
↓
Follow onscreen messages for data tracking*
↓
Follow onscreen messages for worktable setup
↓
Start the protocol
↓
Collect purified nucleic acids
↓
UV decontamination*
* EZ1 Advanced and EZ1 Advanced XL only.
EZ1 DNA Investigator Handbook 04/2009
19
Yield of purified DNA
DNA yields depend on the sample type, number of nucleated cells in the sample, and
the protocol used for DNA purification. Table 1 shows typical yields for some common
reference sample types.
Table 1. DNA yields from common reference sample types using EZ1 DNA Investigator
procedures
Sample type
Sample amount
Protocol
DNA yield
Blood*
10–200 µl
Trace or Tip dance
150 ng–2 µg
Dried blood
4 x 3 mm dics
Tip dance
0.2–0.5 µg
Buccal cells
1 swab
Tip dance
100 ng–2 µg
* Whole blood with 3–7 x 106 white blood cells/ml; elution volume 200 µl.
Precipitate in reagent cartridge
The buffer in well 1 of the reagent cartridge (the well that is nearest to the front of the
EZ1 instrument when the reagent cartridge is loaded) may form a precipitate upon
storage. If necessary, redissolve by mild agitation at 37°C and then place at room
temperature (15–25°C).
Equilibrating reagent cartridges
If reagent cartridges have been stored at 2–8°C, they must be equilibrated to operating
temperature before use. Place the reagent cartridge into a shaker–incubator and
incubate at 30–40°C with mild agitation for at least 2 hours before use. If precipitates
are visible at the bottom of the wells, redissolve by incubating at 30–40°C with mild
agitation for a further 2 hours. Do not use the reagent cartridges if the precipitates do
not redissolve.
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EZ1 DNA Investigator Handbook 04/2009
Lysis with proteinase K
The EZ1 DNA Investigator Kit contains proteinase K, which is the enzyme of choice
for lysis buffers used in EZ1 DNA Investigator protocols. Proteinase K is a recombinant
protein expressed in Pichia pastoris and is particularly suitable for short digestion
times. It possesses a high specific activity and remains stable over a wide range of
temperatures and pH values, with substantially increased activity at higher
temperatures. The activity of the proteinase K solution is 600 mAU/ml solution (or
40 mAU/mg protein). This activity provides optimal results in EZ1 DNA Investigator
protocols.
Additional QIAGEN Proteinase K is required for purification of DNA from hair, bones,
or teeth (see page 57 for ordering information).
Quantification of DNA
Depending on the sample type, the yields of DNA obtained in the purification procedure may be below 1 µg and therefore difficult to quantify using a spectrophotometer.
In addition, eluates prepared with carrier RNA may contain much more carrier RNA
than target nucleic acids. We recommend using quantitative amplification methods to
determine yields.
Carryover of magnetic particles may affect the absorbance reading at 260 nm (A260)
of the purified DNA but should not affect downstream applications. The measured
absorbance at 320 nm (A320) should be subtracted from all absorbance readings.
To eliminate carried-over magnetic particles, the tube containing the eluate should first
be applied to a suitable magnetic separator and the eluate transferred to a clean tube.
EZ1 DNA Investigator Handbook 04/2009
21
Whole Blood
Protocol: Pretreatment for Whole Blood
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
fresh or frozen blood.
Starting material
This protocol is designed for processing up to 200 µl of human whole blood.
Storage of blood samples
Whole blood samples treated with EDTA, ACD, or heparin* can be used, and may be
either fresh or frozen. Frozen samples should be thawed at room temperature
(15–25°C) with mild agitation before beginning the procedure. Yield and quality of the
purified DNA depend on storage conditions of the blood. Fresher blood samples may
yield better results.
■
For short-term storage (up to 10 days), collect blood in tubes containing EDTA as
an anticoagulant, and store the tubes at 2–8°C. However, for applications
requiring maximum fragment size, such as Southern blotting, we recommend
storage at 2–8°C for up to 3 days only, as low levels of DNA degradation will
occur after this time.
■
For long-term storage, collect blood in tubes containing a standard anticoagulant
(preferably EDTA, if high-molecular–weight DNA is required), and store the tubes
at –70°C.
Important points before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
■
Proteinase K is not required in this protocol.
Procedure
1.
2.
Thaw and equilibrate up to 6 whole blood samples at room temperature
(15–25°C).
Transfer 200 µl of each sample into EZ1 sample tubes (2 ml).
For samples <200 µl, bring the volume up to 200 µl with Buffer G2.
3.
Continue with Protocol: DNA Purification (Trace Protocol), page 44.
* When working with chemicals, always wear a suitable lab coat, disposable gloves, and protective
goggles. For more information, consult the appropriate material safety data sheets (MSDSs), available from
the product supplier.
22
EZ1 DNA Investigator Handbook 04/2009
Protocol: Pretreatment for Dried Blood
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
dried blood. The protocol describes sample collection and the preliminary lysis of dried
blood samples using proteinase K.
Starting material
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
As filter paper tends to be absorbent, it is generally necessary to add a greater
volume of digestion buffer to the sample in step 4. To provide sufficient digestion
buffer for absorbent samples, Buffer G2 should be diluted with distilled water
before use. Dilute Buffer G2 in distilled water using a ratio of 1:1 (i.e., one volume
of Buffer G2 to one volume of distilled water) for n+1 samples (where n is the
number of samples to be digested). Use of diluted Buffer G2 does not influence
DNA yield or quality.
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 6.
■
Heat a thermomixer, heating block, or water bath to 95°C for use in step 7.
Procedure
1.
Collect 70 µl of each blood sample onto a ring marked on filter paper. Allow the
blood to air-dry.
Either untreated blood or blood containing an anticoagulant (EDTA, ACD, or
heparin)* can be used.
2.
For each dried blood sample, use the manual paper punch to cut out four 3 mm
diameter discs.
3.
Transfer each set of 4 discs to a 2 ml sample tube.
* When working with chemicals, always wear a suitable lab coat, disposable gloves, and protective
goggles. For more information, consult the appropriate material safety data sheets (MSDSs), available from
the product supplier.
EZ1 DNA Investigator Handbook 04/2009
23
Dried Blood
Drying blood on filter paper is an effective form of storage and samples prepared in
this manner are cheaper and safer to transport. A disc (3 mm diameter) punched out
from filter paper stained with dried blood contains white blood cells from approximately
5 µl whole blood; we recommend using 4 punched-out discs as starting material.
4.
Add 190 µl diluted Buffer G2 to the sample. Check if the sample has absorbed
some or all of the buffer, and if necessary add more diluted Buffer G2 to the sample
tube until the sample volume is 190 µl.
Note: Prepare diluted Buffer G2 as described in “Things to do before starting”.
5.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
6.
Incubate at 56°C for 15 min.
Dried Blood
Vortex the tube once or twice during the incubation, or place in a thermomixer.
7.
Recommended: Incubate at 95°C for 5 min.
Incubating the sample at 95°C may increase the yield of DNA.
8.
9.
If necessary, flick the tube to remove drops from inside the lid.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Using the “tip dance” protocol, there is generally no need to remove solid material
from the tube.
Alternatively, to eliminate the risk of clogging the tips, remove any solid material
from the tube. Using forceps, press the solid material against the inside of the tube
to obtain maximum sample volume. The sample volume should be approximately
200 µl. Continue with Protocol: DNA Purification (Trace Protocol), page 44.
