MagnaMedics
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MagSi-DT Removal
Art.No.
MDKT0004

Product Manual

Version 1.10 | 10/11/2016

MagnaMedics
Move to Simplicity
MagSi-DT Removal
Dye-Terminator RemovalThis product is for Research Use Only (RUO). Not for drug, household or other uses. For more
information, please consult the appropriate Safety Data Sheet (SDS), available on our website atwww.magnamedics.com

Table of Contents
1. General Information............................................................................................................2
2. Materials supplied in the kit................................................................................................3
2.1 Materials Supplied by the User..............................................................................................................3

3. Kit Usage............................................................................................................................ 43.1 Preparations before use.......................................................................................................................4
3.2 Handling guidelines.............................................................................................................................4

4. Protocols............................................................................................................................ 5
4.1 Dye-Terminator Removal in 96 well plate................................................................................................5
4.2 Dye-Terminator Removal in 384 well plate..............................................................................................6

5. Troubleshooting..................................................................................................................7

1. General Information
MagSi-DT Removal provides a convenient tool for ultra-fast and efficient purification of Dye-Terminator
sequencing reactions and removal of unincorporated Dye Terminators and salts. The kit can be used
manually or on automated workstations using 96- and 384-well PCR plates. The kit uses a simple threestep protocol and it can be used directly in the thermal cycling plate. Dye labeled DNA products arebound onto the surface of the magnetic beads, leaving unincorporated Dye Terminators and salts insolution. The DNA fragments are eluted with reagent grade water or 0.1 mM EDTA pH 8.0. The total
preparation time is approximately 20 minutes and hands-on time necessary for the whole procedure is
reduced to a minimum.
The number of preparations depends on the plate format. Please refer to the table below to determine
how many purifications can be performed.
Table 1. Number of preparations for different kits sizes

2

MDKT00040008
8 mL

MDKT00040050
50 mL

MDKT00040500
500 mL96 Well Format

800

5.000

50.000384 Well Format

1600

10.000100.000

PM0012-110_MagSi-DT_Removal

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2. Materials supplied in the kit
Table 2. Materials supplied for different kit sizes
Art.No.

MDKT00040008

MDKT00040050

MDKT00040500

MagSi-DT Removal beads

8 mL

50 mL

500 mL

Product manual111

When stored at 2-8°C the kit is stable for up to 2 years, but no longer than the expiry date on the label.
Do not freeze!

2.1 Materials Supplied by the User
Table 3. Materials supplied by the user
Consumables & Equipment

Multichannel pipettes

Reaction plate

10 µL and 100 µL
96-well PCR Plates, (suggested: ABgene, Cat.No.: AB-0800, AB-1000 or AB-1400 )384-well PCR Plates, (suggested: ABgene, Cat.No.: AB-1111)
MM-Separator 96 PCR (MagnaMedics, Art.No.: MDMG0005): Magnetic separator for 96-well
PCR plates, U and V-bottom microplates. suitable for automated processes

Magnetic separator

MM-Separator 384 PCR (MagnaMedics, Art.No.: MDMG0006): Magnetic separator for 384well PCR. suitable for automated processes

Reagents

Ethanol p.a.

VWR cat# 1.00013.1000

Elution buffer

Reagent grade water or 0.1 mM EDTA pH 8.0

PM0012-110_MagSi-DT_Removal

3

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3. Kit Usage
3.1 Preparations before use•Prepare ethanol solution: Make 25 mL of 85% ethanol per 96 well plate. Ethanol is used for
precipitation of DNA products, so it is critical that the 85% ethanol has been prepared fresh.

•Prepare Elution buffer: Reagent grade water or 0.1 mM EDTA pH 8.0•

Shake MagSi-DT Removal to fully resuspend the magnetic beads. The reagent should behomogeneous and consistent in color.

3.2 Handling guidelines

4•

Drying time may vary due to differences in the laboratory environment. Careful: Do not over-dry
the samples, this may result in loss of signal intensity.

•When transferring purified samples, leave a small volume of liquid behind in order to prevent
carry-over of magnetic beads into a new plate. Residual magnetic beads can interfere withinjection. If beads are present in final sample, perform the separation again.

•When working with chemicals, always wear a suitable lab coat, disposable gloves and protective
goggles. For more information, please consult the appropriate safety data sheets (SDS).

PM0012-110_MagSi-DT_Removal

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4. Protocols
4.1 Dye-Terminator Removal in 96 well plate1.

Before use, shake MagSi-DT Removal to fully resuspend the beads.

2.

Add 10 µL MagSi-DT Removal to each sample in the plate.

