diy magnetic plate for DNA purification?

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Jeswin

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Dec 23, 2014, 8:52:34 AM12/23/14
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Has anyone considered building an 8-well or 96-well magnetic plate for
purification of DNA with magnetic beads? I was looking at the prices
of plates and they're pretty expensive. It seems to me that they're
just a 96 well stand with neodymium magnets placed in between. A 100
neodymium magnets placed between a used pipette rack seems like it
could do the same job and cost 10x less.

Thoughts? What about the magnets and their strengths?

Dakota Hamill

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Dec 23, 2014, 9:51:52 AM12/23/14
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I've seen them in the lab before, never seen anyone use it.  Many companies sell them for purification of DNA with magnetic beads.

 I messed around with one one day out of curiosity and the magnets were falling everywhere, seemed like a pain in the ass to use.




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Jeswin

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Dec 23, 2014, 11:00:29 AM12/23/14
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Yeah, I know of the commercial ones. We got 2, but they're $300 or so.
Pricing the small 0.25 diameter magnets, you can get 100 for $32 from
unitednuclear. I was thinking of placing them on a used pipette tip
rack. That is, unless the magnets the companies use for their stands
are special for magnetic beads? Anyone know?
> https://groups.google.com/d/msgid/diybio/CAGdeWmTj3aBUMEP_EyP8265oOO5U8PJoSJ3%3DoAQUeqmbF%3DBQhA%40mail.gmail.com.

John Griessen

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Dec 23, 2014, 11:40:33 AM12/23/14
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On 12/23/2014 10:00 AM, Jeswin wrote:
> unless the magnets the companies use for their stands
> are special for magnetic beads? Anyone know?

Don't know, but how special could it be. The sales blurb
for 96R & 96S Magnet Plates says get the super "S" when you want more speed is all.

Your DIY idea of shoving ring magnets over pipette tip rack tubes sounds
like maybe something to write up. Do they have the same spacing as well plates?
They would if they are for the multi well pipettes...of course...answered my question.

Another way to use magnets would be small slab magnets with the field aiming
out of the flat sides. Those could be molded into a holder so they fit up between wells in
plates. The beads would be in clumps, rather than a ring, but the bottom of the well
would be clear for similar result for pipetting away supernatant solutions.

See this sketch: http://www.ecosensory.com/diybio/magnetic-plate-design-1.png

Speed? From magnets alone? That would come from the magnetic field reaching up into
the suspension from the bottom. Very small magnetic particles coiuld take a long time to move.
So, to speed that up, instead of stronger magnets, one could agitate the whole thing
while magnets are in plalce near the well bottoms. Speedo-presto even with weaker magnets.

With heavy metal magnetic beads in a suspension swirl agitation to stir things is just a natural.

Jeswin

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Dec 23, 2014, 12:18:36 PM12/23/14
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On Tue, Dec 23, 2014 at 11:40 AM, John Griessen <jo...@industromatic.com> wrote:
> Your DIY idea of shoving ring magnets over pipette tip rack tubes sounds
> like maybe something to write up. Do they have the same spacing as well
> plates?
> They would if they are for the multi well pipettes...of course...answered my
> question.
>
Yep, the tip racks are evenly placed for use in the multi-channel
pipettes. I believe there are accepted engineering specs for 96-well
plates and differences are mainly in the skirts around the
wells/plate.
Does the orientation matter? I was looking at the disc magnets (either
1/8 or 1/4 diameter flat discs). I got an idea from this


The arrangement would be like this:

+--+--+--+--
+O+O+O+--
+--+--+--+--
+O+O+O+--
+--+--+--+
+--

That comes out to 24 magnets, none on the outer edge and each magnet
serving 4 tubes.

Jeswin

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Dec 23, 2014, 12:19:37 PM12/23/14
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sorry, my image didn't go through. I got the idea from this:



John Griessen

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Dec 23, 2014, 1:39:18 PM12/23/14
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On 12/23/2014 11:19 AM, Jeswin wrote:
> Does the orientation matter?

Yes, in my design it does. So you are not thinking
of ring magnets, but flat slabs? Not sure how to interpret your ascii text art sketch.

My sketch is about using small, maybe 1mm X 1mm X 2mm lengthwise polarized inexpensive magnets, with orientations
as in the sketch. Orientation matters to keep from having beads string across a well
bottom.


For your idea of just one magnet between four wells, orientation should not matter,
except probably better all up or all down -- a blob will form
at edge of disc as fields wrap around to other side to concentrate themsleves in the beads.
(Fields concentrating in susceptible media is a potential energy lowering state that explains
the force holding beads together.)