24
EZ1 DNA Investigator Handbook 04/2009
Protocol: Pretreatment for Saliva
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
saliva samples. The protocol describes the preliminary lysis of saliva samples using
proteinase K.
Starting material
The amount of saliva should not exceed 50 µl. For larger volumes, if the sample is very
dilute, see Protocol: DNA Purification (Large-Volume Protocol), page 49.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
Procedure
1.
Place up to 50 µl saliva in a 2 ml sample tube.
2.
Add 140–190 µl Buffer G2 to the sample to bring the total volume up to 190 µl.
3.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
4.
Incubate at 56°C for 15 min.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
5.
If necessary, flick the tube to remove drops from inside the lid.
6.
Continue with Protocol: DNA Purification (Trace Protocol), page 44.
EZ1 DNA Investigator Handbook 04/2009
25
Saliva
■
Protocol: Pretreatment for Forensic Surface and Contact
Swabs
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
forensic surface and contact swabs. The protocol describes the preliminary lysis of
forensic surface and contact swabs using proteinase K.
Starting material
Swabs may be processed on the same day as collection or stored for future processing.
While storage at –20°C is recommended, DNA of suitable quality for single-copy gene
amplification has been documented from swabs stored at room temperature for
24 months.
Forensic Surface and
Contact Swabs
Important points before starting
■
This protocol has been tested using the following swab types: plastic swabs with
cotton or Dacron tips. (Puritan applicators with plastic shafts and cotton or Dacron
tips are available from: Hardwood Products Company, www.hwppuritan.com,
item nos. 25-806 1PC and 25-806 1PD; and from Daigger, www.daigger.com,
cat. nos. EF22008D and EF22008DA). Nylon cytology brushes and other swab
types may also be used.
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
Allow the swab or brush to air-dry for at least 2 h after sample collection.
■
As swabs tend to be absorbent, it is generally necessary to add a greater volume
of digestion buffer to the sample in step 2. To provide sufficient digestion buffer for
absorbent samples, Buffer G2 should be diluted with distilled water before use.
Dilute Buffer G2 in distilled water using a ratio of 1:1 (i.e., one volume of Buffer
G2 to one volume of distilled water) for n+1 samples (where n is the number of
samples to be digested). Use of diluted Buffer G2 does not influence DNA yield
or quality.
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
■
Heat a thermomixer, heating block, or water bath to 95°C for use in step 5.
26
EZ1 DNA Investigator Handbook 04/2009
Procedure
1.
Carefully cut or break off the end part of the swab or brush into a 2 ml sample
tube, using an appropriate tool (e.g., scissors).
2.
Add 290 µl of diluted Buffer G2 to the sample.
Note: Prepare diluted Buffer G2 as described in “Things to do before starting”.
3.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
If processing brush samples, centrifuge the tube briefly (at 10,000 x g for 30 s) to
force the brush to the bottom of the tube.
4.
Incubate at 56°C for 15 min.
Vortex the tube 1–2 times during the incubation, or place in a thermomixer.
5.
Recommended: Incubate at 95°C for 5 min.
Incubating the sample at 95°C may increase the yield of DNA.
6.
If necessary, flick the tube to remove drops from inside the lid.
7.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Alternatively, to eliminate the risk of clogging the tips, remove the swab or brush
from the tube. Using forceps, press the swab or brush against the inside of the tube
to obtain maximum sample volume. The sample volume should be approximately
200 µl. Continue with Protocol: DNA Purification (Trace Protocol), page 44.
EZ1 DNA Investigator Handbook 04/2009
27
Forensic Surface and
Contact Swabs
Using the “tip dance” protocol, there is generally no need to remove the swab or
brush from the tube.
Protocol: Pretreatment for Nail Scrapings
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
forensic nail-scraping samples. The protocol describes the preliminary lysis of nailscraping samples using proteinase K.
Starting material
The amount of biological sample material should not exceed 40 mg.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
Nail Scrapings
Procedure
1.
Place the nail-scraping sample in a 2 ml sample tube.
2.
Add 190 µl Buffer G2 to the sample.
3.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
4.
Incubate at 56°C for 15 min.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
5.
If necessary, flick the tube to remove drops from inside the lid.
6.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Using the “tip dance” protocol, there is generally no need to remove solid material
from the tube.
Alternatively, to eliminate the risk of clogging the tips, remove any solid material
from the tube. Using forceps, press the solid material against the inside of the tube
to obtain maximum sample volume. The sample volume should be approximately
200 µl. Continue with Protocol: DNA Purification (Trace Protocol), page 44.
28
EZ1 DNA Investigator Handbook 04/2009
Protocol: Pretreatment for Chewing Gum
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
forensic chewing-gum samples. The protocol describes the preliminary lysis of chewinggum samples using proteinase K.
Starting material
Use of up to 40 mg of chewing gum cut into small pieces is recommended.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
Procedure
1.
Place the chewing-gum sample in a 2 ml sample tube.
2.
Add 190 µl Buffer G2 to the sample.
3.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
4.
Incubate at 56°C for 15 min.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
If necessary, flick the tube to remove drops from inside the lid.
6.
Remove any solid material from the tube. Using forceps, press the solid material
against the inside of the tube to obtain maximum sample volume. The sample
volume should be approximately 200 µl. Continue with Protocol: DNA Purification
(Trace Protocol), page 44.
EZ1 DNA Investigator Handbook 04/2009
29
Chewing Gum
5.
Cigarette Butts
Protocol: Pretreatment for Cigarette Butts
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
forensic cigarette-butt samples. The protocol describes the preliminary lysis of saliva and
epithelial cells on paper from cigarette butts using proteinase K.
Starting material
Use of approximately 1 cm2 paper from the end of the cigarette or filter is
recommended.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
As cigarette butts tend to be absorbent, it is generally necessary to add a greater
volume of digestion buffer to the sample in step 2. To provide sufficient digestion
buffer for absorbent samples, Buffer G2 should be diluted with distilled water
before use. Dilute Buffer G2 in distilled water using a ratio of 1:1 (i.e., one volume
of Buffer G2 to one volume of distilled water) for n+1 samples (where n is the
number of samples to be digested). Use of diluted Buffer G2 does not influence
DNA yield or quality.
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
■
Heat a thermomixer, heating block, or water bath to 95°C for use in step 5.
Procedure
1.
Place the cigarette-butt sample in a 2 ml sample tube.
2.
Add 190 µl diluted Buffer G2 to the sample. Check if the sample has absorbed
some or all of the buffer, and if necessary add more diluted Buffer G2 to the sample
tube until the sample volume is 190 µl.
Note: Prepare diluted Buffer G2 as described above in “Things to do before
starting”.
3.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
4.
Incubate at 56°C for 15 min.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
5.
Recommended: Incubate at 95°C for 5 min.
Incubating the sample at 95°C may increase the yield of DNA.
30
EZ1 DNA Investigator Handbook 04/2009
6.
If necessary, flick the tube to remove drops from inside the lid.
7.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Alternatively, to eliminate the risk of clogging the tips, remove any solid material
from the tube. Using forceps, press the solid material against the inside of the tube
to obtain maximum sample volume. The sample volume should be approximately
200 µl. Continue with Protocol: DNA Purification (Trace Protocol), page 44.
EZ1 DNA Investigator Handbook 04/2009
31
Cigarette Butts
Using the “tip dance” protocol, there is generally no need to remove solid material
from the tube.
