matrix for spin columns

Paul N Hengen pnh at ncifcrf.gov
Wed Mar 26 12:35:55 EST 1997


Michael Benedik (benedik at uh.edu) wrote:

> Can anyone suggest a suitable matrix for making homemade spin columns
> to separate PCR products from primers. Exclusion should be larger than
> 50nt or so.

Mike:

Try Sephadex G-50 (cut-off is ~ 30,000 MW). The MW of a 50 nt PCR product will
be close to 30,000 if it is 0% CG or 100% GC (all A's or all C's).  If you find
it too close for the cut-off try Sephadex G-25. You can get it from Sigma (see
page 1813), or you can buy pre-loaded push columns from other biotech companies
like Stratagene...very convenient.

Using the dnamwt program gives you the MW of the PCR product,

All A's:

dnamwt 1.08
the number of A's in strand 1 of the sequence is: 50
the number of C's in strand 1 of the sequence is: 0
the number of G's in strand 1 of the sequence is: 0
the number of T's in strand 1 of the sequence is: 0
total number of bases:         50
strand 1 molecular weight: 15678.0 daltons
strand 2 molecular weight: 15228.0 daltons
total molecular weight: 30906.0 daltons
% GC:  0.0

OR

All C's:

dnamwt 1.08
the number of A's in strand 1 of the sequence is: 0
the number of C's in strand 1 of the sequence is: 50
the number of G's in strand 1 of the sequence is: 0
the number of T's in strand 1 of the sequence is: 0
total number of bases:         50
strand 1 molecular weight: 14478.0 daltons
strand 2 molecular weight: 16478.0 daltons
total molecular weight: 30956.0 daltons

Also, if you want the dnamwt program written in pascal, I'll send it to you.

--
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