Patrik D'haeseleer

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Jan 5, 2015, 3:04:54 AM1/5/15
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Sergii Pochekailov

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Mar 29, 2018, 12:13:11 AM3/29/18
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Yes, I have built magnetic racks for different tube sizes. I'm selling them on ebay, you can find them here:



For 96-well plates, compatible with single PCR tubes: https://www.ebay.com/itm/273013056166

For PCR tube stripes, 16 tubes at once: https://www.ebay.com/itm/273027161398

Skyler Gordon

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Mar 29, 2018, 12:15:32 AM3/29/18
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Have you thought about doing them with an electromagnet?

Then you wouldn’t have to switch racks for the elution process.

-SG
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Sergii Pochekailov

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Mar 29, 2018, 4:41:53 AM3/29/18
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Have you thought about doing them with an electromagnet?

That would be very nice to have, but I couldn't yet come up with an acceptable design. Commercial electromagnets cost quite a bit, and such rack would draw significant current.

I'll definitely let you know if I come up with a solution.

- Sergii

Skyler Gordon

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Mar 29, 2018, 3:25:20 PM3/29/18
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For these racks, I believe the neodymium magnets are the most expensive portion.

It has been a long time since I built one, but I believe a 9V battery can provide current sufficient to produce a strong magnetic field - depending on how much copper you used.

If they have an on/off switch they could be plugged into a wall socket.

-SG
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Nathan McCorkle

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Mar 29, 2018, 3:41:34 PM3/29/18
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On Thu, Mar 29, 2018 at 12:25 PM, Skyler Gordon <skg...@gmail.com> wrote:
I believe a 9V battery can provide current sufficient to produce a strong magnetic field - depending on how much copper you used. 

I thought field strength was proportional to current, independent of how thick the wire is (or what the metal was). (sure thinner wire will get hotter faster, and may break... but that's another concern I think)

Skyler Gordon

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Mar 29, 2018, 3:54:01 PM3/29/18
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The current will play a factor, but so will the number of copper coils. That may change the resistance and all boil down to current in the end, but I’m not an electrical engineer.

-SG
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John Griessen

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Mar 29, 2018, 6:07:14 PM3/29/18
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On 03/29/2018 02:41 PM, Nathan McCorkle wrote:
> I thought field strength was proportional to current, independent of how thick the wire is (or what the metal was). (sure thinner
> wire will get hotter faster, and may break... but that's another concern I think)

On 03/29/2018 02:53 PM, Skyler Gordon wrote:
> The current will play a factor, but so will the number of copper coils
Right, it's proportional to current X number of coils.

There's going to be a happy medium for a given field strength, and it probably would take
some testing to find it for an array of holes. When you make many loops in a tight space,
you end up with thin wire, and at some point the resistance decreases current flowing.

Copper wire is very consistent and for any diameter wire it is an easy calc to figure resistance per length.

So this is yet another thing that could be designed by spreadsheet.
Assembling loops of fine wire in tight rows then protecting them from damage in use
could be more expensive than buying Nd magnets... Spreadsheet sizings and price research work will tell. :-;

Skyler Gordon

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Mar 29, 2018, 10:40:39 PM3/29/18
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But if it was possible to run enough current into the electromagnet - not enough to melt the wire - you could possible speed up the process of moving the beads from a viscous solution to the side of your PCR tube. When typical neodymium magnets are used, the speed of the beads will vary widely based on the viscosity of the liquid (ethanol Vs water Vs polymerases and salts) and the amount of beads you’ve added (concentration of polyethylene glycol).

To get magnets that strong you would have to buy larger or multiple and make them stronger.

But if you made them too strong it could lead to loss in yield - if the DNA just whooshed off the bead because it was going too fast.

-SG
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Simon Quellen Field

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Mar 30, 2018, 9:00:50 AM3/30/18
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Magnetomotive force is measured in ampere turns.
It is the current flowing through the wire, multiplied by the number of turns in the coil.
You can think of each loop in the coil as a separate magnet, and they add in series.

There are trade-offs.
If you use thinner wire to get more turns, there is more resistance, and hence less current.
If you use thicker wire to get more current, you get fewer turns in the same space.
You can concentrate the magnetic field by using a core that conducts magnetic flux better than air does,
such as iron or ferrite (an iron oxide ceramic). This works up the the saturation limit of the material,
which varies with different materials.

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Cory J. Geesaman

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Mar 30, 2018, 12:01:32 PM3/30/18
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I'd recommend kjmagnetics over united nuclear - they tend to have a much wider selection with better prices.
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