Protocol: Pretreatment for Postage Stamps
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
postage stamps. The protocol describes the preliminary lysis of postage-stamp samples
using proteinase K.
Postage Stamps
Starting material
Use of a 0.5–2.5 cm2 piece of postage stamp is recommended.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
As postage stamps tend to be absorbent, it is generally necessary to add a greater
volume of digestion buffer to the sample in step 2. To provide sufficient digestion
buffer for absorbent samples, Buffer G2 should be diluted with distilled water
before use. Dilute Buffer G2 in distilled water using a ratio of 1:1 (i.e., one volume
of Buffer G2 to one volume of distilled water) for n+1 samples (where n is the
number of samples to be digested). Use of diluted Buffer G2 does not influence
DNA yield or quality.
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
■
Heat a thermomixer, heating block, or water bath to 95°C for use in step 5.
Procedure
1.
Place the piece of postage stamp in a 2 ml sample tube.
2.
Add 190 µl diluted Buffer G2 to the sample. Check if the sample has absorbed
some or all of the buffer, and if necessary add more diluted Buffer G2 to the sample
tube until the sample volume is 190 µl.
Note: Prepare diluted Buffer G2 as described above in “Things to do before
starting”.
3.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
4.
Incubate at 56°C for 15 min.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
5.
Recommended: Incubate at 95°C for 5 min.
Incubating the sample at 95°C may increase the yield of DNA.
32
EZ1 DNA Investigator Handbook 04/2009
6.
If necessary, flick the tube to remove drops from inside the lid.
7.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Using the “tip dance” protocol, there is generally no need to remove solid material
from the tube.
EZ1 DNA Investigator Handbook 04/2009
33
Postage Stamps
Alternatively, to eliminate the risk of clogging the tips, remove any solid material
from the tube. Using forceps, press the solid material against the inside of the tube
to obtain maximum sample volume. The sample volume should be approximately
200 µl. Continue with Protocol: DNA Purification (Trace Protocol), page 44.
Protocol: Pretreatment for Stains on Fabric
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
stains on fabric (e.g., blood- or saliva-stained fabrics or leather). The protocol describes
the preliminary lysis of stains on fabric using proteinase K. Some samples may require
larger volumes for lysis; see Protocol: DNA Purification (Large-Volume Protocol),
page 49.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Stains on Fabric
Things to do before starting
■
As fabrics tend to be very absorbent, it is generally necessary to add a greater
volume of digestion buffer to the sample in step 2. To provide sufficient digestion
buffer for absorbent samples, Buffer G2 should be diluted with distilled water
before use. Dilute Buffer G2 in distilled water using a ratio of 1:1 (i.e., one volume
of Buffer G2 to one volume of distilled water) for n+1 samples (where n is the
number of samples to be digested). Use of diluted Buffer G2 does not influence
DNA yield or quality.
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
■
Heat a thermomixer, heating block, or water bath to 95°C for use in step 5.
Procedure
1.
Place the fabric sample in a 2 ml sample tube.
2.
Add 190 µl diluted Buffer G2 to the sample. Check if the sample has absorbed
some or all of the buffer, and if necessary add more diluted Buffer G2 to the sample
tube until the sample volume is 190 µl.
Note: Prepare diluted Buffer G2 as described above in “Things to do before
starting”.
3.
4.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
Incubate at 56°C for 15 min.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
34
EZ1 DNA Investigator Handbook 04/2009
5.
Recommended: Incubate at 95°C for 5 min.
Incubating the sample at 95°C may increase the yield of DNA.
6.
If necessary, flick the tube to remove drops from inside the lid.
7.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Using the “tip dance” protocol, there is generally no need to remove solid material
from the tube.
Alternatively, to eliminate the risk of clogging the tips, remove any solid material
from the tube. Using forceps, press the solid material against the inside of the tube
to obtain maximum sample volume. The sample volume should be approximately
200 µl. Continue with Protocol: DNA Purification (Trace Protocol), page 44.
Stains on Fabric
EZ1 DNA Investigator Handbook 04/2009
35
Protocol: Pretreatment for Human Tissues
This protocol is designed for isolation of total (genomic and mitochondrial) DNA
from human tissues. The protocol describes the preliminary lysis of tissues using
proteinase K.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
Human Tissues
Procedure
1.
Transfer the tissue sample into a 1.5 ml screw-capped tube (not supplied).
2.
Add 190 µl Buffer G2.
Ensure that tissue pieces are fully submerged in Buffer G2.
3.
Add 10 µl proteinase K solution and mix by tapping the tube gently.
4.
Incubate at 56°C until the tissue is completely lysed. Vortex 2–3 times per hour
during incubation to disperse the sample, or place in a thermomixer, shaking
water bath, or on a rocking platform.
Lysis time varies depending on the type of tissue processed. Lysis is usually
complete in 3 h. Lysis overnight is possible and does not influence the preparation.
5.
Homogenize the sample by pipetting up and down several times. Transfer the
supernatant to a new 2 ml sample tube.
6.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Using the “tip dance” protocol, there is generally no need to remove solid material
from the tube.
Alternatively, to eliminate the risk of clogging the tips, remove any solid material
from the tube. Remove large pieces of insoluble material and centrifuge at 300 x g
for 1 min. The sample volume should be approximately 200 µl. Continue with
Protocol: DNA Purification (Trace Protocol), page 44.
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EZ1 DNA Investigator Handbook 04/2009
Protocol: Pretreatment for Epithelial Cells Mixed with
Sperm Cells
This protocol is designed for purification of total (genomic and mitochondrial) DNA from
epithelial cells mixed with sperm cells. The protocol describes the preliminary lysis of
samples using proteinase K and dithiothreitol (DTT).
Important points before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
■
As some sample types (e.g., fabrics) tend to be very absorbent, it may be
necessary to add a greater volume of digestion buffer to the sample in step 2.
Things to do before starting
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in steps 4 and 12.
Procedure
Place the forensic sample in a 1.5 ml or 2 ml sample tube.
2.
Add 190 µl Buffer G2 to the sample.
3.
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
4.
Incubate at 56°C for 15 min.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
5.
Centrifuge the tube briefly to remove drops from inside the lid.
6.
Remove any solid material from the tube.
Using forceps, press the solid material against the inside of the tube to obtain
maximum sample volume.
The sample volume should be approximately 200 µl.
7.
Centrifuge the tube at 15,000 x g for 5 min. Carefully transfer the supernatant to
a new tube without disturbing the sperm cell pellet.
DNA from epithelial cells can be purified from the tube containing the supernatant
following Protocol: DNA Purification (Trace Protocol), page 44, or, if the epithelialcell fraction is very dilute, Protocol: DNA Purification (Large-Volume Protocol),
page 49.
Note: The cell pellet may not be visible.
EZ1 DNA Investigator Handbook 04/2009
37
Epithelial Cells Mixed
with Sperm Cells
1.
8.
Wash the sperm cell pellet by resuspending the pellet in 500 µl Buffer G2.
Centrifuge the tube at 15,000 x g for 5 min and discard the supernatant.
9.
Repeat step 8 two or three times.
10. Add 180 µl Buffer G2 to the pellet and resuspend the pellet.
11. Add 10 µl proteinase K and 10 µl 1 M DTT, and mix thoroughly by vortexing for
10 s.
12. Incubate at 56°C overnight at 850 rpm in a shaker–incubator or thermomixer.
13. Centrifuge the tube briefly to remove drops from inside the lid. DNA from sperm
cells can now be purified from this tube.
