[Erik Lehnsherr]

Right now I am trying to optimise a protocol for the purification of 300 pmol freshly synthesised DNA < 50 bases.

How can I calculate the right amount of beads needed? Lacking a better method I simply try ever smaller volumes of the MagPrep Silica beads (roughly 100 µm diameter) and determine the recovery rate in the end. I can already tell you with 5 µL of the delivered suspension you recover basically all 300 pmol…

Is there some formula for m² of surface for a given amount of DNA or bases involved? Also is there an upper dilution limit for these beads? And last but not least: If I use carboxylated beads instead of silica how much does this change?

[admin]

Ahoy,

Unfortunately the answer to all your questions is:

Has to be tested empirically.

It is not possible to estimate/calculate the quantity of Beads needed to achieve best results. This can only be determined empirically. Size dispersity has too much of an effect on bulk density to know the number of beads per volume. If you think of a big box full of soccer balls, you can probably add a surprising amount of golf balls without the bulk volume changing. And things become truly unfathomable once you consider that the beads may not be entirely round. Also, the availability of  hydroxide groups on the bead surface can change between batches and synthesis pathways. So even if you knew the surface area you would not know how much DNA it can hold.

Concerning the upper dilution limit, yes there has to be one but again only empirical tests will tell. Since Beads capture DNA only if it is very, very close, a high dilution means larger distances… Movement and more time may mitigate but again only empirical tests will tell.

I have extensively compared SeraMag carboxylated beads to our homemade Silica beads and not only does it depend on the concentration but also the binding, wash and elution solution (mayor factor) which ends up performing better.

I wish I had answers of more “substance”.

Best of luck,

Tim M

 

 

 

 

 

[Anonymous]

hi You can use below query to get the size of the tables on the Teradata.

select
tablename,
databasename,
sum currentperm/1024 as SIZE_IN_KB
from dbc.allspace
where tablename <> All
and databasename = YOUR_DATABASE_NAME

[Author]

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