Omega Bio-Tek Mag-Bind SeqDTR M1300-05 User manual

Mag-Bind® SeqDTR™
M1300-05 5 mL
M1300-08 50 mL
M1300-50 500 mL
January 2013

1
Introduction and Overview.......................................................2
Illustrated Protocol........................................................................3
Kit Contents and Storage...........................................................4
Mag-Bind® SeqDTR™ 96-well Plate Protocol......................5
Mag-Bind® SeqDTR™ 384-well Plate Protocol.....................7
Troubleshooting Guide...............................................................9
Ordering Information................................................................10
Manual Revision: January 2013
Mag-Bind® SeqDTR™
Table of Contents

2
Introduction and Overview
Excess unincorporated, non-radioactive label can cause high background uorescence
in automated sequencing gels. For optimal sequencing results, remaining labeled
dideoxynucleotides should be removed prior to electrophoresis.
Omega Bio-tek’s Mag-Bind® SeqDTR™ is designed to eectively and reliably remove
unincorporated terminators from sequencing reactions. The system combines Omega
Bio-tek’s proprietary chemistries with the reversible nucleic acid-binding properties
of magnetic beads to eliminate excess nucleotides, primers, and small, non-targeted
amplication products such as primer dimers. This kit is designed for both manual and
fully automated purication of sequencing products.
The Mag-Bind® SeqDTR™ magnetic particles technology provides a better solution
for nucleic acid purication than centrifugation and vacuum-based technologies. The
product can be easily scaled up while providing simple user-friendly handling procedures.
If using the Mag-Bind® SeqDTR™ for the rst time, please read this booklet to become
familiar with the procedures. Sequencing products are mixed with the Mag-Bind®
SeqDTR™. DNA selectively binds to the Mag-Bind® SeqDTR™ particles. With one rapid
wash step, trace contaminants such as nucleotides, primers and small, non-targeted
amplication products are removed. Pure DNA is eluted in low salt buer or water.
Puried DNA can be directly used in downstream applications without the need for
further purication.
New in this edition:
• The manual has been updated to reect the product name change from the old
name of Mag-Bind® SE DTR to the new name of Mag-Bind® SeqDTR™.

3
Illustrated Protocol
Add Mag-Bind®SeqDTR™and 85% Ethanol, Mix
Magnetize and remove cleared supernatant
Wash 2 x with 85% Ethanol
Elute and transfer DNA to a new plate

4
Kit Contents and Storage
Storage and Stability
Mag-Bind® SeqDTR™ is stable for at least 9 months from the date of purchase when stored
at 2-8oC. Contents of the kit should never be frozen at any time.
Product No. M1300-05 M1300-08 M1300-50
Mag-Bind® SeqDTR™ 5 ml 50ml 500 ml
Preparations 500* / 1,000** 5,000* / 10,000** 50,000 */ 100,000**
User Manual P P P
* Based on a typical 10 μL reaction volume in a 96-well format
** Based on a typical 5 μL reaction volume in a 384-well format

5
Mag-Bind® SeqDTR™ - 96-well Plate Protocol
Mag-Bind®SeqDTR™96 Plate Format Protocol
Materials and Equipment to be Supplied by User:
• 85% ethanol (do not use denatured ethanol)
• Magnetic separation device compatible with 96-well PCR plates
• Multichannel pipet
• Reservoirs
• 96-well plate capable of being used in sequencers
• Elution Buer (Cat# PDR048 or 10 mM Tris pH 8.5, TE Buer, 0.1 mM EDTA, or diH₂O)
1. Thoroughly shake the Mag-Bind® SeqDTR™ to fully resuspend the magnetic beads.
2. Add 10 μL Mag-Bind® SeqDTR™ to each well.
Note: Use 10 μL Mag-Bind® SeqDTR™ regardless of the volume of the sequencing
reaction.
3. Add 85% ethanol according to table below and mix the sample thoroughly by
pipetting up and down 7-10 times.
Note: Do not use denatured ethanol. Always prepare fresh 85% ethanol within 3
days of use and store tightly capped.
Reaction volume (μL) 85% Ethanol (μL)
5 30
10 40
15 50
20 60
4. Place the plate on a magnetic separation device to magnetize the Mag-Bind®
SeqDTR™. Let sit at room temperature until the Mag-Bind® SeqDTR™is completely
cleared from solution.
5. Aspirate and discard the supernatant. Do not disturb the Mag-Bind® SeqDTR™.