14. Continue with Protocol: DNA Purification (Trace Protocol), page 44.
Epithelial Cells Mixed
with Sperm Cells
The two tubes in which the epithelial and sperm cells have been separated are
now ready for DNA purification.
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EZ1 DNA Investigator Handbook 04/2009
Protocol: Pretreatment for Hair
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
the root ends of plucked hair samples. The protocol describes the preliminary lysis of
hair samples using proteinase K and dithiothreitol (DTT).
Starting material
We recommend using 0.5–1 cm from the root ends of plucked hair samples.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in steps 4 and 6.
Procedure
1.
Place the hair sample in a 2 ml sample tube.
2.
Add 180 µl Buffer G2 to the sample.
3.
Add 10 µl proteinase K and 10 µl DTT solution, and mix thoroughly by vortexing
for 10 s.
4.
Incubate at 56°C for at least 6 h.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
Add another 10 µl proteinase K and 10 µl DTT solution, and mix thoroughly by
vortexing for 10 s.
6.
Incubate at 56°C for at least 2 h or until the hair samples are completely dissolved.
7.
If necessary, flick the tube to remove drops from inside the lid.
8.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Using the “tip dance” protocol, there is generally no need to remove solid material
from the tube.
Alternatively, to eliminate the risk of clogging the tips, remove any solid material
from the tube. Using forceps, press the solid material against the inside of the tube
to obtain maximum sample volume. Continue with Protocol: DNA Purification
(Trace Protocol), page 44.
EZ1 DNA Investigator Handbook 04/2009
39
Hair
5.
Bones or Teeth
Protocol: Pretreatment for Bones or Teeth
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
bones or teeth. The protocol describes the preliminary grinding, decalcification using
EDTA, and lysis of bone or teeth samples using proteinase K.
Starting material
The amount of biological sample material should not exceed 200 mg.
Important points before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
■
Take time to familiarize yourself with the TissueLyser before starting this protocol.
See the TissueLyser Handbook.
Things to do before starting
■
Heat a thermomixer, heating block, or water bath to 37°C for the decalcification
in step 3.
Procedure
1.
Remove and discard the bone or teeth surfaces. Grind the remaining bone or tooth
root to a fine powder using the TissueLyser system or an equivalent bead mill.
When using the TissueLyser, transfer the bone sample and the ball into the grinding
jar. Pour liquid nitrogen into the grinding jar over the ball and bone fragments.
Allow the temperature to equilibrate (i.e., liquid nitrogen stops boiling). Decant the
excess liquid nitrogen, close the grinding jar with the lid, and transfer it to the
TissueLyser. Grind the bone at 30 Hz for 1 min or until the bone is pulverized
(grinding times depend on type, condition, and size of bone).
2.
Place 150–200 mg of powdered bone into a 2 ml microcentrifuge tube.
3.
Add 600–700 µl 0.5 M EDTA (pH 8.3), and incubate at 37°C for 24–48 h.
After incubation, set the temperature to 56°C for the next incubation step.
4.
Add 20 µl QIAGEN Proteinase K, and incubate at 56°C for 3 h.
5.
Centrifuge at 6000 rpm for 4 min. Transfer 200 µl of the supernatant to an EZ1
sample tube if proceeding with Protocol: DNA Purification (Trace Protocol) or
transfer 500 µl of the supernatant to an EZ1 sample tube if proceeding with
Protocol: DNA Purification (Large-Volume Protocol).
6.
Continue with Protocol: DNA Purification (Trace Protocol), page 44, or Protocol:
DNA Purification (Large-Volume Protocol), page 49.
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EZ1 DNA Investigator Handbook 04/2009
Protocol: Pretreatment for Soil
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
soil. The protocol describes the preliminary lysis of soil samples and adsorption of
inhibitors using InhibitEX tablets (contact QIAGEN Technical Services, see back cover).
Starting material
Up to 0.5 g of soil can be used, depending on the type of soil. With flocculent soil
samples, less starting material should be used.
Soil
Important points before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
■
Proteinase K is not required in this protocol.
■
This protocol requires InhibitEX tablets (contact QIAGEN Technical Services, see
back cover).
Things to do before starting
■
Heat a thermomixer, heating block, or water bath to 95°C for use in step 2.
Procedure
1.
Place the soil sample in a 2 ml sample tube.
2.
Add 900 µl distilled water. Resuspend the soil by vortexing, and incubate at 95°C
for 10 min.
3.
Centrifuge the tube at 4000 x g for 10 min. Transfer the supernatant to another
2 ml sample tube and add 190 µl Buffer G2. Mix by vortexing.
4.
Add 1 InhibitEX tablet and incubate at room temperature (15–25°C) for 1 min.
5.
Mix by vortexing and centrifuge at 10,000 x g for 2 min. Transfer 200 µl of the
supernatant to an EZ1 sample tube if proceeding with Protocol: DNA Purification
(Trace Protocol) or transfer 500 µl of the supernatant to an EZ1 sample tube if
proceeding with Protocol: DNA Purification (Large-Volume Protocol).
6.
Continue with Protocol: DNA Purification (Trace Protocol), page 44, or Protocol:
DNA Purification (Large-Volume Protocol), page 49.
EZ1 DNA Investigator Handbook 04/2009
41
Protocol: Pretreatment for Other Forensic Samples
This protocol is designed as a generic protocol for isolation of total (genomic and
mitochondrial) DNA from various forensic samples. The protocol describes the
preliminary lysis of samples using proteinase K.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Other Forensic Samples
Things to do before starting
■
As some sample types (e.g., bloodstained fabrics) tend to be very absorbent, it
may be necessary to add a greater volume of digestion buffer to the sample in
step 2. To provide sufficient digestion buffer for absorbent samples, Buffer G2 can
be diluted with distilled water before use. If necessary, dilute Buffer G2 in distilled
water using a ratio of 1:1 (i.e., one volume of Buffer G2 to one volume of distilled
water) for n+1 samples (where n is the number of samples to be digested). Use of
diluted Buffer G2 does not influence DNA yield or quality.
■
Heat a thermomixer, heating block, or water bath to 56°C for the proteinase K
digest in step 4.
Procedure
1.
Place the forensic sample in a 2 ml sample tube.
2.
Depending on the type of sample, follow either step 2a (for non-absorbent
samples) or step 2b (for absorbent samples).
2a. Non-absorbent samples:
Add 190 µl Buffer G2 to the sample.
2b. Absorbent samples:
Add 190 µl diluted Buffer G2 to the sample. Check if the sample has absorbed
some or all of the buffer, and if necessary add more diluted Buffer G2 to the sample
tube until the sample volume is 190 µl.
Note: Prepare diluted Buffer G2 as described above in “Things to do before
starting”.
3.
42
Add 10 µl proteinase K, and mix thoroughly by vortexing for 10 s.
EZ1 DNA Investigator Handbook 04/2009
4.
Incubate at 56°C for 15 min.
Vortex the tube once or twice during the incubation, or place in a thermomixer.
5.
If necessary, flick the tube to remove drops from inside the lid.
6.
Continue with Protocol: DNA Purification (“Tip Dance” Protocol), page 46.
Using the “tip dance” protocol, there is generally no need to remove solid material
from the tube.
Alternatively, to eliminate the risk of clogging the tips, remove any solid material
from the tube. Using forceps, press the solid material against the inside of the tube
to obtain maximum sample volume. The sample volume should be approximately
200 µl. Continue with Protocol: DNA Purification (Trace Protocol), page 44.
