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FREQUENTLY
ASKED QUESTIONS
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MagDTR™ Technology
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Additional
Resources
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 800-326-2685
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| Resin
Suspension |
| 1. |
I'm having
trouble with the beads settling. How can I keep them in uniform
suspension while dispensing into the samples?
Shake well or vortex the resin container until the resin is
in complete suspension. For all subsequent pipetting steps,
use a pipet to mix the suspension prior to dispensing into the
sample. |
| 2. |
Can you suggest any other form of mixing besides pipet
mixing?
If using a multichannel pipet reservoir, resin can be resuspended
by rocking the reservoir back and forth 7-10 times.
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| Mixing |
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| 1. |
Is
the number of wash step pipet mixes flexible?
No. A minimum of 15 pipet mixes gives consistent purity and
yields. |
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| 2. |
Can I replace pipet mixing with vortexing throughout
the protocol?
Vortex mixing during the protocol process is not recommended.
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Precipitation
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| 1. |
Can I bind
the sequencing reaction products to the magnetic resin with
solvents other than ethanol?
Other solvents, especially isopropanol, are not recommended. |
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| 2. |
Can I use
80% alcohol to bind the sample to the resin?
Yes. However, 5 volumes of 80% ethanol are required to bind
the sequencing reaction products. This large increase in total
solution volume may obviate the advantages of using a single
alcohol concentration for all steps.
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| 3. |
Can I premix
the resin with ethanol prior to purification?
No. Premixing the MagDTR resin with ethanol negatively impacts
the performance of the product. |
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| 4. |
Can I reduce
the amount of resin for smaller volume reactions and/or for
lower amounts of BigDye®?
The optimum amount of resin to use is 4 µl, and it has been
our observation that this volume is the optimum over a broad
range of conditions. |
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| 5. |
Can I use this technology with other dyes other than
BigDye®?
Yes, including Beckman DTCS™ and Amersham dyes.
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Washing
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| 1. |
Is there
any advantage to washing more than once?
While one wash may be sufficient for very low dye volumes, two
washes give far more reproducible results over a range of dye
volumes up to 4 µl. A third wash step can increase the
consistency of results when using higher dye volumes. |
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| 2. |
Can I use
different concentrations of ethanol for the wash step?
The optimum concentration of ethanol is 80%. Concentrations
as low as 60% and as high as 90% have been tested. These other
concentrations are reasonably effective at washing the resin.
Lower concentrations of ethanol tend to reduce signal strength
and read length especially for samples containing small amounts
of DNA. Increased ethanol concentrations are less effective
at washing away salts and unincorporated dye terminators leading
to an increased frequency of dye blob contamination, noise,
and reduced signal strength. |
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| 3. |
Does residual
ethanol affect the quality of the sequence?
Yes. In most cases, residual ethanol from the wash steps will
contain trace amounts of unincorporated dye terminators. Residual
ethanol must be removed to obtain optimal results. |
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| 4. |
I am seeing
"dye blobs. " What is the cause?
Blobs or unincorporated dye terminator peaks are usually a result
of incomplete removal of ethanol that may contain unincorporated
dye terminators. If residual ethanol is present following the
first aspiration, a second aspiration is recommended. Offset
the pipet to 150 µl, and aspirate as slowly as possible
to remove all residual ethanol. If this step alone does not
solve the problem, then try adding a third wash step to the
process. |
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| 5. |
I can't
seem to get rid of residual ethanol. Any suggestions?
Add an extra aspiration step after each ethanol removal, aspirating
as slowly as possible with the pipet offset to150 µl.
If this doesn't solve the problem, then try adding a third wash
step. |
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| 6. |
Can
I over dry the resin?
Yes. Over dried resin will be attached to the plate well wall
in an obvious manner and will be difficult to work with during
resuspension. Over drying of the resin may result in reduced
signal strength and an increase in the overall failure rate.
To avoid over drying, aspirate all ethanol, and reduce drying
time at room temperature to 3 minutes, or heat at 98°C for
30 seconds. Resuspend immediately. If samples appear over dried
at the elution step, add the recommended volume of deionized
water, and incubate at room temperature for one minute. Pipet
mix to resuspend. |
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| 7. |
How can I tell when the resin is optimally dry?
Resin is optimally dry when there is no visual evidence of
residual ethanol following the drying step.
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| Elution |
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| 1. |
Can I elute
my sample in formamide?
No. However, we recommend that users of this sample purification
system follow the instrument manufacturer's recommendation for
the appropriate solvent to be used in sample injection. If the
sample must be in formamide, the sample can be eluted in water
then dried down and resuspended in formamide. |
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| 2. |
Can I load my plate into the sequencer with the resin
present?
This is not generally recommended since the presence of particulates
in the sample carries the risk of clogging the capillaries
in the DNA analyzers.
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Storage
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| 1. |
Can I store
the sample before eluting from the resin?
Yes, but only after completing the wash steps. The samples should
be sealed to prevent over-drying and stored at 4°C. This
has been tested for up to one week storage. At this time we
do not recommend storage for longer periods. |
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| 2. |
How do I
store the sample after it has been eluted from the resin?
Remove the sample from the resin, and store at - 20°C. |
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| 3. |
Can I store
the sample with resin after it has been eluted?
No. We do not recommend this procedure. |
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| 4. |
Can I store the MagDTR resin in the refrigerator?
The product may be stored at 4°C, but be sure to bring
the resin to room temperature prior to use. Avoid freezing
the product.
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| Magnet |
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| 1. |
What kind of magnet is recommended?
We recommend the Edge
BioSystems' MagWell™ Magnetic Separator 96, Catalog #57624.
The unique configuration of the magnet (milled cavities aligned
on either side of an imbedded bar magnet) places the tip of
the wells below the top of the bar magnets on the plate. This
configuration maximizes the magnetic field strength experienced
by each well while allowing the magnetic particles to be pulled
both to the side and away from the bottom of the plate. In
so doing, it permits effective washing of the particles in
both magnetic and manual liquid handling protocols. It also
permits the user to resuspend in a minimum volume of fluid
e.g. 10 µl. If using an alternative magnet, the protocol
will need to be optimized by the user.
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Troubleshooting
Guide 
Product
Protocol