3.

Add 85% ethanol according to the table below. Mix by pipetting up and down 10 times until ahomogeneous suspension is obtained. It is very important to mix to completely bind the sequencing
products.
Sequencing reaction volume (µL)

Volume of 85% ethanol (µL)

531

10421552

20622573

For other volumes use this calculation: Volume of 85% ethanol = 2.077 x (10 µL + Sample Volume)
4.

Place the sample plate on the magnetic separator for 3 minutes to collect the magnetic beads
until a clear solution is obtained.

5.

Remove the cleared supernatant from the beads and discard.
This step must be performed while the plate is on the magnet. Remove the supernatant as much as
possible.

6.

Add 100 µL of 85% ethanol and incubate for 30 seconds to allow the beads to settle to the magnet
again. This step can be performed while the plate is placed on the magnet. (It is not necessary toresuspend the beads)

7.

Completely discard the supernatant.
This step must be performed while the plate is on the magnet.

8.

Repeat steps 6-7 once more for a total of 2 washing steps.

9.

Air-dry the magnetic beads for 10 minutes.
The beads can be dried while the plate is on the magnet. Note: Excessive drying can lead to degradationof the fluorescent dye.

10.

Add 40 µL Elution Buffer and incubate for 5 minutes to elute.
This step can be performed while the plate is placed on the magnet. Elution is fast but can be facilitatedby pipetting up and down 7 times.

11.

Transfer the supernatant to the final plate.
Leave 5-10 µL liquid behind to prevent transfer of beads into the final plate.

PM0012-110_MagSi-DT_Removal

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4.2 Dye-Terminator Removal in 384 well plate1.

Before use, shake MagSi-DT Removal to fully resuspend the beads.

2.

Add 5 µL MagSi-DT Removal to each sample in the plate.

3.

Add 85% ethanol according to the table below. Mix by pipetting up and down 10 times until ahomogeneous suspension is obtained. It is very important to mix to completely bind the sequencing
products.
Sequencing reaction volume (µL)

Volume of 85% ethanol (µL)

514.3

1021.41528.6For other volumes use this calculation: Volume of 85% ethanol = 1.428 x (5 µL + Sample Volume)

64.

Place the sample plate on the magnetic separator for 2-3 minutes to collect the magnetic beads
until a clear solution is obtained.

5.

Remove the cleared supernatant from the beads and discard.
This step must be performed while the plate is on the magnet. Remove the supernatant as much as
possible.

6.

Add 30 µL of 85% ethanol and incubate for 30 seconds to allow the beads to settle to the magnet
again. This step can be performed while the plate is placed on the magnet. (It is not necessary toresuspend the beads)

7.

Completely discard the supernatant.
This step must be performed while the plate is on the magnet.

8.

Repeat steps 6-7 once more for a total of 2 washing steps.

9.

Air-dry the magnetic beads for 10 minutes.
The beads can be dried while the plate is on the magnet. Note: Excessive drying can lead to degradationof the fluorescent dye.

10.

Add 15-30 µL Elution Buffer and incubate for 5 minutes to elute.
This step can be performed while the plate is placed on the magnet. Elution is fast but can be facilitatedby pipetting up and down 7 times.

11.

Transfer the supernatant to the final plate.
Leave 2-5 µL liquid behind to prevent transfer of beads into the final plate.

PM0012-110_MagSi-DT_Removal

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5. Troubleshooting
Problem

Probable cause

Dye Blobs

Insufficient supernatant removal

Suggestion- Check the plate visually after discarding supernatant
and wash solutions and make sure they are removed
completely(dye peaks usually at 70 and100 bases)
Too much BigDye- Use less BigDye per sequencing reaction- Make sure the elution volume is sufficient, theappropriate number of mixes are performed andInsufficient mixing

visually check for proper homogenization- Optionally resuspend the sample 1-2 times duringbinding step.

Low signal(signal intensity is similar tointensity of background noise)- Make sure no magnetic particles are aspirated by
Loss of magnetic particles

proper positioning of the pipette, dispense backsupernatant when aspiration of beads occurs

Low ethanol concentrationhigh)PM0012-110_MagSi-DT_Removalof clean-up and correct volumes are added- Use less BigDye per sequencing reaction; transferOverload(signal intensity is extremely- Make sure 85% ethanol is prepared freshly on the day

Too much BigDye

only part of the eluant for loading; use alternativeelution buffer; decrease the sample injection time ofthe sequencer

7

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Tel: +31-(0)46-820 0206
Fax: +31-(0)46-410 6825
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