Other Forensic Samples
EZ1 DNA Investigator Handbook 04/2009
43
Protocol: DNA Purification (Trace Protocol)
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
forensic samples that have been pretreated as described in the relevant protocols in this
handbook (pages 22–43). The protocol describes the simple procedure for setting up
the EZ1 instrument and starting a run.
Important points before starting
■
■
If using the EZ1 DNA Investigator Kit for the first time, read “Important Notes“ (page 15).
■
Perform all steps of the protocol at room temperature (15–25°C). During the setup
procedure, work quickly.
■
In some steps of the procedure, one of 2 choices can be made. Choose 쑿 (blue) if using
the EZ1 Advanced or the EZ1 Advanced XL; choose 앬 (red) if using the BioRobot EZ1.
The reagent cartridges contain guanidine salts and are therefore not compatible
with disinfecting reagents containing bleach. See page 8 for safety information.
DNA Purification
(Trace Protocol)
Things to do before starting
■
If reagent cartridges have been stored at 2–8°C, equilibrate to operating
temperature before use. See “Equilibrating reagent cartridges”, page 20.
■
Remove any solid material from the sample tube. Using forceps, press the solid
material against the inside of the tube to obtain maximum sample volume.
■
The lysis buffer in the reagent cartridge may form a precipitate during storage.
If necessary, redissolve by warming at 37°C, and then place at room temperature
(15–25°C).
Procedure
1.
Insert 쑿 the EZ1 Advanced DNA Investigator Card completely into the EZ1
Advanced Card slot of the EZ1 Advanced or the EZ1 Advanced XL DNA Investigator
Card completely into the EZ1 Advanced XL Card slot of the EZ1 Advanced XL or 앬
the EZ1 DNA Investigator Card completely into the EZ1 Card slot of the BioRobot EZ1.
2.
Switch on the EZ1 instrument.
3.
Press “START” to start protocol setup. 쑿 Follow the onscreen instructions for data
tracking.
4.
Press “1” (for Trace protocol).
5.
Choose the elution buffer and volume: press “1” to elute in water or “2” to elute
in TE buffer. Then press “1”, “2”, or “3”, (or “4”, EZ1 Advanced XL only) to select
the elution volume.
6.
Press any key to proceed through the text shown on the display and start
worktable setup.
The text summarizes the following steps which describe loading of the worktable.
Wear gloves when loading the required items on the worktable.
44
EZ1 DNA Investigator Handbook 04/2009
7.
Open the instrument door.
8.
Invert reagent cartridges twice to mix the magnetic particles. Then tap the
cartridges to deposit the reagents at the bottom of their wells. Check that the
magnetic particles are completely resuspended.
9.
Load the reagent cartridges into the cartridge rack.
Note: After sliding a reagent cartridge into the cartridge rack, ensure that you
press down on the cartridge until it clicks into place.
10. Load opened elution tubes into the first row of the tip rack.
11. Load tip holders containing filter-tips into the second row of the tip rack.
12. Load opened sample tubes containing digested samples into the back row of the
tip rack.
Pretreat the samples following the individual protocols in this handbook.
Note: When using the data tracking option, ensure that the sample ID follows the
same order as the samples on the worktable to avoid data mixup.
13. Close the instrument door.
14. Press “START” to start the purification procedure.
The EZ1 Advanced and the EZ1 Advanced XL can store up to 10 report files. Report
files can be printed directly on a connected printer or transferred to a computer.
16. Open the instrument door.
17. Retrieve the elution tubes containing the purified DNA. The DNA is ready to use,
or can be stored at 2–8°C for 24 h or at –20°C for longer periods. Discard the
sample-preparation waste.*
If the purified DNA is to be analyzed by real-time PCR, tubes containing eluate
should first be applied to a suitable magnetic separator and the eluate transferred
to a clean tube in order to minimize the risk of magnetic-particle carryover.
18. 쑿 Optional: Follow the onscreen instructions to perform UV decontamination of
the worktable surfaces.
19. To run another protocol, press “ESC”, prepare samples as described in the relevant
protocol, and follow the procedure from step 4 onward. Otherwise, press “STOP”
twice to return to the first screen of the display, close the instrument door, and
switch off the EZ1 instrument.
20. Clean the EZ1 instrument.
Follow the maintenance instructions in the user manual supplied with your EZ1
instrument.
* Sample waste contains guanidine salts and is therefore not compatible with bleach. See page 8 for safety
information.
EZ1 DNA Investigator Handbook 04/2009
45
DNA Purification
(Trace Protocol)
The automated purification procedure takes 15–20 min.
15. When the protocol ends, the display shows “Protocol finished”. 쑿 Press “ENT” to
generate the report file.
Protocol: DNA Purification (“Tip Dance” Protocol)
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
forensic samples that have been pretreated as described in the relevant protocols in this
handbook (pages 22–43). This protocol describes the simple procedure for setting up
the EZ1 instrument and starting a run.
In the “tip dance” protocol, the filter-tip moves back-and-forth relative to the worktable
platform while pipetting. This enables processing of solid materials, such as swabs,
fabrics, blood discs, or cigarette butts, directly in the sample tube. There is generally
no need for prior centrifugation to remove solid materials that could clog the tip.
However, when processing fluffy sample material such as cotton wool, we recommend
removing solid material if you cannot process a replicate sample or the sample material
is precious. (Using forceps, press the solid material against the inside of the tube to
obtain maximum sample volume.)
DNA Purification
(“Tip Dance“ Protocol)
Important points before starting
■
If using the EZ1 DNA Investigator Kit for the first time, read “Important Notes“
(page 15).
■
The reagent cartridges contain guanidine salts and are therefore not compatible
with disinfecting reagents containing bleach. See page 8 for safety information.
■
Perform all steps of the protocol at room temperature (15–25°C). During the setup
procedure, work quickly.
■
In some steps of the procedure, one of 2 choices can be made. Choose 쑿 (blue)
if using the EZ1 Advanced or the EZ1 Advanced XL; choose 앬 (red) if using the
BioRobot EZ1.
Things to do before starting
■
If reagent cartridges have been stored at 2–8°C, equilibrate to operating
temperature before use. See “Equilibrating reagent cartridges”, page 20.
■
The lysis buffer in the reagent cartridge may form a precipitate during storage.
If necessary, redissolve by warming at 37°C, and then place at room temperature
(15–25°C).
Procedure
1.
46
Insert 쑿 the EZ1 Advanced DNA Investigator Card completely into the EZ1
Advanced Card slot of the EZ1 Advanced or the EZ1 Advanced XL DNA Investigator
Card completely into the EZ1 Advanced XL Card slot of the EZ1 Advanced XL or 앬
the EZ1 DNA Investigator Card completely into the EZ1 Card slot of the BioRobot EZ1.
EZ1 DNA Investigator Handbook 04/2009
2.
Switch on the EZ1 instrument.
3.
Press “START” to start protocol setup. 쑿 Follow the onscreen instructions for data
tracking.
4.
Press “2” (for Trace TD protocol).
5.
Choose the elution buffer and volume: press “1” to elute in water or “2” to elute
in TE. Then press “1”, “2”, or “3”, (or “4”, EZ1 Advanced XL only) to select the
elution volume.
6.
Press any key to proceed through the text shown on the display and start
worktable setup.
The text summarizes the following steps which describe loading of the worktable.
Wear gloves when loading the required items on the worktable.
7.
Open the instrument door.
8.