6
6. Add 100 μL 85% ethanol to each well. It is not necessary to resuspend the Mag-Bind®
SeqDTR™.
7. Let sit at room temperature until the Mag-Bind® SeqDTR™is completely cleared from
solution.
8. Aspirate and discard the supernatant. Do not disturb the Mag-Bind® SeqDTR™.
9. Repeat Steps 6-8 for a second 85% ethanol wash step.
10. Leave the plate on the magnetic separation device for 10-15 minutes to air dry the
Mag-Bind® SeqDTR™. Remove any residue liquid with a pipettor.
Note: It is important to dry the Mag-Bind® SeqDTR™before elution. Residual ethanol
may interfere with downstream applications.
11. Add 40 μL Elution Buer (or 10 mM Tris pH 8.5, TE Buer, 0.1 mM EDTA, or diH2O) to
each well.
12. Pipet up and down 20 times to mix thoroughly.
13. Let sit at room temperature for 5 minutes.
14. Place the plate on a magnetic separation device to magnetize the Mag-Bind®
SeqDTR™. Let sit at room temperature until the Mag-Bind® SeqDTR™is completely
cleared from solution.
15. Transfer 30-35 µL cleared supernatant containing puried sequencing product to a
new plate capable of being used in sequencer.
Mag-Bind® SeqDTR™ - 96-well Plate Protocol

7
Mag-Bind®SeqDTR™- 384-well Plate Protocol
Additional Materials Supplied by User:
• 85% ethanol (do not use denatured ethanol)
• Magnetic separation device compatible with 384-well microplates
• Multichannel pipet
• Reservoirs
• 384-well plate capable of being used in sequencers
• Elution Buer (Cat# PDR048 or 10 mM Tris pH 8.5, TE Buer, 0.1 mM EDTA, or diH₂O)
1. Thoroughly shake the Mag-Bind® SeqDTR™ to fully resuspend the magnetic beads.
2. Add 5 μL Mag-Bind® SeqDTR™ to each well.
Note: Use 5 μL Mag-Bind® SeqDTR™ regardless of the volume of the sequencing
reaction.
3. Add 85% ethanol according to table below and mix the sample thoroughly by
pipetting up and down 7-10 times.
Note: Do not use denatured ethanol. Always prepare fresh 85% ethanol within 3
days of use and store tightly capped.
Reaction volume (μL) 85% Ethanol (μL)
5 14.3
10 21.4
15 28.6
4. Place the plate on a magnetic separation device to magnetize the Mag-Bind®
SeqDTR™. Let sit at room temperature until the Mag-Bind® SeqDTR™is completely
cleared from solution.
5. Aspirate and discard the supernatant. Do not disturb the Mag-Bind® SeqDTR™.
6. Add 30 μL 85% ethanol to each well. It is not necessary to resuspend the Mag-Bind®
SeqDTR™.
Mag-Bind® SeqDTR™ - 384-well Plate Protocol

8
7. Let sit at room temperature until the Mag-Bind® SeqDTR™is completely cleared from
solution.
8. Aspirate and discard the supernatant. Do not disturb the Mag-Bind® SeqDTR™.
9. Repeat Steps 6-8 for a second 85% ethanol wash step.
10. Leave the plate on the magnetic separation device for 10-15 minutes to air dry the
Mag-Bind® SeqDTR™. Remove any residue liquid with a pipettor.
Note: It is important to dry the Mag-Bind® SeqDTR™before elution. Residual ethanol
may interfere with downstream applications.
11. Add 15-20 μL Elution Buer (or 10 mM Tris pH 8.5, TE Buer, 0.1 mM EDTA, or diH2O)
to each well.
12. Pipet up and down 20 times to mix thoroughly.
13. Let sit at room temperature for 5 minutes.
14. Place the plate on a magnetic separation device to magnetize the Mag-Bind®
SeqDTR™. Let sit at room temperature until the Mag-Bind® SeqDTR™is completely
cleared from solution.
15. Transfer the cleared supernatant containing puried sequencing product to a new
plate capable of being used in sequencer.
Mag-Bind® SeqDTR™ - 384-well Plate Protocol