Invert reagent cartridges twice to mix the magnetic particles. Then tap the
cartridges to deposit the reagents at the bottom of their wells. Check that the
magnetic particles are completely resuspended.
9.
Load the reagent cartridges into the cartridge rack.
Note: After sliding a reagent cartridge into the cartridge rack, ensure that you
press down on the cartridge until it clicks into place.
10. Load opened elution tubes into the first row of the tip rack.
11. Load tip holders containing filter-tips into the second row of the tip rack.
Pretreat the samples following the individual protocols in this handbook.
Note: When using the data tracking option, ensure that the sample ID follows the
same order as the samples on the worktable to avoid data mixup.
13. Close the instrument door.
14. Press “START” to start the purification procedure.
The automated purification procedure takes 15–20 min.
15. When the protocol ends, the display shows “Protocol finished”. 쑿 Press “ENT” to
generate the report file.
The EZ1 Advanced and the EZ1 Advanced XL can store up to 10 report files.
Report files can be printed directly on a connected printer or transferred to a computer.
16. Open the instrument door.
EZ1 DNA Investigator Handbook 04/2009
47
DNA Purification
(“Tip Dance“ Protocol)
12. Load opened sample tubes containing digested samples into the back row of the
tip rack.
17. Retrieve the elution tubes containing the purified DNA. The DNA is ready to use,
or can be stored at 2–8°C for 24 h or at –20°C for longer periods. Discard the
sample-preparation waste.*
If the purified DNA is to be analyzed by real-time PCR, tubes containing eluate
should first be applied to a suitable magnetic separator and the eluate transferred
to a clean tube in order to minimize the risk of magnetic-particle carryover.
18. 쑿 Optional: Follow the onscreen instructions to perform UV decontamination of
the worktable surfaces.
19. To run another protocol, press “ESC”, prepare samples as described in the relevant
protocol, and follow the procedure from step 4 onward. Otherwise, press “STOP”
twice to return to the first screen of the display, close the instrument door, and
switch off the EZ1 instrument.
20. Clean the EZ1 instrument.
DNA Purification
(“Tip Dance“ Protocol)
Follow the maintenance instructions in the user manual supplied with your EZ1
instrument.
* Sample waste contains guanidine salts and is therefore not compatible with bleach. See page 8 for safety
information.
48
EZ1 DNA Investigator Handbook 04/2009
Protocol: DNA Purification (Large-Volume Protocol)
This protocol is designed for isolation of total (genomic and mitochondrial) DNA from
forensic samples that have been pretreated as described in the relevant protocols in this
handbook (pages 22–43). This protocol describes the simple procedure for setting up
the EZ1 instrument and starting a run.
Starting material
Using this protocol, up to 500 µl of pretreated sample can be processed. This not only
allows efficient DNA purification from dilute samples with low concentrations of DNA,
such as diffuse stains, but also enables purification from samples that require larger
volumes for thorough lysis. For these samples, increase the amount of Buffer G2 as
required. The amount of proteinase K generally does not need to be increased.
The ability to process larger sample volumes — with the same elution volume as the
standard trace protocol — enables higher yields of more concentrated DNA for greater
sensitivity in downstream applications.
Important points before starting
If using the EZ1 DNA Investigator Kit for the first time, read “Important Notes“
(page 15).
■
The reagent cartridges contain guanidine salts and are therefore not compatible
with disinfecting reagents containing bleach. See page 8 for safety information.
■
Perform all steps of the protocol at room temperature (15–25°C). During the setup
procedure, work quickly.
■
This protocol requires extra Buffer MTL (contact QIAGEN Technical Services, see
back cover).
■
In some steps of the procedure, one of 2 choices can be made. Choose 쑿 (blue)
if using the EZ1 Advanced or the EZ1 Advanced XL; choose 앬 (red) if using the
BioRobot EZ1.
Things to do before starting
■
If reagent cartridges have been stored at 2–8°C, equilibrate to operating
temperature before use. See “Equilibrating reagent cartridges”, page 20.
■
Remove any solid material from the sample tube. Using forceps, press the solid
material against the inside of the tube to obtain maximum sample volume.
■
The lysis buffer in the reagent cartridge may form a precipitate during storage.
If necessary, redissolve by warming at 37°C, and then place at room temperature
(15–25°C).
EZ1 DNA Investigator Handbook 04/2009
49
DNA Purification
(Large-Volume Protocol)
■
Procedure
1.
Insert 쑿 the EZ1 Advanced DNA Investigator Card completely into the EZ1
Advanced Card slot of the EZ1 Advanced or the EZ1 Advanced XL DNA Investigator
Card completely into the EZ1 Advanced XL Card slot of the EZ1 Advanced XL or 앬
the EZ1 DNA Investigator Card completely into the EZ1 Card slot of the BioRobot EZ1.
2.
Switch on the EZ1 instrument.
3.
Press “START” to start protocol setup. 쑿 Follow the onscreen instructions for data
tracking.
4.
Press “3” (for Large-Volume protocol).
5.
Choose the elution buffer and volume: press “1” to elute in water or “2” to elute
in TE buffer. Then press “1”, “2”, or “3”, (or “4”, EZ1 Advanced XL only) to select
the elution volume.
6.
Press any key to proceed through the text shown on the display and start
worktable setup.
The text summarizes the following steps which describe loading of the worktable.
Wear gloves when loading the required items on the worktable.
7.
Open the instrument door.
8.
Invert reagent cartridges twice to mix the magnetic particles. Then tap the
cartridges to deposit the reagents at the bottom of their wells. Check that the
magnetic particles are completely resuspended.
9.
Load the reagent cartridges into the cartridge rack.
Note: After sliding a reagent cartridge into the cartridge rack, ensure that you
press down on the cartridge until it clicks into place.
10. Load opened elution tubes into the first row of the tip rack.
DNA Purification
(Large-Volume Protocol)
11. Load tip holders containing filter-tips into the second row of the tip rack.
12. Add 400 µl Buffer MTL to each sample tube containing digested samples. Load
opened sample tubes containing Buffer MTL and digested samples into the back
row of the tip rack.
Pretreat the samples following the individual protocols in this handbook.
Note: When using the data tracking option, ensure that the sample ID follows the
same order as the samples on the worktable to avoid data mixup.
13. Close the instrument door.
14. Press “START” to start the purification procedure.
The automated purification procedure takes 15–20 min.
50
EZ1 DNA Investigator Handbook 04/2009
15. When the protocol ends, the display shows “Protocol finished”. 쑿 Press “ENT” to
generate the report file.
The EZ1 Advanced and the EZ1 Advanced XL can store up to 10 report files. Report
files can be printed directly on a connected printer or transferred to a computer.
16. Open the instrument door.
17. Retrieve the elution tubes containing the purified DNA. The DNA is ready to use,
or can be stored at 2–8°C for 24 h or at –20°C for longer periods. Discard the
sample-preparation waste.*
If the purified DNA is to be analyzed by real-time PCR, tubes containing eluate
should first be applied to a suitable magnetic separator and the eluate transferred
to a clean tube in order to minimize the risk of magnetic-particle carryover.
18. 쑿 Optional: Follow the onscreen instructions to perform UV decontamination of
the worktable surfaces.
19. To run another protocol, press “ESC”, prepare samples as described in the relevant
protocol, and follow the procedure from step 4 onward. Otherwise, press “STOP”
twice to return to the first screen of the display, close the instrument door, and
switch off the EZ1 instrument.
20. Clean the EZ1 instrument.
Follow the maintenance instructions in the user manual supplied with your EZ1
instrument.
DNA Purification
(Large-Volume Protocol)
* Sample waste contains guanidine salts and is therefore not compatible with bleach. See page 8 for safety
information.
EZ1 DNA Investigator Handbook 04/2009
51
Troubleshooting Guide
This troubleshooting guide may be helpful in solving any problems that may arise. For
more information, see also the Frequently Asked Questions page at our Technical
Support Center: www.qiagen.com/FAQ/FAQList.aspx. The scientists in QIAGEN
Technical Services are always happy to answer any questions you may have
about either the information and protocols in this handbook or sample and assay
technologies (for contact information, see back cover or visit www.qiagen.com)
Comments and suggestions
General handling
a)
Error message in
instrument display
Refer to the user manual supplied with your
EZ1 instrument.
b)
Report file not printed
Check whether the printer is connected to the
EZ1 Advanced or EZ1 Advanced XL via the
“PC/Printer” serial port.
Check whether the serial port is set for use
with a printer.
c)
Report file not sent to the PC
Check whether the PC is connected to the
EZ1 Advanced or EZ1 Advanced XL via the
“PC/Printer” serial port.
Check whether the serial port is set for use
with a PC.
d)
Wrong Q-Card ID entered
If the wrong ID was entered instead of the
Q-Card ID, the EZ1 Advanced/EZ1
Advanced XL will not accept the ID and will
prompt for the Q-Card ID until the correct ID
is entered. Press “STOP” twice to go to the
main menu.
Low DNA yield
a)
Magnetic particles not
completely resuspended
Ensure that you invert the reagent cartridges
several times to resuspend the magnetic
particles.
b)
Insufficient reagent aspirated
After inverting the reagent cartridges to
resuspend the magnetic particles, ensure
that you tap the cartridges to deposit the
reagents at the bottom of the wells.
52
EZ1 DNA Investigator Handbook 04/2009
Comments and suggestions
c)
Purified DNA stored in water
Elute in TE buffer instead of water. Elution in
TE buffer gives comparable performance
and provides increased stability for longterm storage of small amounts of purified
DNA.
d)
Varying pipetting volumes
To ensure pipetting accuracy, it is important
that buffer volumes in the reagent cartridges
are correct and that the filter tips fit optimally
to the tip adapter. Ensure that samples are
thoroughly mixed and that reagent cartridges
have not passed their expiry date. Perform
regular maintenance as described in the
instrument user manual. Check the fit of the
filter tips regularly as described in the user
manual.
DNA does not perform well in downstream applications
a)
Insufficient DNA used in
downstream applications
If possible, repeat the downstream
application using more eluate.
b)
Excess DNA used in
downstream application
Excess DNA can inhibit some enzymatic
reactions. Dilute the eluate or use less in the
downstream application. Quantify the
purified DNA by measurement of the
absorbance using an appropriate method.
EZ1 DNA Investigator Handbook 04/2009
53
Appendix A: Purification of Low Amounts of DNA
This protocol is designed for purification of isolation of total (genomic and
mitochondrial) DNA from forensic samples that contain <100 ng DNA. The protocol
describes the addition of carrier RNA to sample lysates. For full details, refer to Kishore,
R., Hardy, W.R., Anderson, V.J., Sanchez, N.A., and Buoncristiani, M.P.H. (2006)
Optimization of DNA extraction from low-yield and degraded samples using the
BioRobot EZ1 and BioRobot M48. J. Forensic Sci. Vol. 51, No. 5, 1055.
The procedure has not been thoroughly tested and optimized by QIAGEN.
Important point before starting
■
Before beginning the procedure, read “Important Notes”, page 15.
Things to do before starting
■
Add 310 µl nuclease-free water or TE buffer to the tube containing carrier RNA
(310 µg) to obtain a solution of 1 µg/µl.
■
Dissolve the carrier RNA thoroughly, divide it into single-use aliquots, and store at
–70°C.
Procedure
1.
Pretreat samples according to the appropriate pretreatment protocol given on
pages 22–43 of this handbook.
2.
Add 1 µl of thawed carrier RNA solution (1 µg) to each lysate. It is not necessary
to incubate the carrier RNA and sample lysate.
3.
Continue immediately with Protocol: DNA Purification (Trace Protocol), Protocol:
DNA Purification (“Tip Dance” Protocol), or Protocol: DNA Purification (LargeVolume Protocol) on pages 44, 46, or 49 of this handbook.
54
EZ1 DNA Investigator Handbook 04/2009
Appendix B: Example of an EZ1 Advanced Report File
This appendix shows a typical report file generated on the EZ1 Advanced. The values
for each parameter will differ from the report file generated on your EZ1 Advanced.
Please note that “User ID” is allowed a maximum of 9 characters, and that “Assay kit
ID” and “Note“ are allowed a maximum of 14 characters.
The EZ1 Advanced XL generates a similar report file containing instrument and protocol
information relevant to the EZ1 Advanced XL and information for channels 1–14.
REPORT - FILE EZ1 Advanced:
__________________
Serial No. EZ1 Advanced: _ _ _ _ _ _ _ _ 0301F0172
User ID: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 4121
Firmware version:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ V 1.0.0
Installation date of instr.:
_ _ _ _ _ _ _ _ Jan 05, 2008
Weekly maintenance done on: _ _ _ _ _ Apr 15, 2008
Yearly maintenance done on: _ _ _ _ _ _ Mar 10, 2008
Date of last UV-run: _ _ _ _ _ _ _ _ _ _ _ Apr 20, 2008
Start of last UV-run:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 16:06
End of last UV-run: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 16:26
Status UV-run: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _o.k.
Protocol name: _ _ _ _ _ _ _ _ _ _ _ _ DNA Investigator
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Trace
Date of run:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ Aprl 21, 2008
Start of run:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 12:57
End of run: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 13:31
Status run:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ o.k.
Error Code: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Sample input Vol [ul]:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 200
Elution volume [ul]: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 100
Channel A:
Sample ID:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 123456789
Reagen Kit number: _ _ _ _ _ _ _ _ _ _ _ _ _ 9801301
Reagen Lot number:
_ _ _ _ _ _ _ _ _ _ _ _ 23456789
Reagent Expiry date: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1208
Assay kit ID: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 848373922
Note: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2000
EZ1 DNA Investigator Handbook 04/2009
55
Channel B:
Sample ID:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 234567890
Reagen Kit number: _ _ _ _ _ _ _ _ _ _ _ _ _ 9801301
Reagen Lot number:
_ _ _ _ _ _ _ _ _ _ _ _ 23456789
Reagent Expiry date: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1208
Assay kit ID: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 836266738
Note:
__________________________
Channel C:
Sample ID:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 345678901
Reagen Kit number: _ _ _ _ _ _ _ _ _ _ _ _ _ 9801301
Reagen Lot number:
_ _ _ _ _ _ _ _ _ _ _ _ 23456789
Reagent Expiry date: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1208
Assay kit ID: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 883727832
Notes: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _1000
Channel D:
Sample ID:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 456789012
Reagen Kit number: _ _ _ _ _ _ _ _ _ _ _ _ _ 9801301
Reagen Lot number:
_ _ _ _ _ _ _ _ _ _ _ _ 23456789
Reagent Expiry date: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1208
Assay kit ID: _ _ _ __ _ _ _ _ _ _ _ _ _ _ _ 763684837
Note: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Channel E:
Sample ID:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 567890123
Reagen Kit number: _ _ _ _ _ _ _ _ _ _ _ _ _ 9801301
Reagen Lot number:
_ _ _ _ _ _ _ _ _ _ _ _ 23456789
Reagent Expiry date: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1208
Assay kit ID: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 4387728002
Note: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Channel F:
Sample ID:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 678901234
Reagen Kit number: _ _ _ _ _ _ _ _ _ _ _ _ _ 9801301
Reagen Lot number:
_ _ _ _ _ _ _ _ _ _ _ _ 23456789
Reagent Expiry date: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 1208
Assay kit ID: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 509389403
Note:
56
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 50
EZ1 DNA Investigator Handbook 04/2009
Ordering Information
Product
Contents
Cat. no.
EZ1 DNA Investigator Kit (48)
For 48 preps: Reagent Cartridges,
Disposable Tip Holders, Disposable
Filter-Tips, Sample Tubes, Elution
Tubes, Buffers and Reagents;
includes Certificate of Analysis
952034
EZ1 Advanced XL
Robotic instrument for automated
purification of nucleic acids from
up to 14 samples using EZ1 Kits,
1-year warranty on parts and labor*
9001492
EZ1 Advanced
Robotic instrument for automated
purification of nucleic acids using
EZ1 Kits, 1-year warranty on parts
and labor*
9001410
EZ1 Advanced XL DNA
Investigator Card
Preprogrammed card for EZ1
Advanced XL DNA Investigator
protocols on the EZ1 Advanced XL
9018699
EZ1 Advanced DNA
Investigator Card
Preprogrammed card for EZ1
9018302
Advanced DNA Investigator protocols
EZ1 DNA Investigator Card
Preprogrammed card for BioRobot
EZ1 DNA Investigator protocols
9016387
Filter-Tips and Holders,
EZ1 (50)
50 Disposable Filter-Tips,
50 Disposable Tip Holders;
additional tips and holders for use
with EZ1 Kits
994900
12-Tube Magnet
Magnet for separating magnetic
particles in 12 x 1.5 ml or 2 ml tubes
Buffer G2 (260 ml)
Lysis buffer for EZ1 DNA procedures 1014636
QIAGEN Proteinase K (2 ml)
2 ml (>600 mAU/ml, solution)
19131
QIAGEN Proteinase K (10 ml)
10 ml (>600 mAU/ml, solution)
19133
TissueLyser II
Universal laboratory mixer-mill
disruptor
85300
Accessories
36912
* Warranty PLUS 2 (cat. no. 9237720) recommended: 3-year warranty, 1 preventive maintenance visit per
year, 48-hour priority response, all labor, travel, and repair parts.
EZ1 DNA Investigator Handbook 04/2009
57
Ordering Information
Product
Contents
Cat. no.
Grinding Jar Set,
S. Steel (2 x 10 ml)
2 Grinding Jars (10 ml), 2 Stainless
Steel Grinding Balls (20 mm)
69985
PC and TFT Monitor, 17”
PC capable of connection with up
9016643
to 4 EZ1 Advanced or EZ1 Advanced
XL instruments; Monitor for use with PC
Printer
Printer for connection with
EZ1 Advanced or EZ1 Advanced
XL instrument
9018464
Printer Accessory Package
Accessories for printer connected to
EZ1 Advanced or EZ1 Advanced
XL instrument
9018465
QIAcard FTA One Spot (100)
For collection and storage of
100 samples: 100 QIAcard FTA
One Spots
159201
QIAcard FTA Two Spots (100)
For collection and storage of
100 x 2 samples: 100 QIAcard
FTA Two Spots
159203
QIAcard FTA Four Spots (100)
For collection and storage of
100 x 4 samples: 100 QIAcard
FTA Four Spots
159205
QIAcard FTA Indicator
Four Spots (25)
For collection and storage of
25 x 4 samples: 25 QIAcard
FTA Indicator Four Spots
159214
QIAcard FTA Purification
Reagent (500 ml)
For use with QIAcard FTA Spots:
500 ml QIAcard FTA Purification
Reagent
159300
EZ1 DNA Blood 200 µl
Kit (48)
48 Reagent Cartridges,
50 Disposable Tip Holders,
50 Disposable Filter-Tips, 50 Sample
Tubes, 50 Elution Tubes
951034
EZ1 DNA Blood 350 µl
Kit (48)
48 Reagent Cartridges,
50 Disposable Tip Holders,
50 Disposable Filter-Tips, 50 Sample
Tubes, 50 Elution Tubes
951054
Related products
58
EZ1 DNA Investigator Handbook 04/2009
Ordering Information
Product
Contents
Cat. no.
EZ1 DNA Tissue Kit (48)
48 Reagent Cartridges,
50 Disposable Tip Holders,
50 Disposable Filter-Tips, 50 Sample
Tubes, 50 Elution Tubes, Buffer G2,
Proteinase K
953034
EZ1 Virus Mini Kit v2.0 (48)
For 48 virus nucleic acid preps:
Reagent Cartridges (Virus Mini v2.0),
Disposable Tips, Disposable
Tip-Holders, Sample Tubes, Elution
Tubes, Buffers
955134
For up-to-date licensing information and product-specific disclaimers, see the respective
QIAGEN kit handbook or user manual. QIAGEN kit handbooks and user manuals are
available at www.qiagen.com or can be requested from QIAGEN Technical Services
or your local distributor.
Visit www.qiagen.com/goto/EZ1Advanced to find out more about other EZ1 Kits!
EZ1 DNA Investigator Handbook 04/2009
59
Notes
60
EZ1 DNA Investigator Handbook 04/2009
Notes
EZ1 DNA Investigator Handbook 04/2009
61
Notes
62
EZ1 DNA Investigator Handbook 04/2009
Trademarks: QIAGEN®, QIAcard®, BioRobot®, EZ1®, InhibitEX® (QIAGEN Group); 903® (S&S Biosciences, Inc.); Dacron® (E. I. du
Pont de Nemours and Company); FTA® (Whatman PLC); Puritan® (Hardwood Products Company).
Limited License Agreement
Use of this product signifies the agreement of any purchaser or user of the EZ1 DNA Investigator Kit to the following terms:
1. The EZ1 DNA Investigator Kit may be used solely in accordance with the EZ1 DNA Investigator Handbook and for use
with components contained in the Kit only. QIAGEN grants no license under any of its intellectual property to use or
incorporate the enclosed components of this Kit with any components not included within this Kit except as described in the
EZ1 DNA Investigator Handbook and additional protocols available at www.qiagen.com.
2. Other than expressly stated licenses, QIAGEN makes no warranty that this Kit and/or its use(s) do not infringe the rights of
third-parties.
3. This Kit and its components are licensed for one-time use and may not be reused, refurbished, or resold.
4. QIAGEN specifically disclaims any other licenses, expressed or implied other than those expressly stated.
5. The purchaser and user of the Kit agree not to take or permit anyone else to take any steps that could lead to or facilitate
any acts prohibited above. QIAGEN may enforce the prohibitions of this Limited License Agreement in any Court, and shall
recover all its investigative and Court costs, including attorney fees, in any action to enforce this Limited License Agreement or
any of its intellectual property rights relating to the Kit and/or its components.
For updated license terms, see www.qiagen.com.
© 2009 QIAGEN, all rights reserved.
63
www.qiagen.com
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1056888 04/2009
Sample & Assay Technologies
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